[Bio] / FigKernelPackages / Tracer.pm Repository:
ViewVC logotype

Diff of /FigKernelPackages/Tracer.pm

Parent Directory Parent Directory | Revision Log Revision Log | View Patch Patch

revision 1.4, Thu Jan 27 00:32:17 2005 UTC revision 1.129, Tue Jan 5 17:25:48 2010 UTC
# Line 1  Line 1 
1    # -*- perl -*-
2    ########################################################################
3    # Copyright (c) 2003-2006 University of Chicago and Fellowship
4    # for Interpretations of Genomes. All Rights Reserved.
5    #
6    # This file is part of the SEED Toolkit.
7    #
8    # The SEED Toolkit is free software. You can redistribute
9    # it and/or modify it under the terms of the SEED Toolkit
10    # Public License.
11    #
12    # You should have received a copy of the SEED Toolkit Public License
13    # along with this program; if not write to the University of Chicago
14    # at info@ci.uchicago.edu or the Fellowship for Interpretation of
15    # Genomes at veronika@thefig.info or download a copy from
16    # 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);  
         @EXPORT_OK = qw(GetFile GetOptions Merge MergeOptions ParseCommand ParseRecord UnEscape);  
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;
30        use PageBuilder;
31        use Digest::MD5;
32        use File::Basename;
33        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<Setup> 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    To generate a trace message, use the following syntax.
61    
62  C<< Trace($message) if T(errors => 4); >>      Trace($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 34  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  To set up tracing, you call the C</Setup> method. The method takes as input a trace level, a list  In scripts, where no package name is available, the category defaults to C<main>.
78  of category names, and a set of options. The trace level and list of category names are  
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 custom tracing, you call the L</TSetup> method. The method takes as input a trace level,
86    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
92    specifies that messages should be sent to the standard output.
93    
94  sets the trace level to 3, activated the C<errors>, C<Sprout>, and C<ERDB> categories, and  To turn on tracing for ALL categories, use an asterisk. The call below sets every category to
95  specifies that messages should be output as HTML paragraphs. The idea is to make it easier to  level 3 and writes the output to the standard error output. This sort of thing might be
96  input tracing configuration on a web form.  useful in a CGI environment.
97    
98  In addition to HTML and file output for trace messages, you can specify that the trace messages      TSetup('3 *', 'WARN');
99    
100    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
125    a suggestion.
126    
127    =over 4
128    
129    =item Error 0
130    
131    Message indicates an error that may lead to incorrect results or that has stopped the
132    application entirely.
133    
134    =item Warning 1
135    
136    Message indicates something that is unexpected but that probably did not interfere
137    with program execution.
138    
139    =item Notice 2
140    
141    Message indicates the beginning or end of a major task.
142    
143    =item Information 3
144    
145    Message indicates a subtask. In the FIG system, a subtask generally relates to a single
146    genome. This would be a big loop that is not expected to execute more than 500 times or so.
147    
148    =item Detail 4
149    
150    Message indicates a low-level loop iteration.
151    
152    =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
201                                # 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
209    my $LastLevel = 0;          # level of the last test call
210    my $SetupCount = 0;         # number of times TSetup called
211    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 Public Methods  =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    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 90  Line 249 
249    
250  The destination for the trace output. To send the trace output to a file, specify the file  The destination for the trace output. To send the trace output to a file, specify the file
251  name preceded by a ">" symbol. If a double symbol is used (">>"), then the data is appended  name preceded by a ">" symbol. If a double symbol is used (">>"), then the data is appended
252  to the file. Otherwise the file is cleared before tracing begins. In addition to sending  to the file. Otherwise the file is cleared before tracing begins. Precede the first ">"
253  the trace messages to a file, you can specify a special destination. C<HTML> will  symbol with a C<+> to echo output to a file AND to the standard output. In addition to
254    sending the trace messages to a file, you can specify a special destination. C<HTML> will
255  cause tracing to the standard output with each line formatted as an HTML paragraph. C<TEXT>  cause tracing to the standard output with each line formatted as an HTML paragraph. C<TEXT>
256  will cause tracing to the standard output as ordinary text. C<QUEUE> will cause trace messages  will cause tracing to the standard output as ordinary text. C<ERROR> will cause trace
257  to be stored in a queue for later retrieval by the L</QTrace> method. C<WARN> will cause  messages to be sent to the standard error output as ordinary text. C<QUEUE> will cause trace
258  trace messages to be emitted as warnings using the B<warn> directive.  C<NONE> will cause  messages to be stored in a queue for later retrieval by the L</QTrace> method. C<WARN> will
259  tracing to be suppressed.  cause trace messages to be emitted as warnings using the B<warn> directive.  C<NONE> will
260    cause tracing to be suppressed.
261    
262  =back  =back
263    
# Line 109  Line 270 
270          my @categoryData = split /\s+/, $categoryList;          my @categoryData = split /\s+/, $categoryList;
271          # Extract the trace level.          # Extract the trace level.
272          $TraceLevel = shift @categoryData;          $TraceLevel = shift @categoryData;
273          # Build the category hash.      # Presume category-based tracing until we learn otherwise.
274        $AllTrace = 0;
275        # Build the category hash. Note that if we find a "*", we turn on non-category
276        # tracing. We must also clear away any pre-existing data.
277        %Categories = ( main => 1 );
278          for my $category (@categoryData) {          for my $category (@categoryData) {
279                  $Categories{$category} = 1;          if ($category eq '*') {
280                $AllTrace = 1;
281            } else {
282                $Categories{lc $category} = 1;
283            }
284          }          }
285          # Now we need to process the destination information. The most important special          # Now we need to process the destination information. The most important special
286          # case is the single ">", which requires we clear the file first. After doing      # case is when we're writing to a file. This is indicated by ">" (overwrite) and
287          # so, we tack on another ">" sign so that future trace messages are appended.      # ">>" (append). A leading "+" for either indicates that we are also writing to
288        # the standard output (tee mode).
289        if ($target =~ m/^\+?>>?/) {
290            if ($target =~ m/^\+/) {
291                $TeeFlag = 1;
292                $target = substr($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                  $Destination = uc($target);              $Destination = $target;
303          }          }
304        } else {
305            $Destination = uc($target);
306  }  }
307        # Increment the setup counter.
308  =head3 Now      $SetupCount++;
   
 C<< my $string = Tracer::Now(); >>  
   
 Return a displayable time stamp containing the local time.  
   
 =cut  
   
 sub Now {  
         my ($sec,$min,$hour,$mday,$mon,$year,$wday,$yday,$isdst) = localtime(time);  
         my $retVal = _p2($mon+1) . "/" . _p2($mday) . "/" . ($year + 1900) . " " .  
                                  _p2($hour) . ":" . _p2($min) . ":" . _p2($sec);  
         return $retVal;  
 }  
   
 # Pad a number to 2 digits.  
 sub _p2 {  
         my ($value) = @_;  
         $value = "0$value" if ($value < 10);  
         return $value;  
309  }  }
310    
311  =head3 LogErrors  =head3 SetLevel
312    
313  C<< Tracer::LogErrors($fileName); >>      Tracer::SetLevel($newLevel);
314    
315  Route the standard error output to a log file.  Modify the trace level. A higher trace level will cause more messages to appear.
316    
317  =over 4  =over 4
318    
319  =item fileName  =item newLevel
320    
321  Name of the file to receive the error output.  Proposed new trace level.
322    
323  =back  =back
324    
325  =cut  =cut
326    
327  sub LogErrors {  sub SetLevel {
328          # Get the file name.      $TraceLevel = $_[0];
         my ($fileName) = @_;  
         # Open the file as the standard error output.  
         open STDERR, '>', $fileName;  
329  }  }
330    
331  =head3 GetOptions  =head3 ParseDate
332    
333  C<< Tracer::GetOptions(\%defaults, \%options); >>      my $time = Tracer::ParseDate($dateString);
334    
335  Merge a specified set of options into a table of defaults. This method takes two hash references  Convert a date into a PERL time number. This method expects a date-like string
336  as input and uses the data from the second to update the first. If the second does not exist,  and parses it into a number. The string must be vaguely date-like or it will
337  there will be no effect. An error will be thrown if one of the entries in the second hash does not  return an undefined value. Our requirement is that a month and day be
338  exist in the first.  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  Consider the following example.  If a time of day is present, it must be in military time with two digits for
342    everything but the hour.
343    
344  C<< my $optionTable = GetOptions({ dbType => 'mySQL', trace => 0 }, $options); >>  The year must be exactly four digits.
345    
346  In this example, the variable B<$options> is expected to contain at most two options-- B<dbType> and  Additional stuff can be in the string. We presume it's time zones or weekdays or something
347  B<trace>. The default database type is C<mySQL> and the default trace level is C<0>. If the value of  equally innocuous. This means, however, that a sufficiently long sentence with date-like
348  B<$options> is C<< {dbType => 'Oracle'} >>, then the database type will be changed to C<Oracle> and  parts in it may be interpreted as a date. Hopefully this will not be a problem.
 the trace level will remain at 0. If B<$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  
349    
350  C<< {databaseType => 'Oracle'} >>  It should be guaranteed that this method will parse the output of the L</Now> function.
351    
352  an error will occur because the B<databaseType> option does not exist.  The parameters are as follows.
353    
354  =over 4  =over 4
355    
356  =item defaults  =item dateString
   
 Table of default option values.  
   
 =item options  
357    
358  Table of overrides, if any.  The date string to convert.
359    
360  =item RETURN  =item RETURN
361    
362  Returns a reference to the default table passed in as the first parameter.  Returns a PERL time, that is, a number of seconds since the epoch, or C<undef> if
363    the date string is invalid. A valid date string must contain a month and day.
364    
365  =back  =back
366    
367  =cut  =cut
368    
369  sub GetOptions {  # Universal month conversion table.
370    use constant MONTHS => {    Jan =>  0, January   =>  0, '01' =>  0,  '1' =>  0,
371                                Feb =>  1, February  =>  1, '02' =>  1,  '2' =>  1,
372                                Mar =>  2, March     =>  2, '03' =>  2,  '3' =>  2,
373                                Apr =>  3, April     =>  3, '04' =>  3,  '4' =>  3,
374                                May =>  4, May       =>  4, '05' =>  4,  '5' =>  4,
375                                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.          # Get the parameters.
386          my ($defaults, $options) = @_;      my ($dateString) = @_;
387          # Check for overrides.      # Declare the return variable.
388          if ($options) {      my $retVal;
389                  # Loop through the overrides.      # Find the month and day of month. There are two ways that can happen. We check for the
390                  while (my ($option, $setting) = each %{$options}) {      # numeric style first. That way, if the user's done something like "Sun 12/22", then we
391                          # Insure this override exists.      # won't be fooled into thinking the month is Sunday.
392                          if (!exists $defaults->{$option}) {      if ($dateString =~ m#\b(\d{1,2})/(\d{1,2})\b# || $dateString =~ m#\b(\w+)\s(\d{1,2})\b#) {
393                                  croak "Unrecognized option $option encountered.";          my ($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 {                          } else {
406                                  # Apply the override.                  # Get the default year, which is this one. Note we must convert it to
407                                  $defaults->{$option} = $setting;                  # 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 merged table.      # Return the result.
415          return $defaults;      return $retVal;
416  }  }
417    
418  =head3 MergeOptions  =head3 LogErrors
419    
420  C<< Tracer::MergeOptions(\%table, \%defaults); >>      Tracer::LogErrors($fileName);
421    
422  Merge default values into a hash table. This method looks at the key-value pairs in the  Route the standard error output to a log file.
 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.  
423    
424  =over 4  =over 4
425    
426  =item table  =item fileName
   
 Hash table to be updated with the default values.  
   
 =item defaults  
427    
428  Default values to be merged into the first hash table if they are not already present.  Name of the file to receive the error output.
429    
430  =back  =back
431    
432  =cut  =cut
433    
434  sub MergeOptions {  sub LogErrors {
435          # Get the parameters.      # Get the file name.
436          my ($table, $defaults) = @_;      my ($fileName) = @_;
437          # Loop through the defaults.      # Open the file as the standard error output.
438          while (my ($key, $value) = each %{$defaults}) {      open STDERR, '>', $fileName;
                 if (!exists $table->{$key}) {  
                         $table->{$key} = $value;  
                 }  
         }  
439  }  }
440    
441  =head3 Trace  =head3 Trace
442    
443  C<< Trace($message); >>      Trace($message);
444    
445  Write a trace message to the target location specified in L</TSetup>. If there has not been  Write a trace message to the target location specified in L</TSetup>. If there has not been
446  any prior call to B<TSetup>.  any prior call to B<TSetup>.
# Line 286  Line 458 
458  sub Trace {  sub Trace {
459          # Get the parameters.          # Get the parameters.
460          my ($message) = @_;          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.          # Get the timestamp.
470          my $timeStamp = Now();          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 $stripped";
476          # Process according to the destination.          # Process according to the destination.
477          if ($Destination eq "TEXT") {          if ($Destination eq "TEXT") {
478                  # Write the message to the standard output.                  # Write the message to the standard output.
479                  print "$timeStamp $message\n";          print "$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") {          } elsif ($Destination eq "QUEUE") {
489                  # Push the message into the queue.                  # Push the message into the queue.
490                  push @Queue, "$timeStamp $message";          push @Queue, "$formatted";
491          } elsif ($Destination eq "HTML") {          } elsif ($Destination eq "HTML") {
492                  # Convert the message to HTML and write it to the standard output.          # Convert the message to HTML.
493                  my $escapedMessage = CGI::escapeHTML($message);          my $escapedMessage = CGI::escapeHTML($stripped);
494                  print "<p>$timeStamp $message</p>\n";          # The stuff after the first line feed should be pre-formatted.
495      } elsif ($Destination eq "WARN") {          my @lines = split /\s*\n/, $escapedMessage;
496         # Emit the message as a warning.          # Get the normal portion.
497         warn $message;          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/^>>/) {          } elsif ($Destination =~ m/^>>/) {
503                  # Write the trace message to an output file.                  # Write the trace message to an output file.
504                  open TRACING, $Destination;          open(TRACING, $Destination) || die "Tracing open for \"$Destination\" failed: $!";
505                  print TRACING "$timeStamp $message\n";          # Lock the file.
506            flock TRACING, LOCK_EX;
507            print TRACING "$formatted\n";
508                  close TRACING;                  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($message);
519    
520    Output a trace message that includes memory size information.
521    
522    =over 4
523    
524    =item message
525    
526    Message to display. The message will be followed by a sentence about the memory size.
527    
528    =back
529    
530    =cut
531    
532    sub MemTrace {
533        # Get the parameters.
534        my ($message) = @_;
535        my $memory = GetMemorySize();
536        Trace("$message $memory in use.");
537          }          }
538    
539    
540    =head3 TraceDump
541    
542        TraceDump($title, $object);
543    
544    Dump an object to the trace log. This method simply calls the C<Dumper>
545    function, but routes the output to the trace log instead of returning it
546    as a string. The output is arranged so that it comes out monospaced when
547    it appears in an HTML trace dump.
548    
549    =over 4
550    
551    =item title
552    
553    Title to give to the object being dumped.
554    
555    =item object
556    
557    Reference to a list, hash, or object to dump.
558    
559    =back
560    
561    =cut
562    
563    sub TraceDump {
564        # Get the parameters.
565        my ($title, $object) = @_;
566        # Trace the object.
567        Trace("Object dump for $title:\n" . Dumper($object));
568  }  }
569    
570  =head3 T  =head3 T
571    
572  C<< my $switch = T($category, $traceLevel); >>      my $switch = T($category, $traceLevel);
573    
574          or          or
575    
576  C<< my $switch = T($traceLevel); >>      my $switch = T($traceLevel);
577    
578  Return TRUE if the trace level is at or above a specified value and the specified category  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.  is active, else FALSE. If no category is specified, the caller's package name is used.
# Line 349  Line 606 
606                  my ($category, $traceLevel) = @_;                  my ($category, $traceLevel) = @_;
607                  if (!defined $traceLevel) {                  if (!defined $traceLevel) {
608                          # Here we have no category, so we need to get the calling package.                          # 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;                          $traceLevel = $category;
614                          my ($package, $fileName, $line) = caller;                          my ($package, $fileName, $line) = caller;
615              # If there is no calling package, we default to "main".              # If there is no calling package, we default to "main".
616                          if (!$package) {                          if (!$package) {
617                  $category = "main";                  $category = "main";
618                          } else {                          } else {
619                                  $category = $package;                  my @cats = split /::/, $package;
620                    $category = $cats[$#cats];
621                          }                          }
622                  }                  }
623                  # Use the package and tracelevel to compute the result.          # Save the category name and level.
624                  $retVal = ($traceLevel <= $TraceLevel && exists $Categories{$category});          $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.          # Return the computed result.
638      return $retVal;      return $retVal;
639  }  }
640    
641  =head3 ParseCommand  =head3 QTrace
   
 C<< my ($options, @arguments) = Tracer::ParseCommand(\%optionTable, @inputList); >>  
642    
643  Parse a command line consisting of a list of parameters. The initial parameters may be option      my $data = QTrace($format);
 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.  
644    
645  C<< my ($options, @arguments) = ParseCommand({ errors => 0, logFile => 'trace.log'}, @words); >>  Return the queued trace data in the specified format.
646    
647  In this case, the list @words will be treated as a command line. There are two options available,  =over 4
 B<errors> and B<logFile>. If @words has the following format  
648    
649  C<< -logFile=error.log apple orange rutabaga >>  =item format
650    
651  then at the end of the invocation, C<$options> will be  C<html> to format the data as an HTML list, C<text> to format it as straight text.
652    
653  C<< { errors => 0, logFile => 'error.log' } >>  =back
654    
655  and C<@arguments> will contain  =cut
656    
657  C<< apple orange rutabaga >>  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 $retVal;
682    }
683    
684  The parser allows for some escape sequences. See L</UnEscape> for a description. There is no  =head3 Confess
 support for quote characters.  
685    
686  =over 4      Confess($message);
687    
688  =item optionTable  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  Table of default options.      Assert($recNum >= 0) || Confess("Invalid record number $recNum.");
693    
694  =item inputList  Will abort the program with a stack trace if the value of C<$recNum> is negative.
695    
696  List of words on the command line.  =over 4
697    
698  =item RETURN  =item message
699    
700  Returns a reference to the option table and a list of the positional arguments.  Message to include in the trace.
701    
702  =back  =back
703    
704  =cut  =cut
705    
706  sub ParseCommand {  sub Confess {
707          # Get the parameters.          # Get the parameters.
708          my ($optionTable, @inputList) = @_;      my ($message) = @_;
709          # Process any options in the input list.      # Set up the category and level.
710          my %overrides = ();      $LastCategory = "(confess)";
711          while ((@inputList > 0) && ($inputList[0] =~ /^-/)) {      $LastLevel = 0;
712                  # Get the current option.      # Trace the call stack.
713                  my $arg = shift @inputList;      Cluck($message);
714                  # Pull out the option name.      # Increment the confession count.
715                  $arg =~ /^-([^=]*)/g;      $Confessions++;
716                  my $name = $1;      # Abort the program.
717                  # Check for an option value.      croak(">>> $message");
                 if ($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;  
                 }  
718          }          }
719          # Merge the options into the defaults.  
720          GetOptions($optionTable, \%overrides);  =head3 Confessions
721          # Translate the remaining parameters.  
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 = ();          my @retVal = ();
1052          for my $inputParm (@inputList) {      my $confession = longmess("");
1053                  push @retVal, UnEscape($inputParm);      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 && (my $stat = stat($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 ($now) = gettimeofday;
1135            if ($now - $stat->mtime <= $expire) {
1136                # Emergency tracing is on. Pull off the destination and
1137                # the trace level;
1138                $dest = shift @tracing;
1139                my $level = shift @tracing;
1140                # Insure Tracer is specified.
1141                my %moduleHash = map { $_ => 1 } @tracing;
1142                $moduleHash{Tracer} = 1;
1143                # Set the trace parameter.
1144                $tracing = join(" ", $level, sort keys %moduleHash);
1145            }
1146        }
1147        # Convert the destination to a real tracing destination.
1148        $dest = EmergencyTracingDest($tkey, $dest);
1149        # Setup the tracing we've determined from all the stuff above.
1150        TSetup($tracing, $dest);
1151        # Check to see if we're a web script.
1152        if (defined $SavedCGI) {
1153            # Yes we are. Trace the form and environment data if it's not suppressed.
1154            if (! $noParms) {
1155                TraceParms($SavedCGI);
1156            }
1157            # Check for RAW mode. In raw mode, we print a fake header so that we see everything
1158            # emitted by the script in its raw form.
1159            if (T(Raw => 3)) {
1160                print CGI::header(-type => 'text/plain', -tracing => 'Raw');
1161            }
1162        }
1163    }
1164    
1165    =head3 EmergencyFileName
1166    
1167        my $fileName = Tracer::EmergencyFileName($tkey);
1168    
1169    Return the emergency tracing file name. This is the file that specifies
1170    the tracing information.
1171    
1172    =over 4
1173    
1174    =item tkey
1175    
1176    Tracing key for the current program.
1177    
1178    =item RETURN
1179    
1180    Returns the name of the file to contain the emergency tracing information.
1181    
1182    =back
1183    
1184    =cut
1185    
1186    sub EmergencyFileName {
1187        # Get the parameters.
1188        my ($tkey) = @_;
1189        # Compute the emergency tracing file name.
1190        return "$FIG_Config::temp/Emergency$tkey.txt";
1191    }
1192    
1193    =head3 EmergencyFileTarget
1194    
1195        my $fileName = Tracer::EmergencyFileTarget($tkey);
1196    
1197    Return the emergency tracing target file name. This is the file that receives
1198    the tracing output for file-based tracing.
1199    
1200    =over 4
1201    
1202    =item tkey
1203    
1204    Tracing key for the current program.
1205    
1206    =item RETURN
1207    
1208    Returns the name of the file to contain the trace output.
1209    
1210    =back
1211    
1212    =cut
1213    
1214    sub EmergencyFileTarget {
1215        # Get the parameters.
1216        my ($tkey) = @_;
1217        # Compute the emergency tracing file name.
1218        return "$FIG_Config::temp/trace$tkey.log";
1219    }
1220    
1221    =head3 EmergencyTracingDest
1222    
1223        my $dest = Tracer::EmergencyTracingDest($tkey, $myDest);
1224    
1225    This method converts an emergency tracing destination to a real
1226    tracing destination. The main difference is that if the
1227    destination is C<FILE> or C<APPEND>, we convert it to file
1228    output. If the destination is C<DUAL>, we convert it to file
1229    and standard output.
1230    
1231    =over 4
1232    
1233    =item tkey
1234    
1235    Tracing key for this environment.
1236    
1237    =item myDest
1238    
1239    Destination from the emergency tracing file.
1240    
1241    =item RETURN
1242    
1243    Returns a destination that can be passed into L</TSetup>.
1244    
1245    =back
1246    
1247    =cut
1248    
1249    sub EmergencyTracingDest {
1250        # Get the parameters.
1251        my ($tkey, $myDest) = @_;
1252        # Declare the return variable.
1253        my $retVal = $myDest;
1254        # Process according to the destination value.
1255        if ($myDest eq 'FILE') {
1256            $retVal = ">" . EmergencyFileTarget($tkey);
1257        } elsif ($myDest eq 'APPEND') {
1258            $retVal = ">>" . EmergencyFileTarget($tkey);
1259        } elsif ($myDest eq 'DUAL') {
1260            $retVal = "+>" . EmergencyFileTarget($tkey);
1261        } elsif ($myDest eq 'WARN') {
1262            $retVal = "WARN";
1263        }
1264        # Return the result.
1265        return $retVal;
1266    }
1267    
1268    =head3 Emergency
1269    
1270        Emergency($key, $hours, $dest, $level, @modules);
1271    
1272    Turn on emergency tracing. This method is normally invoked over the web from
1273    a debugging console, but it can also be called by the C<trace.pl> script.
1274    The caller specifies the duration of the emergency in hours, the desired tracing
1275    destination, the trace level, and a list of the trace modules to activate.
1276    For the length of the duration, when a program in an environment with the
1277    specified tracing key active invokes a Sprout CGI script, tracing will be
1278    turned on automatically. See L</TSetup> for more about tracing setup and
1279    L</ETracing> for more about emergency tracing.
1280    
1281    =over 4
1282    
1283    =item tkey
1284    
1285    The tracing key. This is used to identify the control file and the trace file.
1286    
1287    =item hours
1288    
1289    Number of hours to keep emergency tracing alive.
1290    
1291    =item dest
1292    
1293    Tracing destination. If no path information is specified for a file
1294    destination, it is put in the FIG temporary directory.
1295    
1296    =item level
1297    
1298    Tracing level. A higher level means more trace messages.
1299    
1300    =item modules
1301    
1302    A list of the tracing modules to activate.
1303    
1304    =back
1305    
1306    =cut
1307    
1308    sub Emergency {
1309        # Get the parameters.
1310        my ($tkey, $hours, $dest, $level, @modules) = @_;
1311        # Create the emergency file.
1312        my $specFile = EmergencyFileName($tkey);
1313        my $outHandle = Open(undef, ">$specFile");
1314        print $outHandle join("\n", $hours, $dest, $level, @modules, "");
1315    }
1316    
1317    =head3 EmergencyKey
1318    
1319        my $tkey = EmergencyKey($parameter);
1320    
1321    Return the Key to be used for emergency tracing. This could be an IP address,
1322     a session ID, or a user name, depending on the environment.
1323    
1324    =over 4
1325    
1326    =item parameter
1327    
1328    Parameter defining the method for finding the tracing key. If it is a scalar,
1329    then it is presumed to be the tracing key itself. If it is a CGI object, then
1330    the tracing key is taken from the C<IP> cookie. Otherwise, the tracing key is
1331    taken from the C<TRACING> environment variable.
1332    
1333    =item RETURN
1334    
1335    Returns the key to be used for labels in emergency tracing.
1336    
1337    =back
1338    
1339    =cut
1340    
1341    sub EmergencyKey {
1342        # Get the parameters.
1343        my ($parameter) = @_;
1344        # Declare the return variable.
1345        my $retVal;
1346        # Determine the parameter type.
1347        if (! defined $parameter) {
1348            # Here we're supposed to check the environment. If that fails, we
1349            # get the effective login ID.
1350            $retVal = $ENV{TRACING} || scalar getpwuid($<);
1351        } else {
1352            my $ptype = ref $parameter;
1353            if ($ptype eq 'CGI') {
1354                # Here we were invoked from a web page. Look for a cookie.
1355                $retVal = $parameter->cookie('IP');
1356            } elsif (! $ptype) {
1357                # Here the key was passed in.
1358                $retVal = $parameter;
1359            }
1360        }
1361        # If no luck finding a key, use the PID.
1362        if (! defined $retVal) {
1363            $retVal = $$;
1364        }
1365        # Return the result.
1366        return $retVal;
1367    }
1368    
1369    
1370    =head3 TraceParms
1371    
1372        Tracer::TraceParms($cgi);
1373    
1374    Trace the CGI parameters at trace level CGI => 3 and the environment variables
1375    at level CGI => 4. A self-referencing URL is traced at level CGI => 2.
1376    
1377    =over 4
1378    
1379    =item cgi
1380    
1381    CGI query object containing the parameters to trace.
1382    
1383    =back
1384    
1385    =cut
1386    
1387    sub TraceParms {
1388        # Get the parameters.
1389        my ($cgi) = @_;
1390        if (T(CGI => 2)) {
1391            # Here we trace the GET-style URL for the script, but only if it's
1392            # relatively small.
1393            my $url = $cgi->url(-relative => 1, -query => 1);
1394            my $len = length($url);
1395            if ($len < 500) {
1396                Trace("[URL] $url");
1397            } elsif ($len > 2048) {
1398                Trace("[URL] URL is too long to use with GET ($len characters).");
1399            } else {
1400                Trace("[URL] URL length is $len characters.");
1401            }
1402        }
1403        if (T(CGI => 3)) {
1404            # Here we want to trace the parameter data.
1405            my @names = $cgi->param;
1406            for my $parmName (sort @names) {
1407                # Note we skip the Trace parameters, which are for our use only.
1408                if ($parmName ne 'Trace' && $parmName ne 'TF') {
1409                    my @values = $cgi->param($parmName);
1410                    Trace("[CGI] $parmName = " . join(", ", @values));
1411                }
1412            }
1413            # Display the request method.
1414            my $method = $cgi->request_method();
1415            Trace("Method: $method");
1416        }
1417        if (T(CGI => 4)) {
1418            # Here we want the environment data too.
1419            for my $envName (sort keys %ENV) {
1420                Trace("[ENV] $envName = $ENV{$envName}");
1421            }
1422        }
1423    }
1424    
1425    =head3 TraceImages
1426    
1427        Tracer::TraceImages($htmlString);
1428    
1429    Trace information about all of an html document's images. The tracing
1430    will be for type "IMG" at level 3. The image's source string
1431    will be displayed. This is generally either the URL of the image or
1432    raw data for the image itself. If the source is too long, only the first 300
1433    characters will be shown at trace level 3. The entire source will be shown,
1434    however, at trace level 4. This method is not very smart, and might catch
1435    Javascript code, but it is still useful when debugging the arcane
1436    behavior of images in multiple browser environments.
1437    
1438    =over 4
1439    
1440    =item htmlString
1441    
1442    HTML text for an outgoing web page.
1443    
1444    =back
1445    
1446    =cut
1447    
1448    sub TraceImages {
1449        # Only proceed if we're at the proper trace level.
1450        if (T(IMG => 3)) {
1451            # For performance reasons we're manipulating $_[0] instead of retrieving the string
1452            # into a variable called "$htmlString". This is because we expect html strings to be
1453            # long, and don't want to copy them any more than we have to.
1454            Trace(length($_[0]) . " characters in web page.");
1455            # Loop through the HTML, culling image tags.
1456            while ($_[0] =~ /<img\s+[^>]+?src="([^"]+)"/sgi) {
1457                # Extract the source string and determine whether or not it's too long.
1458                my $srcString = $1;
1459                my $pos = pos($_[0]) - length($srcString);
1460                my $excess = length($srcString) - 300;
1461                # We'll put the display string in here.
1462                my $srcDisplay = $srcString;
1463                # If it's a data string, split it at the comma.
1464                $srcDisplay =~ s/^(data[^,]+,)/$1\n/;
1465                # If there's no excess or we're at trace level 4, we're done. At level 3 with
1466                # a long string, however, we only show the first 300 characters.
1467                if ($excess > 0 && ! T(IMG => 4)) {
1468                    $srcDisplay = substr($srcDisplay,0,300) . "\nplus $excess characters.";
1469                }
1470                # Output the trace message.
1471                Trace("Image tag at position $pos:\n$srcDisplay");
1472            }
1473        }
1474    }
1475    
1476    =head2 Command-Line Utility Methods
1477    
1478    =head3 SendSMS
1479    
1480        my $msgID = Tracer::SendSMS($phoneNumber, $msg);
1481    
1482    Send a text message to a phone number using Clickatell. The FIG_Config file must contain the
1483    user name, password, and API ID for the relevant account in the hash reference variable
1484    I<$FIG_Config::phone>, using the keys C<user>, C<password>, and C<api_id>. For
1485    example, if the user name is C<BruceTheHumanPet>, the password is C<silly>, and the API ID
1486    is C<2561022>, then the FIG_Config file must contain
1487    
1488        $phone =  { user => 'BruceTheHumanPet',
1489                    password => 'silly',
1490                    api_id => '2561022' };
1491    
1492    The original purpose of this method was to insure Bruce would be notified immediately when the
1493    Sprout Load terminates. Care should be taken if you do not wish Bruce to be notified immediately
1494    when you call this method.
1495    
1496    The message ID will be returned if successful, and C<undef> if an error occurs.
1497    
1498    =over 4
1499    
1500    =item phoneNumber
1501    
1502    Phone number to receive the message, in international format. A United States phone number
1503    would be prefixed by "1". A British phone number would be prefixed by "44".
1504    
1505    =item msg
1506    
1507    Message to send to the specified phone.
1508    
1509    =item RETURN
1510    
1511    Returns the message ID if successful, and C<undef> if the message could not be sent.
1512    
1513    =back
1514    
1515    =cut
1516    
1517    sub SendSMS {
1518        # Get the parameters.
1519        my ($phoneNumber, $msg) = @_;
1520        # Declare the return variable. If we do not change it, C<undef> will be returned.
1521        my $retVal;
1522        # Only proceed if we have phone support.
1523        if (! defined $FIG_Config::phone) {
1524            Trace("Phone support not present in FIG_Config.") if T(1);
1525        } else {
1526            # Get the phone data.
1527            my $parms = $FIG_Config::phone;
1528            # Get the Clickatell URL.
1529            my $url = "http://api.clickatell.com/http/";
1530            # Create the user agent.
1531            my $ua = LWP::UserAgent->new;
1532            # Request a Clickatell session.
1533            my $resp = $ua->post("$url/sendmsg", { user => $parms->{user},
1534                                         password => $parms->{password},
1535                                         api_id => $parms->{api_id},
1536                                         to => $phoneNumber,
1537                                         text => $msg});
1538            # Check for an error.
1539            if (! $resp->is_success) {
1540                Trace("Alert failed.") if T(1);
1541            } else {
1542                # Get the message ID.
1543                my $rstring = $resp->content;
1544                if ($rstring =~ /^ID:\s+(.*)$/) {
1545                    $retVal = $1;
1546                } else {
1547                    Trace("Phone attempt failed with $rstring") if T(1);
1548                }
1549            }
1550        }
1551        # Return the result.
1552        return $retVal;
1553    }
1554    
1555    =head3 StandardSetup
1556    
1557        my ($options, @parameters) = StandardSetup(\@categories, \%options, $parmHelp, @ARGV);
1558    
1559    This method performs standard command-line parsing and tracing setup. The return
1560    values are a hash of the command-line options and a list of the positional
1561    parameters. Tracing is automatically set up and the command-line options are
1562    validated.
1563    
1564    This is a complex method that does a lot of grunt work. The parameters can
1565    be more easily understood, however, once they are examined individually.
1566    
1567    The I<categories> parameter is the most obtuse. It is a reference to a list of
1568    special-purpose tracing categories. Most tracing categories are PERL package
1569    names. So, for example, if you wanted to turn on tracing inside the B<Sprout>,
1570    B<ERDB>, and B<SproutLoad> packages, you would specify the categories
1571    
1572        ["Sprout", "SproutLoad", "ERDB"]
1573    
1574    This would cause trace messages in the specified three packages to appear in
1575    the output. There are two special tracing categories that are automatically
1576    handled by this method. In other words, if you used L</TSetup> you would need
1577    to include these categories manually, but if you use this method they are turned
1578    on automatically.
1579    
1580    =over 4
1581    
1582    =item SQL
1583    
1584    Traces SQL commands and activity.
1585    
1586    =item Tracer
1587    
1588    Traces error messages and call stacks.
1589    
1590    =back
1591    
1592    C<SQL> is only turned on if the C<-sql> option is specified in the command line.
1593    The trace level is specified using the C<-trace> command-line option. For example,
1594    the following command line for C<TransactFeatures> turns on SQL tracing and runs
1595    all tracing at level 3.
1596    
1597        TransactFeatures -trace=3 -sql register ../xacts IDs.tbl
1598    
1599    Standard tracing is output to the standard output and echoed to the file
1600    C<trace>I<$$>C<.log> in the FIG temporary directory, where I<$$> is the
1601    process ID. You can also specify the C<user> parameter to put a user ID
1602    instead of a process ID in the trace file name. So, for example
1603    
1604    The default trace level is 2. To get all messages, specify a trace level of 4.
1605    For a genome-by-genome update, use 3.
1606    
1607        TransactFeatures -trace=3 -sql -user=Bruce register ../xacts IDs.tbl
1608    
1609    would send the trace output to C<traceBruce.log> in the temporary directory.
1610    
1611    The I<options> parameter is a reference to a hash containing the command-line
1612    options, their default values, and an explanation of what they mean. Command-line
1613    options may be in the form of switches or keywords. In the case of a switch, the
1614    option value is 1 if it is specified and 0 if it is not specified. In the case
1615    of a keyword, the value is separated from the option name by an equal sign. You
1616    can see this last in the command-line example above.
1617    
1618    You can specify a different default trace level by setting C<$options->{trace}>
1619    prior to calling this method.
1620    
1621    An example at this point would help. Consider, for example, the command-line utility
1622    C<TransactFeatures>. It accepts a list of positional parameters plus the options
1623    C<safe>, C<noAlias>, C<start>, and C<tblFiles>. To start up this command, we execute
1624    the following code.
1625    
1626        my ($options, @parameters) = Tracer::StandardSetup(["DocUtils"],
1627                            { safe => [0, "use database transactions"],
1628                              noAlias => [0, "do not expect aliases in CHANGE transactions"],
1629                              start => [' ', "start with this genome"],
1630                              tblFiles => [0, "output TBL files containing the corrected IDs"] },
1631                            "<command> <transactionDirectory> <IDfile>",
1632                          @ARGV);
1633    
1634    
1635    The call to C<ParseCommand> specifies the default values for the options and
1636    stores the actual options in a hash that is returned as C<$options>. The
1637    positional parameters are returned in C<@parameters>.
1638    
1639    The following is a sample command line for C<TransactFeatures>.
1640    
1641        TransactFeatures -trace=2 -noAlias register ../xacts IDs.tbl
1642    
1643    Single and double hyphens are equivalent. So, you could also code the
1644    above command as
1645    
1646        TransactFeatures --trace=2 --noAlias register ../xacts IDs.tbl
1647    
1648    In this case, C<register>, C<../xacts>, and C<IDs.tbl> are the positional
1649    parameters, and would find themselves in I<@parameters> after executing the
1650    above code fragment. The tracing would be set to level 2, and the categories
1651    would be C<Tracer>, and <DocUtils>. C<Tracer> is standard,
1652    and C<DocUtils> was included because it came in within the first parameter
1653    to this method. The I<$options> hash would be
1654    
1655        { trace => 2, sql => 0, safe => 0,
1656          noAlias => 1, start => ' ', tblFiles => 0 }
1657    
1658    Use of C<StandardSetup> in this way provides a simple way of performing
1659    standard tracing setup and command-line parsing. Note that the caller is
1660    not even aware of the command-line switches C<-trace> and C<-sql>, which
1661    are used by this method to control the tracing. If additional tracing features
1662    need to be added in the future, they can be processed by this method without
1663    upsetting the command-line utilities.
1664    
1665    If the C<background> option is specified on the command line, then the
1666    standard and error outputs will be directed to files in the temporary
1667    directory, using the same suffix as the trace file. So, if the command
1668    line specified
1669    
1670        -user=Bruce -background
1671    
1672    then the trace output would go to C<traceBruce.log>, the standard output to
1673    C<outBruce.log>, and the error output to C<errBruce.log>. This is designed to
1674    simplify starting a command in the background.
1675    
1676    The user name is also used as the tracing key for L</Emergency Tracing>.
1677    Specifying a value of C<E> for the trace level causes emergency tracing to
1678    be used instead of custom tracing. If the user name is not specified,
1679    the tracing key is taken from the C<Tracing> environment variable. If there
1680    is no value for that variable, the tracing key will be computed from the active
1681    login ID.
1682    
1683    Since the default situation in StandardSetup is to trace to the standard
1684    output, errors that occur in command-line scripts will not generate
1685    RSS events. To force the events, use the C<warn> option.
1686    
1687        TransactFeatures -background -warn register ../xacts IDs.tbl
1688    
1689    Finally, if the special option C<-help> is specified, the option
1690    names will be traced at level 0 and the program will exit without processing.
1691    This provides a limited help capability. For example, if the user enters
1692    
1693        TransactFeatures -help
1694    
1695    he would see the following output.
1696    
1697        TransactFeatures [options] <command> <transactionDirectory> <IDfile>
1698            -trace    tracing level (default E)
1699            -sql      trace SQL commands
1700            -safe     use database transactions
1701            -noAlias  do not expect aliases in CHANGE transactions
1702            -start    start with this genome
1703            -tblFiles output TBL files containing the corrected IDs
1704            -forked   do not erase the trace file before tracing
1705    
1706    The caller has the option of modifying the tracing scheme by placing a value
1707    for C<trace> in the incoming options hash. The default value can be overridden,
1708    or the tracing to the standard output can be turned off by suffixing a minus
1709    sign to the trace level. So, for example,
1710    
1711        { trace => [0, "tracing level (default 0)"],
1712           ...
1713    
1714    would set the default trace level to 0 instead of E, while
1715    
1716        { trace => ["2-", "tracing level (default 2)"],
1717           ...
1718    
1719    would set the default to 2, but trace only to the log file, not to the
1720    standard output.
1721    
1722    The parameters to this method are as follows.
1723    
1724    =over 4
1725    
1726    =item categories
1727    
1728    Reference to a list of tracing category names. These should be names of
1729    packages whose internal workings will need to be debugged to get the
1730    command working.
1731    
1732    =item options
1733    
1734    Reference to a hash containing the legal options for the current command mapped
1735    to their default values and descriptions. The user can override the defaults
1736    by specifying the options as command-line switches prefixed by a hyphen.
1737    Tracing-related options may be added to this hash. If the C<-h> option is
1738    specified on the command line, the option descriptions will be used to
1739    explain the options. To turn off tracing to the standard output, add a
1740    minus sign to the value for C<trace> (see above).
1741    
1742    =item parmHelp
1743    
1744    A string that vaguely describes the positional parameters. This is used
1745    if the user specifies the C<-h> option.
1746    
1747    =item argv
1748    
1749    List of command line parameters, including the option switches, which must
1750    precede the positional parameters and be prefixed by a hyphen.
1751    
1752    =item RETURN
1753    
1754    Returns a list. The first element of the list is the reference to a hash that
1755    maps the command-line option switches to their values. These will either be the
1756    default values or overrides specified on the command line. The remaining
1757    elements of the list are the position parameters, in order.
1758    
1759    =back
1760    
1761    =cut
1762    
1763    sub StandardSetup {
1764        # Get the parameters.
1765        my ($categories, $options, $parmHelp, @argv) = @_;
1766        # Get the default tracing key.
1767        my $tkey = EmergencyKey();
1768        # Save the command line.
1769        $CommandLine = join(" ", $0, map { $_ =~ /\s/ ? "\"$_\"" : $_ } @argv);
1770        # Add the tracing options.
1771        if (! exists $options->{trace}) {
1772            $options->{trace} = ['2', "tracing level (E for emergency tracing)"];
1773        }
1774        if (! exists $options->{forked}) {
1775            $options->{forked} = [0, "keep old trace file"];
1776        }
1777        $options->{sql} = [0, "turn on SQL tracing"];
1778        $options->{help} = [0, "display command-line options"];
1779        $options->{user} = [$tkey, "tracing key"];
1780        $options->{background} = [0, "spool standard and error output"];
1781        $options->{warn} = [0, "send errors to RSS feed"];
1782        $options->{moreTracing} = ["", "comma-delimited list of additional trace modules for debugging"];
1783        # Create a parsing hash from the options hash. The parsing hash
1784        # contains the default values rather than the default value
1785        # and the description. While we're at it, we'll memorize the
1786        # length of the longest option name.
1787        my $longestName = 0;
1788        my %parseOptions = ();
1789        for my $key (keys %{$options}) {
1790            if (length $key > $longestName) {
1791                $longestName = length $key;
1792            }
1793            $parseOptions{$key} = $options->{$key}->[0];
1794        }
1795        # Parse the command line.
1796        my ($retOptions, @retParameters) = ParseCommand(\%parseOptions, @argv);
1797        # Get the logfile suffix.
1798        my $suffix = $retOptions->{user};
1799        # We'll put the trace file name in here. We need it later if background
1800        # mode is on.
1801        my $traceFileName;
1802        # Now we want to set up tracing. First, we need to know if the user
1803        # wants emergency tracing.
1804        if ($retOptions->{trace} eq 'E') {
1805            ETracing($retOptions->{user});
1806        } else {
1807            # Here the tracing is controlled from the command line.
1808            my @cats = @{$categories};
1809            if ($retOptions->{sql}) {
1810                push @cats, "SQL";
1811            }
1812            if ($retOptions->{warn}) {
1813                push @cats, "Feed";
1814            }
1815            # Add the default categories.
1816            push @cats, "Tracer";
1817            # Check for more tracing groups.
1818            if ($retOptions->{moreTracing}) {
1819                push @cats, split /,/, $retOptions->{moreTracing};
1820            }
1821            # Next, we create the category string by joining the categories.
1822            my $cats = join(" ", @cats);
1823            # Check to determine whether or not the caller wants to turn off tracing
1824            # to the standard output.
1825            my $traceLevel = $retOptions->{trace};
1826            my $textOKFlag = 1;
1827            if ($traceLevel =~ /^(.)-/) {
1828                $traceLevel = $1;
1829                $textOKFlag = 0;
1830            }
1831            # Now we set up the trace mode.
1832            my $traceMode;
1833            # Verify that we can open a file in the FIG temporary directory.
1834            my $traceFileName = "$FIG_Config::temp/trace$suffix.log";
1835            my $traceFileSpec = ($retOptions->{forked} ? ">>$traceFileName" : ">$traceFileName");
1836            if (open TESTTRACE, "$traceFileSpec") {
1837                # Here we can trace to a file.
1838                $traceMode = ">>$traceFileName";
1839                if ($textOKFlag) {
1840                    # Echo to standard output if the text-OK flag is set.
1841                    $traceMode = "+$traceMode";
1842                }
1843                # Close the test file.
1844                close TESTTRACE;
1845            } else {
1846                # Here we can't trace to a file. Complain about this.
1847                warn "Could not open trace file $traceFileName: $!\n";
1848                # We trace to the standard output if it's
1849                # okay, and the error log otherwise.
1850                if ($textOKFlag) {
1851                    $traceMode = "TEXT";
1852                } else {
1853                    $traceMode = "WARN";
1854                }
1855            }
1856            # Now set up the tracing.
1857            TSetup("$traceLevel $cats", $traceMode);
1858        }
1859        # Check for background mode.
1860        if ($retOptions->{background}) {
1861            my $outFileName = "$FIG_Config::temp/out$suffix$$.log";
1862            my $errFileName = "$FIG_Config::temp/err$suffix$$.log";
1863            # Spool the output.
1864            open STDOUT, ">$outFileName";
1865            # If we have a trace file, trace the errors to the log. Otherwise,
1866            # spool the errors.
1867            if (defined $traceFileName) {
1868                open STDERR, "| Tracer $traceFileName";
1869            } else {
1870                open STDERR, ">$errFileName";
1871            }
1872            # Check for phone support. If we have phone support and a phone number,
1873            # we want to turn it on.
1874            if ($ENV{PHONE} && defined($FIG_Config::phone)) {
1875                $retOptions->{phone} = $ENV{PHONE};
1876            }
1877        }
1878        # Check for the "help" option. If it is specified, dump the command-line
1879        # options and exit the program.
1880        if ($retOptions->{help}) {
1881            $0 =~ m#[/\\](\w+)(\.pl)?$#i;
1882            print "$1 [options] $parmHelp\n";
1883            for my $key (sort keys %{$options}) {
1884                my $name = Pad($key, $longestName, 0, ' ');
1885                my $desc = $options->{$key}->[1];
1886                if ($options->{$key}->[0]) {
1887                    $desc .= " (default " . $options->{$key}->[0] . ")";
1888                }
1889                print "  $name $desc\n";
1890            }
1891            exit(0);
1892        }
1893        # Trace the options, if applicable.
1894        if (T(3)) {
1895            my @parms = grep { $retOptions->{$_} } keys %{$retOptions};
1896            Trace("Selected options: " . join(", ", sort @parms) . ".");
1897        }
1898        # Return the parsed parameters.
1899        return ($retOptions, @retParameters);
1900    }
1901    
1902    =head3 ReadOptions
1903    
1904        my %options = Tracer::ReadOptions($fileName);
1905    
1906    Read a set of options from a file. Each option is encoded in a line of text that has the
1907    format
1908    
1909    I<optionName>C<=>I<optionValue>C<; >I<comment>
1910    
1911    The option name must consist entirely of letters, digits, and the punctuation characters
1912    C<.> and C<_>, and is case sensitive. Blank lines and lines in which the first nonblank
1913    character is a semi-colon will be ignored. The return hash will map each option name to
1914    the corresponding option value.
1915    
1916    =over 4
1917    
1918    =item fileName
1919    
1920    Name of the file containing the option data.
1921    
1922    =item RETURN
1923    
1924    Returns a hash mapping the option names specified in the file to their corresponding option
1925    value.
1926    
1927    =back
1928    
1929    =cut
1930    
1931    sub ReadOptions {
1932        # Get the parameters.
1933        my ($fileName) = @_;
1934        # Open the file.
1935        (open CONFIGFILE, "<$fileName") || Confess("Could not open option file $fileName.");
1936        # Count the number of records read.
1937        my ($records, $comments) = 0;
1938        # Create the return hash.
1939        my %retVal = ();
1940        # Loop through the file, accumulating key-value pairs.
1941        while (my $line = <CONFIGFILE>) {
1942            # Denote we've read a line.
1943            $records++;
1944            # Determine the line type.
1945            if ($line =~ /^\s*[\n\r]/) {
1946                # A blank line is a comment.
1947                $comments++;
1948            } elsif ($line =~ /^\s*([A-Za-z0-9_\.]+)=([^;]*);/) {
1949                # Here we have an option assignment.
1950                retVal{$1} = $2;
1951            } elsif ($line =~ /^\s*;/) {
1952                # Here we have a text comment.
1953                $comments++;
1954            } else {
1955                # Here we have an invalid line.
1956                Trace("Invalid option statement in record $records.") if T(0);
1957            }
1958        }
1959        # Return the hash created.
1960        return %retVal;
1961    }
1962    
1963    =head3 GetOptions
1964    
1965        Tracer::GetOptions(\%defaults, \%options);
1966    
1967    Merge a specified set of options into a table of defaults. This method takes two hash references
1968    as input and uses the data from the second to update the first. If the second does not exist,
1969    there will be no effect. An error will be thrown if one of the entries in the second hash does not
1970    exist in the first.
1971    
1972    Consider the following example.
1973    
1974        my $optionTable = GetOptions({ dbType => 'mySQL', trace => 0 }, $options);
1975    
1976    In this example, the variable B<$options> is expected to contain at most two options-- B<dbType> and
1977    B<trace>. The default database type is C<mySQL> and the default trace level is C<0>. If the value of
1978    B<$options> is C<< {dbType => 'Oracle'} >>, then the database type will be changed to C<Oracle> and
1979    the trace level will remain at 0. If B<$options> is undefined, then the database type and trace level
1980    will remain C<mySQL> and C<0>. If, on the other hand, B<$options> is defined as
1981    
1982        {databaseType => 'Oracle'}
1983    
1984    an error will occur because the B<databaseType> option does not exist.
1985    
1986    =over 4
1987    
1988    =item defaults
1989    
1990    Table of default option values.
1991    
1992    =item options
1993    
1994    Table of overrides, if any.
1995    
1996    =item RETURN
1997    
1998    Returns a reference to the default table passed in as the first parameter.
1999    
2000    =back
2001    
2002    =cut
2003    
2004    sub GetOptions {
2005        # Get the parameters.
2006        my ($defaults, $options) = @_;
2007        # Check for overrides.
2008        if ($options) {
2009            # Loop through the overrides.
2010            while (my ($option, $setting) = each %{$options}) {
2011                # Insure this override exists.
2012                if (!exists $defaults->{$option}) {
2013                    croak "Unrecognized option $option encountered.";
2014                } else {
2015                    # Apply the override.
2016                    $defaults->{$option} = $setting;
2017                }
2018            }
2019        }
2020        # Return the merged table.
2021        return $defaults;
2022    }
2023    
2024    =head3 MergeOptions
2025    
2026        Tracer::MergeOptions(\%table, \%defaults);
2027    
2028    Merge default values into a hash table. This method looks at the key-value pairs in the
2029    second (default) hash, and if a matching key is not found in the first hash, the default
2030    pair is copied in. The process is similar to L</GetOptions>, but there is no error-
2031    checking and no return value.
2032    
2033    =over 4
2034    
2035    =item table
2036    
2037    Hash table to be updated with the default values.
2038    
2039    =item defaults
2040    
2041    Default values to be merged into the first hash table if they are not already present.
2042    
2043    =back
2044    
2045    =cut
2046    
2047    sub MergeOptions {
2048        # Get the parameters.
2049        my ($table, $defaults) = @_;
2050        # Loop through the defaults.
2051        while (my ($key, $value) = each %{$defaults}) {
2052            if (!exists $table->{$key}) {
2053                $table->{$key} = $value;
2054            }
2055        }
2056    }
2057    
2058    =head3 UnparseOptions
2059    
2060        my $optionString = Tracer::UnparseOptions(\%options);
2061    
2062    Convert an option hash into a command-line string. This will not
2063    necessarily be the same text that came in, but it will nonetheless
2064    produce the same ultimate result when parsed by L</StandardSetup>.
2065    
2066    =over 4
2067    
2068    =item options
2069    
2070    Reference to a hash of options to convert into an option string.
2071    
2072    =item RETURN
2073    
2074    Returns a string that will parse to the same set of options when
2075    parsed by L</StandardSetup>.
2076    
2077    =back
2078    
2079    =cut
2080    
2081    sub UnparseOptions {
2082        # Get the parameters.
2083        my ($options) = @_;
2084        # The option segments will be put in here.
2085        my @retVal = ();
2086        # Loop through the options.
2087        for my $key (keys %$options) {
2088            # Get the option value.
2089            my $value = $options->{$key};
2090            # Only use it if it's nonempty.
2091            if (defined $value && $value ne "") {
2092                my $segment = "--$key=$value";
2093                # Quote it if necessary.
2094                if ($segment =~ /[ |<>*]/) {
2095                    $segment = '"' . $segment . '"';
2096                }
2097                # Add it to the return list.
2098                push @retVal, $segment;
2099            }
2100        }
2101        # Return the result.
2102        return join(" ", @retVal);
2103    }
2104    
2105    =head3 ParseCommand
2106    
2107        my ($options, @arguments) = Tracer::ParseCommand(\%optionTable, @inputList);
2108    
2109    Parse a command line consisting of a list of parameters. The initial parameters may be option
2110    specifiers of the form C<->I<option> or C<->I<option>C<=>I<value>. The options are stripped
2111    off and merged into a table of default options. The remainder of the command line is
2112    returned as a list of positional arguments. For example, consider the following invocation.
2113    
2114        my ($options, @arguments) = ParseCommand({ errors => 0, logFile => 'trace.log'}, @words);
2115    
2116    In this case, the list @words will be treated as a command line and there are two options available,
2117    B<errors> and B<logFile>. If @words has the following format
2118    
2119        -logFile=error.log apple orange rutabaga
2120    
2121    then at the end of the invocation, C<$options> will be
2122    
2123        { errors => 0, logFile => 'error.log' }
2124    
2125    and C<@arguments> will contain
2126    
2127        apple orange rutabaga
2128    
2129    The parser allows for some escape sequences. See L</UnEscape> for a description. There is no
2130    support for quote characters. Options can be specified with single or double hyphens.
2131    
2132    =over 4
2133    
2134    =item optionTable
2135    
2136    Table of default options.
2137    
2138    =item inputList
2139    
2140    List of words on the command line.
2141    
2142    =item RETURN
2143    
2144    Returns a reference to the option table and a list of the positional arguments.
2145    
2146    =back
2147    
2148    =cut
2149    
2150    sub ParseCommand {
2151        # Get the parameters.
2152        my ($optionTable, @inputList) = @_;
2153        # Process any options in the input list.
2154        my %overrides = ();
2155        while ((@inputList > 0) && ($inputList[0] =~ /^--?/)) {
2156            # Get the current option.
2157            my $arg = shift @inputList;
2158            # Pull out the option name.
2159            $arg =~ /^--?([^=]*)/g;
2160            my $name = $1;
2161            # Check for an option value.
2162            if ($arg =~ /\G=(.*)$/g) {
2163                # Here we have a value for the option.
2164                $overrides{$name} = UnEscape($1);
2165            } else {
2166                # Here there is no value, so we use 1.
2167                $overrides{$name} = 1;
2168            }
2169        }
2170        # Merge the options into the defaults.
2171        GetOptions($optionTable, \%overrides);
2172        # Translate the remaining parameters.
2173        my @retVal = ();
2174        for my $inputParm (@inputList) {
2175            push @retVal, UnEscape($inputParm);
2176        }
2177        # Return the results.
2178        return ($optionTable, @retVal);
2179    }
2180    
2181    
2182    =head2 File Utility Methods
2183    
2184    =head3 GetFile
2185    
2186        my @fileContents = Tracer::GetFile($fileName);
2187    
2188        or
2189    
2190        my $fileContents = Tracer::GetFile($fileName);
2191    
2192    Return the entire contents of a file. In list context, line-ends are removed and
2193    each line is a list element. In scalar context, line-ends are replaced by C<\n>.
2194    
2195    =over 4
2196    
2197    =item fileName
2198    
2199    Name of the file to read.
2200    
2201    =item RETURN
2202    
2203    In a list context, returns the entire file as a list with the line terminators removed.
2204    In a scalar context, returns the entire file as a string. If an error occurs opening
2205    the file, an empty list will be returned.
2206    
2207    =back
2208    
2209    =cut
2210    
2211    sub GetFile {
2212        # Get the parameters.
2213        my ($fileName) = @_;
2214        # Declare the return variable.
2215        my @retVal = ();
2216        # Open the file for input.
2217        my $handle = Open(undef, "<$fileName");
2218        # Read the whole file into the return variable, stripping off any terminator
2219        # characters.
2220        my $lineCount = 0;
2221        while (my $line = <$handle>) {
2222            $lineCount++;
2223            $line = Strip($line);
2224            push @retVal, $line;
2225        }
2226        # Close it.
2227        close $handle;
2228        my $actualLines = @retVal;
2229        Trace("$actualLines lines read from file $fileName.") if T(File => 2);
2230        # Return the file's contents in the desired format.
2231        if (wantarray) {
2232            return @retVal;
2233        } else {
2234            return join "\n", @retVal;
2235        }
2236    }
2237    
2238    =head3 PutFile
2239    
2240        Tracer::PutFile($fileName, \@lines);
2241    
2242    Write out a file from a list of lines of text.
2243    
2244    =over 4
2245    
2246    =item fileName
2247    
2248    Name of the output file.
2249    
2250    =item lines
2251    
2252    Reference to a list of text lines. The lines will be written to the file in order, with trailing
2253    new-line characters. Alternatively, may be a string, in which case the string will be written without
2254    modification.
2255    
2256    =back
2257    
2258    =cut
2259    
2260    sub PutFile {
2261        # Get the parameters.
2262        my ($fileName, $lines) = @_;
2263        # Open the output file.
2264        my $handle = Open(undef, ">$fileName");
2265        # Count the lines written.
2266        if (ref $lines ne 'ARRAY') {
2267            # Here we have a scalar, so we write it raw.
2268            print $handle $lines;
2269            Trace("Scalar put to file $fileName.") if T(File => 3);
2270        } else {
2271            # Write the lines one at a time.
2272            my $count = 0;
2273            for my $line (@{$lines}) {
2274                print $handle "$line\n";
2275                $count++;
2276            }
2277            Trace("$count lines put to file $fileName.") if T(File => 3);
2278        }
2279        # Close the output file.
2280        close $handle;
2281    }
2282    
2283    =head3 ParseRecord
2284    
2285        my @fields = Tracer::ParseRecord($line);
2286    
2287    Parse a tab-delimited data line. The data line is split into field values. Embedded tab
2288    and new-line characters in the data line must be represented as C<\t> and C<\n>, respectively.
2289    These will automatically be converted.
2290    
2291    =over 4
2292    
2293    =item line
2294    
2295    Line of data containing the tab-delimited fields.
2296    
2297    =item RETURN
2298    
2299    Returns a list of the fields found in the data line.
2300    
2301    =back
2302    
2303    =cut
2304    
2305    sub ParseRecord {
2306        # Get the parameter.
2307        my ($line) = @_;
2308        # Remove the trailing new-line, if any.
2309        chomp $line;
2310        # Split the line read into pieces using the tab character.
2311        my @retVal = split /\t/, $line;
2312        # Trim and fix the escapes in each piece.
2313        for my $value (@retVal) {
2314            # Trim leading whitespace.
2315            $value =~ s/^\s+//;
2316            # Trim trailing whitespace.
2317            $value =~ s/\s+$//;
2318            # Delete the carriage returns.
2319            $value =~ s/\r//g;
2320            # Convert the escapes into their real values.
2321            $value =~ s/\\t/"\t"/ge;
2322            $value =~ s/\\n/"\n"/ge;
2323        }
2324        # Return the result.
2325        return @retVal;
2326    }
2327    
2328    =head3 Merge
2329    
2330        my @mergedList = Tracer::Merge(@inputList);
2331    
2332    Sort a list of strings and remove duplicates.
2333    
2334    =over 4
2335    
2336    =item inputList
2337    
2338    List of scalars to sort and merge.
2339    
2340    =item RETURN
2341    
2342    Returns a list containing the same elements sorted in ascending order with duplicates
2343    removed.
2344    
2345    =back
2346    
2347    =cut
2348    
2349    sub Merge {
2350        # Get the input list in sort order.
2351        my @inputList = sort @_;
2352        # Only proceed if the list has at least two elements.
2353        if (@inputList > 1) {
2354            # Now we want to move through the list splicing out duplicates.
2355            my $i = 0;
2356            while ($i < @inputList) {
2357                # Get the current entry.
2358                my $thisEntry = $inputList[$i];
2359                # Find out how many elements duplicate the current entry.
2360                my $j = $i + 1;
2361                my $dup1 = $i + 1;
2362                while ($j < @inputList && $inputList[$j] eq $thisEntry) { $j++; };
2363                # If the number is nonzero, splice out the duplicates found.
2364                if ($j > $dup1) {
2365                    splice @inputList, $dup1, $j - $dup1;
2366                }
2367                # Now the element at position $dup1 is different from the element before it
2368                # at position $i. We push $i forward one position and start again.
2369                $i++;
2370            }
2371        }
2372        # Return the merged list.
2373        return @inputList;
2374    }
2375    
2376    =head3 Open
2377    
2378        my $handle = Open($fileHandle, $fileSpec, $message);
2379    
2380    Open a file.
2381    
2382    The I<$fileSpec> is essentially the second argument of the PERL C<open>
2383    function. The mode is specified using Unix-like shell information. So, for
2384    example,
2385    
2386        Open(\*LOGFILE, '>>/usr/spool/news/twitlog', "Could not open twit log.");
2387    
2388    would open for output appended to the specified file, and
2389    
2390        Open(\*DATASTREAM, "| sort -u >$outputFile", "Could not open $outputFile.");
2391    
2392    would open a pipe that sorts the records written and removes duplicates. Note
2393    the use of file handle syntax in the Open call. To use anonymous file handles,
2394    code as follows.
2395    
2396        my $logFile = Open(undef, '>>/usr/spool/news/twitlog', "Could not open twit log.");
2397    
2398    The I<$message> parameter is used if the open fails. If it is set to C<0>, then
2399    the open returns TRUE if successful and FALSE if an error occurred. Otherwise, a
2400    failed open will throw an exception and the third parameter will be used to construct
2401    an error message. If the parameter is omitted, a standard message is constructed
2402    using the file spec.
2403    
2404        Could not open "/usr/spool/news/twitlog"
2405    
2406    Note that the mode characters are automatically cleaned from the file name.
2407    The actual error message from the file system will be captured and appended to the
2408    message in any case.
2409    
2410        Could not open "/usr/spool/news/twitlog": file not found.
2411    
2412    In some versions of PERL the only error message we get is a number, which
2413    corresponds to the C++ C<errno> value.
2414    
2415        Could not open "/usr/spool/news/twitlog": 6.
2416    
2417    =over 4
2418    
2419    =item fileHandle
2420    
2421    File handle. If this parameter is C<undef>, a file handle will be generated
2422    and returned as the value of this method.
2423    
2424    =item fileSpec
2425    
2426    File name and mode, as per the PERL C<open> function.
2427    
2428    =item message (optional)
2429    
2430    Error message to use if the open fails. If omitted, a standard error message
2431    will be generated. In either case, the error information from the file system
2432    is appended to the message. To specify a conditional open that does not throw
2433    an error if it fails, use C<0>.
2434    
2435    =item RETURN
2436    
2437    Returns the name of the file handle assigned to the file, or C<undef> if the
2438    open failed.
2439    
2440    =back
2441    
2442    =cut
2443    
2444    sub Open {
2445        # Get the parameters.
2446        my ($fileHandle, $fileSpec, $message) = @_;
2447        # Attempt to open the file.
2448        my $rv = open $fileHandle, $fileSpec;
2449        # If the open failed, generate an error message.
2450        if (! $rv) {
2451            # Save the system error message.
2452            my $sysMessage = $!;
2453            # See if we need a default message.
2454            if (!$message) {
2455                # Clean any obvious mode characters and leading spaces from the
2456                # filename.
2457                my ($fileName) = FindNamePart($fileSpec);
2458                $message = "Could not open \"$fileName\"";
2459            }
2460            # Terminate with an error using the supplied message and the
2461            # error message from the file system.
2462            Confess("$message: $!");
2463        }
2464        # Return the file handle.
2465        return $fileHandle;
2466    }
2467    
2468    =head3 FindNamePart
2469    
2470        my ($fileName, $start, $len) = Tracer::FindNamePart($fileSpec);
2471    
2472    Extract the portion of a file specification that contains the file name.
2473    
2474    A file specification is the string passed to an C<open> call. It specifies the file
2475    mode and name. In a truly complex situation, it can specify a pipe sequence. This
2476    method assumes that the file name is whatever follows the first angle bracket
2477    sequence.  So, for example, in the following strings the file name is
2478    C</usr/fig/myfile.txt>.
2479    
2480        >>/usr/fig/myfile.txt
2481        </usr/fig/myfile.txt
2482        | sort -u > /usr/fig/myfile.txt
2483    
2484    If the method cannot find a file name using its normal methods, it will return the
2485    whole incoming string.
2486    
2487    =over 4
2488    
2489    =item fileSpec
2490    
2491    File specification string from which the file name is to be extracted.
2492    
2493    =item RETURN
2494    
2495    Returns a three-element list. The first element contains the file name portion of
2496    the specified string, or the whole string if a file name cannot be found via normal
2497    methods. The second element contains the start position of the file name portion and
2498    the third element contains the length.
2499    
2500    =back
2501    
2502    =cut
2503    #: Return Type $;
2504    sub FindNamePart {
2505        # Get the parameters.
2506        my ($fileSpec) = @_;
2507        # Default to the whole input string.
2508        my ($retVal, $pos, $len) = ($fileSpec, 0, length $fileSpec);
2509        # Parse out the file name if we can.
2510        if ($fileSpec =~ m/(<|>>?)(.+?)(\s*)$/) {
2511            $retVal = $2;
2512            $len = length $retVal;
2513            $pos = (length $fileSpec) - (length $3) - $len;
2514        }
2515        # Return the result.
2516        return ($retVal, $pos, $len);
2517    }
2518    
2519    =head3 OpenDir
2520    
2521        my @files = OpenDir($dirName, $filtered, $flag);
2522    
2523    Open a directory and return all the file names. This function essentially performs
2524    the functions of an C<opendir> and C<readdir>. If the I<$filtered> parameter is
2525    set to TRUE, all filenames beginning with a period (C<.>), dollar sign (C<$>),
2526    or pound sign (C<#>) and all filenames ending with a tilde C<~>) will be
2527    filtered out of the return list. If the directory does not open and I<$flag> is not
2528    set, an exception is thrown. So, for example,
2529    
2530        my @files = OpenDir("/Volumes/fig/contigs", 1);
2531    
2532    is effectively the same as
2533    
2534        opendir(TMP, "/Volumes/fig/contigs") || Confess("Could not open /Volumes/fig/contigs.");
2535        my @files = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir(TMP);
2536    
2537    Similarly, the following code
2538    
2539        my @files = grep { $_ =~ /^\d/ } OpenDir("/Volumes/fig/orgs", 0, 1);
2540    
2541    Returns the names of all files in C</Volumes/fig/orgs> that begin with digits and
2542    automatically returns an empty list if the directory fails to open.
2543    
2544    =over 4
2545    
2546    =item dirName
2547    
2548    Name of the directory to open.
2549    
2550    =item filtered
2551    
2552    TRUE if files whose names begin with a period (C<.>) should be automatically removed
2553    from the list, else FALSE.
2554    
2555    =item flag
2556    
2557    TRUE if a failure to open is okay, else FALSE
2558    
2559    =back
2560    
2561    =cut
2562    #: Return Type @;
2563    sub OpenDir {
2564        # Get the parameters.
2565        my ($dirName, $filtered, $flag) = @_;
2566        # Declare the return variable.
2567        my @retVal = ();
2568        # Open the directory.
2569        if (opendir(my $dirHandle, $dirName)) {
2570            # The directory opened successfully. Get the appropriate list according to the
2571            # strictures of the filter parameter.
2572            if ($filtered) {
2573                @retVal = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir $dirHandle;
2574            } else {
2575                @retVal = readdir $dirHandle;
2576            }
2577            closedir $dirHandle;
2578        } elsif (! $flag) {
2579            # Here the directory would not open and it's considered an error.
2580            Confess("Could not open directory $dirName.");
2581        }
2582        # Return the result.
2583        return @retVal;
2584    }
2585    
2586    
2587    =head3 Insure
2588    
2589        Insure($dirName, $chmod);
2590    
2591    Insure a directory is present.
2592    
2593    =over 4
2594    
2595    =item dirName
2596    
2597    Name of the directory to check. If it does not exist, it will be created.
2598    
2599    =item chmod (optional)
2600    
2601    Security privileges to be given to the directory if it is created.
2602    
2603    =back
2604    
2605    =cut
2606    
2607    sub Insure {
2608        my ($dirName, $chmod) = @_;
2609        if (! -d $dirName) {
2610            Trace("Creating $dirName directory.") if T(2);
2611            eval {
2612                mkpath $dirName;
2613                # If we have permissions specified, set them here.
2614                if (defined($chmod)) {
2615                    chmod $chmod, $dirName;
2616                }
2617            };
2618            if ($@) {
2619                Confess("Error creating $dirName: $@");
2620            }
2621        }
2622    }
2623    
2624    =head3 ChDir
2625    
2626        ChDir($dirName);
2627    
2628    Change to the specified directory.
2629    
2630    =over 4
2631    
2632    =item dirName
2633    
2634    Name of the directory to which we want to change.
2635    
2636    =back
2637    
2638    =cut
2639    
2640    sub ChDir {
2641        my ($dirName) = @_;
2642        if (! -d $dirName) {
2643            Confess("Cannot change to directory $dirName: no such directory.");
2644        } else {
2645            Trace("Changing to directory $dirName.") if T(File => 4);
2646            my $okFlag = chdir $dirName;
2647            if (! $okFlag) {
2648                Confess("Error switching to directory $dirName.");
2649            }
2650        }
2651    }
2652    
2653    =head3 SetPermissions
2654    
2655        Tracer::SetPermissions($dirName, $group, $mask, %otherMasks);
2656    
2657    Set the permissions for a directory and all the files and folders inside it.
2658    In addition, the group ownership will be changed to the specified value.
2659    
2660    This method is more vulnerable than most to permission and compatability
2661    problems, so it does internal error recovery.
2662    
2663    =over 4
2664    
2665    =item dirName
2666    
2667    Name of the directory to process.
2668    
2669    =item group
2670    
2671    Name of the group to be assigned.
2672    
2673    =item mask
2674    
2675    Permission mask. Bits that are C<1> in this mask will be ORed into the
2676    permission bits of any file or directory that does not already have them
2677    set to 1.
2678    
2679    =item otherMasks
2680    
2681    Map of search patterns to permission masks. If a directory name matches
2682    one of the patterns, that directory and all its members and subdirectories
2683    will be assigned the new pattern. For example, the following would
2684    assign 0664 to most files, but would use 0777 for directories named C<tmp>.
2685    
2686        Tracer::SetPermissions($dirName, 'fig', 01664, '^tmp$' => 01777);
2687    
2688    The list is ordered, so the following would use 0777 for C<tmp1> and
2689    0666 for C<tmp>, C<tmp2>, or C<tmp3>.
2690    
2691        Tracer::SetPermissions($dirName, 'fig', 01664, '^tmp1' => 0777,
2692                                                       '^tmp' => 0666);
2693    
2694    Note that the pattern matches are all case-insensitive, and only directory
2695    names are matched, not file names.
2696    
2697    =back
2698    
2699    =cut
2700    
2701    sub SetPermissions {
2702        # Get the parameters.
2703        my ($dirName, $group, $mask, @otherMasks) = @_;
2704        # Set up for error recovery.
2705        eval {
2706            # Switch to the specified directory.
2707            ChDir($dirName);
2708            # Get the group ID.
2709            my $gid = getgrnam($group);
2710            # Get the mask for tracing.
2711            my $traceMask = sprintf("%04o", $mask) . "($mask)";
2712            Trace("Fixing permissions for directory $dirName using group $group($gid) and mask $traceMask.") if T(File => 2);
2713            my $fixCount = 0;
2714            my $lookCount = 0;
2715            # @dirs will be a stack of directories to be processed.
2716            my @dirs = (getcwd());
2717            while (scalar(@dirs) > 0) {
2718                # Get the current directory.
2719                my $dir = pop @dirs;
2720                # Check for a match to one of the specified directory names. To do
2721                # that, we need to pull the individual part of the name off of the
2722                # whole path.
2723                my $simpleName = $dir;
2724                if ($dir =~ m!/([^/]+)$!) {
2725                    $simpleName = $1;
2726                }
2727                Trace("Simple directory name for $dir is $simpleName.") if T(File => 4);
2728                # Search for a match.
2729                my $match = 0;
2730                my $i;
2731                for ($i = 0; $i < $#otherMasks && ! $match; $i += 2) {
2732                    my $pattern = $otherMasks[$i];
2733                    if ($simpleName =~ /$pattern/i) {
2734                        $match = 1;
2735                    }
2736                }
2737                # Find out if we have a match. Note we use $i-1 because the loop added 2
2738                # before terminating due to the match.
2739                if ($match && $otherMasks[$i-1] != $mask) {
2740                    # This directory matches one of the incoming patterns, and it's
2741                    # a different mask, so we process it recursively with that mask.
2742                    SetPermissions($dir, $group, $otherMasks[$i-1], @otherMasks);
2743                } else {
2744                    # Here we can process normally. Get all of the non-hidden members.
2745                    my @submems = OpenDir($dir, 1);
2746                    for my $submem (@submems) {
2747                        # Get the full name.
2748                        my $thisMem = "$dir/$submem";
2749                        Trace("Checking member $thisMem.") if T(4);
2750                        $lookCount++;
2751                        if ($lookCount % 1000 == 0) {
2752                            Trace("$lookCount members examined. Current is $thisMem. Mask is $traceMask") if T(File => 3);
2753                        }
2754                        # Fix the group.
2755                        chown -1, $gid, $thisMem;
2756                        # Insure this member is not a symlink.
2757                        if (! -l $thisMem) {
2758                            # Get its info.
2759                            my $fileInfo = stat $thisMem;
2760                            # Only proceed if we got the info. Otherwise, it's a hard link
2761                            # and we want to skip it anyway.
2762                            if ($fileInfo) {
2763                                my $fileMode = $fileInfo->mode;
2764                                if (($fileMode & $mask) != $mask) {
2765                                    # Fix this member.
2766                                    $fileMode |= $mask;
2767                                    chmod $fileMode, $thisMem;
2768                                    $fixCount++;
2769                                }
2770                                # If it's a subdirectory, stack it.
2771                                if (-d $thisMem) {
2772                                    push @dirs, $thisMem;
2773                                }
2774                            }
2775                        }
2776                    }
2777                }
2778            }
2779            Trace("$lookCount files and directories processed, $fixCount fixed.") if T(File => 2);
2780        };
2781        # Check for an error.
2782        if ($@) {
2783            Confess("SetPermissions error: $@");
2784        }
2785    }
2786    
2787    =head3 GetLine
2788    
2789        my @data = Tracer::GetLine($handle);
2790    
2791    Read a line of data from a tab-delimited file.
2792    
2793    =over 4
2794    
2795    =item handle
2796    
2797    Open file handle from which to read.
2798    
2799    =item RETURN
2800    
2801    Returns a list of the fields in the record read. The fields are presumed to be
2802    tab-delimited. If we are at the end of the file, then an empty list will be
2803    returned. If an empty line is read, a single list item consisting of a null
2804    string will be returned.
2805    
2806    =back
2807    
2808    =cut
2809    
2810    sub GetLine {
2811        # Get the parameters.
2812        my ($handle) = @_;
2813        # Declare the return variable.
2814        my @retVal = ();
2815        Trace("File position is " . tell($handle) . ". EOF flag is " . eof($handle) . ".") if T(File => 4);
2816        # Read from the file.
2817        my $line = <$handle>;
2818        # Only proceed if we found something.
2819        if (defined $line) {
2820            # Remove the new-line. We are a bit over-cautious here because the file may be coming in via an
2821            # upload control and have a nonstandard EOL combination.
2822            $line =~ s/(\r|\n)+$//;
2823            # Here we do some fancy tracing to help in debugging complicated EOL marks.
2824            if (T(File => 4)) {
2825                my $escapedLine = $line;
2826                $escapedLine =~ s/\n/\\n/g;
2827                $escapedLine =~ s/\r/\\r/g;
2828                $escapedLine =~ s/\t/\\t/g;
2829                Trace("Line read: -->$escapedLine<--");
2830            }
2831            # If the line is empty, return a single empty string; otherwise, parse
2832            # it into fields.
2833            if ($line eq "") {
2834                push @retVal, "";
2835            } else {
2836                push @retVal, split /\t/,$line;
2837            }
2838        } else {
2839            # Trace the reason the read failed.
2840            Trace("End of file: $!") if T(File => 3);
2841        }
2842        # Return the result.
2843        return @retVal;
2844    }
2845    
2846    =head3 PutLine
2847    
2848        Tracer::PutLine($handle, \@fields, $eol);
2849    
2850    Write a line of data to a tab-delimited file. The specified field values will be
2851    output in tab-separated form, with a trailing new-line.
2852    
2853    =over 4
2854    
2855    =item handle
2856    
2857    Output file handle.
2858    
2859    =item fields
2860    
2861    List of field values.
2862    
2863    =item eol (optional)
2864    
2865    End-of-line character (default is "\n").
2866    
2867    =back
2868    
2869    =cut
2870    
2871    sub PutLine {
2872        # Get the parameters.
2873        my ($handle, $fields, $eol) = @_;
2874        # Write the data.
2875        print $handle join("\t", @{$fields}) . ($eol || "\n");
2876    }
2877    
2878    
2879    =head3 PrintLine
2880    
2881        Tracer::PrintLine($line);
2882    
2883    Print a line of text with a trailing new-line.
2884    
2885    =over 4
2886    
2887    =item line
2888    
2889    Line of text to print.
2890    
2891    =back
2892    
2893    =cut
2894    
2895    sub PrintLine {
2896        # Get the parameters.
2897        my ($line) = @_;
2898        # Print the line.
2899        print "$line\n";
2900    }
2901    
2902    
2903    =head2 Other Useful Methods
2904    
2905    =head3 IDHASH
2906    
2907        my $hash = SHTargetSearch::IDHASH(@keys);
2908    
2909    This is a dinky little method that converts a list of values to a reference
2910    to hash of values to labels. The values and labels are the same.
2911    
2912    =cut
2913    
2914    sub IDHASH {
2915        my %retVal = map { $_ => $_ } @_;
2916        return \%retVal;
2917    }
2918    
2919    =head3 Pluralize
2920    
2921        my $plural = Tracer::Pluralize($word);
2922    
2923    This is a very simple pluralization utility. It adds an C<s> at the end
2924    of the input word unless it already ends in an C<s>, in which case it
2925    adds C<es>.
2926    
2927    =over 4
2928    
2929    =item word
2930    
2931    Singular word to pluralize.
2932    
2933    =item RETURN
2934    
2935    Returns the probable plural form of the word.
2936    
2937    =back
2938    
2939    =cut
2940    
2941    sub Pluralize {
2942        # Get the parameters.
2943        my ($word) = @_;
2944        # Declare the return variable.
2945        my $retVal;
2946        if ($word =~ /s$/) {
2947            $retVal = $word . 'es';
2948        } else {
2949            $retVal = $word . 's';
2950        }
2951        # Return the result.
2952        return $retVal;
2953    }
2954    
2955    =head3 Numeric
2956    
2957        my $okFlag = Tracer::Numeric($string);
2958    
2959    Return the value of the specified string if it is numeric, or an undefined value
2960    if it is not numeric.
2961    
2962    =over 4
2963    
2964    =item string
2965    
2966    String to check.
2967    
2968    =item RETURN
2969    
2970    Returns the numeric value of the string if successful, or C<undef> if the string
2971    is not numeric.
2972    
2973    =back
2974    
2975    =cut
2976    
2977    sub Numeric {
2978        # Get the parameters.
2979        my ($string) = @_;
2980        # We'll put the value in here if we succeed.
2981        my $retVal;
2982        # Get a working copy of the string.
2983        my $copy = $string;
2984        # Trim leading and trailing spaces.
2985        $copy =~ s/^\s+//;
2986        $copy =~ s/\s+$//;
2987        # Check the result.
2988        if ($copy =~ /^[+-]?\d+$/) {
2989            $retVal = $copy;
2990        } elsif ($copy =~ /^([+-]\d+|\d*)[eE][+-]?\d+$/) {
2991            $retVal = $copy;
2992        } elsif ($copy =~ /^([+-]\d+|\d*)\.\d*([eE][+-]?\d+)?$/) {
2993            $retVal = $copy;
2994        }
2995        # Return the result.
2996        return $retVal;
2997    }
2998    
2999    
3000    =head3 ParseParm
3001    
3002        my $listValue = Tracer::ParseParm($string);
3003    
3004    Convert a parameter into a list reference. If the parameter is undefined,
3005    an undefined value will be returned. Otherwise, it will be parsed as a
3006    comma-separated list of values.
3007    
3008    =over 4
3009    
3010    =item string
3011    
3012    Incoming string.
3013    
3014    =item RETURN
3015    
3016    Returns a reference to a list of values, or C<undef> if the incoming value
3017    was undefined.
3018    
3019    =back
3020    
3021    =cut
3022    
3023    sub ParseParm {
3024        # Get the parameters.
3025        my ($string) = @_;
3026        # Declare the return variable.
3027        my $retVal;
3028        # Check for data.
3029        if (defined $string) {
3030            # We have some, so split it into a list.
3031            $retVal = [ split /\s*,\s*/, $string];
3032        }
3033        # Return the result.
3034        return $retVal;
3035    }
3036    
3037    =head3 Now
3038    
3039        my $string = Tracer::Now();
3040    
3041    Return a displayable time stamp containing the local time. Whatever format this
3042    method produces must be parseable by L</ParseDate>.
3043    
3044    =cut
3045    
3046    sub Now {
3047        return DisplayTime(time);
3048    }
3049    
3050    =head3 DisplayTime
3051    
3052        my $string = Tracer::DisplayTime($time);
3053    
3054    Convert a time value to a displayable time stamp. Whatever format this
3055    method produces must be parseable by L</ParseDate>.
3056    
3057    =over 4
3058    
3059    =item time
3060    
3061    Time to display, in seconds since the epoch, or C<undef> if the time is unknown.
3062    
3063    =item RETURN
3064    
3065    Returns a displayable time, or C<(n/a)> if the incoming time is undefined.
3066    
3067    =back
3068    
3069    =cut
3070    
3071    sub DisplayTime {
3072        my ($time) = @_;
3073        my $retVal = "(n/a)";
3074        if (defined $time) {
3075            my ($sec,$min,$hour,$mday,$mon,$year,$wday,$yday,$isdst) = localtime($time);
3076            $retVal = _p2($mon+1) . "/" . _p2($mday) . "/" . ($year + 1900) . " " .
3077                      _p2($hour) . ":" . _p2($min) . ":" . _p2($sec);
3078        }
3079        return $retVal;
3080    }
3081    
3082    # Pad a number to 2 digits.
3083    sub _p2 {
3084        my ($value) = @_;
3085        $value = "0$value" if ($value < 10);
3086        return $value;
3087    }
3088    
3089    =head3 Escape
3090    
3091        my $codedString = Tracer::Escape($realString);
3092    
3093    Escape a string for use in a command. Tabs will be replaced by C<\t>, new-lines
3094    replaced by C<\n>, carriage returns will be deleted, and backslashes will be doubled. The
3095    result is to reverse the effect of L</UnEscape>.
3096    
3097    =over 4
3098    
3099    =item realString
3100    
3101    String to escape.
3102    
3103    =item RETURN
3104    
3105    Escaped equivalent of the real string.
3106    
3107    =back
3108    
3109    =cut
3110    
3111    sub Escape {
3112        # Get the parameter.
3113        my ($realString) = @_;
3114        # Initialize the return variable.
3115        my $retVal = "";
3116        # Loop through the parameter string, looking for sequences to escape.
3117        while (length $realString > 0) {
3118            # Look for the first sequence to escape.
3119            if ($realString =~ /^(.*?)([\n\t\r\\])/) {
3120                # Here we found it. The text preceding the sequence is in $1. The sequence
3121                # itself is in $2. First, move the clear text to the return variable.
3122                $retVal .= $1;
3123                # Strip the processed section off the real string.
3124                $realString = substr $realString, (length $2) + (length $1);
3125                # Get the matched character.
3126                my $char = $2;
3127                # If we have a CR, we are done.
3128                if ($char ne "\r") {
3129                    # It's not a CR, so encode the escape sequence.
3130                    $char =~ tr/\t\n/tn/;
3131                    $retVal .= "\\" . $char;
3132                }
3133            } else {
3134                # Here there are no more escape sequences. The rest of the string is
3135                # transferred unmodified.
3136                $retVal .= $realString;
3137                $realString = "";
3138            }
3139        }
3140        # Return the result.
3141        return $retVal;
3142    }
3143    
3144    =head3 UnEscape
3145    
3146        my $realString = Tracer::UnEscape($codedString);
3147    
3148    Replace escape sequences with their actual equivalents. C<\t> will be replaced by
3149    a tab, C<\n> by a new-line character, and C<\\> by a backslash. C<\r> codes will
3150    be deleted.
3151    
3152    =over 4
3153    
3154    =item codedString
3155    
3156    String to un-escape.
3157    
3158    =item RETURN
3159    
3160    Returns a copy of the original string with the escape sequences converted to their actual
3161    values.
3162    
3163    =back
3164    
3165    =cut
3166    
3167    sub UnEscape {
3168        # Get the parameter.
3169        my ($codedString) = @_;
3170        # Initialize the return variable.
3171        my $retVal = "";
3172        # Only proceed if the incoming string is nonempty.
3173        if (defined $codedString) {
3174            # Loop through the parameter string, looking for escape sequences. We can't do
3175            # translating because it causes problems with the escaped slash. ("\\t" becomes
3176            # "\<tab>" no matter what we do.)
3177            while (length $codedString > 0) {
3178                # Look for the first escape sequence.
3179                if ($codedString =~ /^(.*?)\\(\\|n|t|r)/) {
3180                    # Here we found it. The text preceding the sequence is in $1. The sequence
3181                    # itself is in $2. First, move the clear text to the return variable.
3182                    $retVal .= $1;
3183                    $codedString = substr $codedString, (2 + length $1);
3184                    # Get the escape value.
3185                    my $char = $2;
3186                    # If we have a "\r", we are done.
3187                    if ($char ne 'r') {
3188                        # Here it's not an 'r', so we convert it.
3189                        $char =~ tr/\\tn/\\\t\n/;
3190                        $retVal .= $char;
3191                    }
3192                } else {
3193                    # Here there are no more escape sequences. The rest of the string is
3194                    # transferred unmodified.
3195                    $retVal .= $codedString;
3196                    $codedString = "";
3197                }
3198            }
3199        }
3200        # Return the result.
3201        return $retVal;
3202    }
3203    
3204    =head3 Percent
3205    
3206        my $percent = Tracer::Percent($number, $base);
3207    
3208    Returns the percent of the base represented by the given number. If the base
3209    is zero, returns zero.
3210    
3211    =over 4
3212    
3213    =item number
3214    
3215    Percent numerator.
3216    
3217    =item base
3218    
3219    Percent base.
3220    
3221    =item RETURN
3222    
3223    Returns the percentage of the base represented by the numerator.
3224    
3225    =back
3226    
3227    =cut
3228    
3229    sub Percent {
3230        # Get the parameters.
3231        my ($number, $base) = @_;
3232        # Declare the return variable.
3233        my $retVal = 0;
3234        # Compute the percent.
3235        if ($base != 0) {
3236            $retVal = $number * 100 / $base;
3237        }
3238        # Return the result.
3239        return $retVal;
3240    }
3241    
3242    =head3 In
3243    
3244        my $flag = Tracer::In($value, $min, $max);
3245    
3246    Return TRUE if the value is between the minimum and the maximum, else FALSE.
3247    
3248    =cut
3249    
3250    sub In {
3251        return ($_[0] <= $_[2] && $_[0] >= $_[1]);
3252    }
3253    
3254    
3255    =head3 Constrain
3256    
3257        my $constrained = Constrain($value, $min, $max);
3258    
3259    Modify a numeric value to bring it to a point in between a maximum and a minimum.
3260    
3261    =over 4
3262    
3263    =item value
3264    
3265    Value to constrain.
3266    
3267    =item min (optional)
3268    
3269    Minimum permissible value. If this parameter is undefined, no minimum constraint will be applied.
3270    
3271    =item max (optional)
3272    
3273    Maximum permissible value. If this parameter is undefined, no maximum constraint will be applied.
3274    
3275    =item RETURN
3276    
3277    Returns the incoming value, constrained according to the other parameters.
3278    
3279    =back
3280    
3281    =cut
3282    
3283    sub Constrain {
3284        # Get the parameters.
3285        my ($value, $min, $max) = @_;
3286        # Declare the return variable.
3287        my $retVal = $value;
3288        # Apply the minimum constraint.
3289        if (defined $min && $retVal < $min) {
3290            $retVal = $min;
3291        }
3292        # Apply the maximum constraint.
3293        if (defined $max && $retVal > $max) {
3294            $retVal = $max;
3295        }
3296        # Return the result.
3297        return $retVal;
3298    }
3299    
3300    =head3 Min
3301    
3302        my $min = Min($value1, $value2, ... $valueN);
3303    
3304    Return the minimum argument. The arguments are treated as numbers.
3305    
3306    =over 4
3307    
3308    =item $value1, $value2, ... $valueN
3309    
3310    List of numbers to compare.
3311    
3312    =item RETURN
3313    
3314    Returns the lowest number in the list.
3315    
3316    =back
3317    
3318    =cut
3319    
3320    sub Min {
3321        # Get the parameters. Note that we prime the return value with the first parameter.
3322        my ($retVal, @values) = @_;
3323        # Loop through the remaining parameters, looking for the lowest.
3324        for my $value (@values) {
3325            if ($value < $retVal) {
3326                $retVal = $value;
3327            }
3328        }
3329        # Return the minimum found.
3330        return $retVal;
3331    }
3332    
3333    =head3 Max
3334    
3335        my $max = Max($value1, $value2, ... $valueN);
3336    
3337    Return the maximum argument. The arguments are treated as numbers.
3338    
3339    =over 4
3340    
3341    =item $value1, $value2, ... $valueN
3342    
3343    List of numbers to compare.
3344    
3345    =item RETURN
3346    
3347    Returns the highest number in the list.
3348    
3349    =back
3350    
3351    =cut
3352    
3353    sub Max {
3354        # Get the parameters. Note that we prime the return value with the first parameter.
3355        my ($retVal, @values) = @_;
3356        # Loop through the remaining parameters, looking for the highest.
3357        for my $value (@values) {
3358            if ($value > $retVal) {
3359                $retVal = $value;
3360            }
3361        }
3362        # Return the maximum found.
3363        return $retVal;
3364    }
3365    
3366    =head3 Strip
3367    
3368        my $string = Tracer::Strip($line);
3369    
3370    Strip all line terminators off a string. This is necessary when dealing with files
3371    that may have been transferred back and forth several times among different
3372    operating environments.
3373    
3374    =over 4
3375    
3376    =item line
3377    
3378    Line of text to be stripped.
3379    
3380    =item RETURN
3381    
3382    The same line of text with all the line-ending characters chopped from the end.
3383    
3384    =back
3385    
3386    =cut
3387    
3388    sub Strip {
3389        # Get a copy of the parameter string.
3390        my ($string) = @_;
3391        my $retVal = (defined $string ? $string : "");
3392        # Strip the line terminator characters.
3393        $retVal =~ s/(\r|\n)+$//g;
3394        # Return the result.
3395        return $retVal;
3396    }
3397    
3398    =head3 Trim
3399    
3400        my $string = Tracer::Trim($line);
3401    
3402    Trim all spaces from the beginning and ending of a string.
3403    
3404    =over 4
3405    
3406    =item line
3407    
3408    Line of text to be trimmed.
3409    
3410    =item RETURN
3411    
3412    The same line of text with all whitespace chopped off either end.
3413    
3414    =back
3415    
3416    =cut
3417    
3418    sub Trim {
3419        # Get a copy of the parameter string.
3420        my ($string) = @_;
3421        my $retVal = (defined $string ? $string : "");
3422        # Strip the front spaces.
3423        $retVal =~ s/^\s+//;
3424        # Strip the back spaces.
3425        $retVal =~ s/\s+$//;
3426        # Return the result.
3427        return $retVal;
3428    }
3429    
3430    =head3 Pad
3431    
3432        my $paddedString = Tracer::Pad($string, $len, $left, $padChar);
3433    
3434    Pad a string to a specified length. The pad character will be a
3435    space, and the padding will be on the right side unless specified
3436    in the third parameter.
3437    
3438    =over 4
3439    
3440    =item string
3441    
3442    String to be padded.
3443    
3444    =item len
3445    
3446    Desired length of the padded string.
3447    
3448    =item left (optional)
3449    
3450    TRUE if the string is to be left-padded; otherwise it will be padded on the right.
3451    
3452    =item padChar (optional)
3453    
3454    Character to use for padding. The default is a space.
3455    
3456    =item RETURN
3457    
3458    Returns a copy of the original string with the pad character added to the
3459    specified end so that it achieves the desired length.
3460    
3461    =back
3462    
3463    =cut
3464    
3465    sub Pad {
3466        # Get the parameters.
3467        my ($string, $len, $left, $padChar) = @_;
3468        # Compute the padding character.
3469        if (! defined $padChar) {
3470            $padChar = " ";
3471        }
3472        # Compute the number of spaces needed.
3473        my $needed = $len - length $string;
3474        # Copy the string into the return variable.
3475        my $retVal = $string;
3476        # Only proceed if padding is needed.
3477        if ($needed > 0) {
3478            # Create the pad string.
3479            my $pad = $padChar x $needed;
3480            # Affix it to the return value.
3481            if ($left) {
3482                $retVal = $pad . $retVal;
3483            } else {
3484                $retVal .= $pad;
3485            }
3486        }
3487        # Return the result.
3488        return $retVal;
3489    }
3490    
3491    =head3 Quoted
3492    
3493        my $string = Tracer::Quoted($var);
3494    
3495    Convert the specified value to a string and enclose it in single quotes.
3496    If it's undefined, the string C<undef> in angle brackets will be used
3497    instead.
3498    
3499    =over 4
3500    
3501    =item var
3502    
3503    Value to quote.
3504    
3505    =item RETURN
3506    
3507    Returns a string enclosed in quotes, or an indication the value is undefined.
3508    
3509    =back
3510    
3511    =cut
3512    
3513    sub Quoted {
3514        # Get the parameters.
3515        my ($var) = @_;
3516        # Declare the return variable.
3517        my $retVal;
3518        # Are we undefined?
3519        if (! defined $var) {
3520            $retVal = "<undef>";
3521        } else {
3522            # No, so convert to a string and enclose in quotes.
3523            $retVal = $var;
3524            $retVal =~ s/'/\\'/;
3525            $retVal = "'$retVal'";
3526        }
3527        # Return the result.
3528        return $retVal;
3529    }
3530    
3531    =head3 EOF
3532    
3533    This is a constant that is lexically greater than any useful string.
3534    
3535    =cut
3536    
3537    sub EOF {
3538        return "\xFF\xFF\xFF\xFF\xFF";
3539    }
3540    
3541    =head3 TICK
3542    
3543        my @results = TICK($commandString);
3544    
3545    Perform a back-tick operation on a command. If this is a Windows environment, any leading
3546    dot-slash (C<./> will be removed. So, for example, if you were doing
3547    
3548        `./protein.cgi`
3549    
3550    from inside a CGI script, it would work fine in Unix, but would issue an error message
3551    in Windows complaining that C<'.'> is not a valid command. If instead you code
3552    
3553        TICK("./protein.cgi")
3554    
3555    it will work correctly in both environments.
3556    
3557    =over 4
3558    
3559    =item commandString
3560    
3561    The command string to pass to the system.
3562    
3563    =item RETURN
3564    
3565    Returns the standard output from the specified command, as a list.
3566    
3567    =back
3568    
3569    =cut
3570    #: Return Type @;
3571    sub TICK {
3572        # Get the parameters.
3573        my ($commandString) = @_;
3574        # Chop off the dot-slash if this is Windows.
3575        if ($FIG_Config::win_mode) {
3576            $commandString =~ s!^\./!!;
3577        }
3578        # Activate the command and return the result.
3579        return `$commandString`;
3580    }
3581    
3582    
3583    =head3 CommaFormat
3584    
3585        my $formatted = Tracer::CommaFormat($number);
3586    
3587    Insert commas into a number.
3588    
3589    =over 4
3590    
3591    =item number
3592    
3593    A sequence of digits.
3594    
3595    =item RETURN
3596    
3597    Returns the same digits with commas strategically inserted.
3598    
3599    =back
3600    
3601    =cut
3602    
3603    sub CommaFormat {
3604        # Get the parameters.
3605        my ($number) = @_;
3606        # Pad the length up to a multiple of three.
3607        my $padded = "$number";
3608        $padded = " " . $padded while length($padded) % 3 != 0;
3609        # This is a fancy PERL trick. The parentheses in the SPLIT pattern
3610        # cause the delimiters to be included in the output stream. The
3611        # GREP removes the empty strings in between the delimiters.
3612        my $retVal = join(",", grep { $_ ne '' } split(/(...)/, $padded));
3613        # Clean out the spaces.
3614        $retVal =~ s/ //g;
3615        # Return the result.
3616        return $retVal;
3617    }
3618    
3619    
3620    =head3 GetMemorySize
3621    
3622        my $string = Tracer::GetMemorySize();
3623    
3624    Return a memory size string for the current process. The string will be
3625    in comma format, with a size indicator (K, M, G) at the end.
3626    
3627    =cut
3628    
3629    sub GetMemorySize {
3630        # Get the memory size from Unix.
3631        my ($retVal) = `ps h -o vsz $$`;
3632        # Remove the ending new-line.
3633        chomp $retVal;
3634        # Format and return the result.
3635        return CommaFormat($retVal) . "K";
3636    }
3637    
3638    =head3 CompareLists
3639    
3640        my ($inserted, $deleted) = Tracer::CompareLists(\@newList, \@oldList, $keyIndex);
3641    
3642    Compare two lists of tuples, and return a hash analyzing the differences. The lists
3643    are presumed to be sorted alphabetically by the value in the $keyIndex column.
3644    The return value contains a list of items that are only in the new list
3645    (inserted) and only in the old list (deleted).
3646    
3647    =over 4
3648    
3649    =item newList
3650    
3651    Reference to a list of new tuples.
3652    
3653    =item oldList
3654    
3655    Reference to a list of old tuples.
3656    
3657    =item keyIndex (optional)
3658    
3659    Index into each tuple of its key field. The default is 0.
3660    
3661    =item RETURN
3662    
3663    Returns a 2-tuple consisting of a reference to the list of items that are only in the new
3664    list (inserted) followed by a reference to the list of items that are only in the old
3665    list (deleted).
3666    
3667    =back
3668    
3669    =cut
3670    
3671    sub CompareLists {
3672        # Get the parameters.
3673        my ($newList, $oldList, $keyIndex) = @_;
3674        if (! defined $keyIndex) {
3675            $keyIndex = 0;
3676        }
3677        # Declare the return variables.
3678        my ($inserted, $deleted) = ([], []);
3679        # Loop through the two lists simultaneously.
3680        my ($newI, $oldI) = (0, 0);
3681        my ($newN, $oldN) = (scalar @{$newList}, scalar @{$oldList});
3682        while ($newI < $newN || $oldI < $oldN) {
3683            # Get the current object in each list. Note that if one
3684            # of the lists is past the end, we'll get undef.
3685            my $newItem = $newList->[$newI];
3686            my $oldItem = $oldList->[$oldI];
3687            if (! defined($newItem) || defined($oldItem) && $newItem->[$keyIndex] gt $oldItem->[$keyIndex]) {
3688                # The old item is not in the new list, so mark it deleted.
3689                push @{$deleted}, $oldItem;
3690                $oldI++;
3691            } elsif (! defined($oldItem) || $oldItem->[$keyIndex] gt $newItem->[$keyIndex]) {
3692                # The new item is not in the old list, so mark it inserted.
3693                push @{$inserted}, $newItem;
3694                $newI++;
3695            } else {
3696 &