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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    
21      require Exporter;      require Exporter;
22      @ISA = ('Exporter');      @ISA = ('Exporter');
23      @EXPORT = qw(Trace T TSetup QTrace Confess Cluck Min Max Assert Open OpenDir TICK);      @EXPORT = qw(Trace T TSetup QTrace Confess Cluck Min Max Assert Open OpenDir TICK StandardSetup EmergencyKey ETracing Constrain Insure ChDir Emergency);
24      @EXPORT_OK = qw(GetFile GetOptions Merge MergeOptions ParseCommand ParseRecord UnEscape Escape);      @EXPORT_OK = qw(GetFile GetOptions Merge MergeOptions ParseCommand ParseRecord UnEscape Escape PrintLine PutLine);
25      use strict;      use strict;
26      use Carp qw(longmess croak);      use Carp qw(longmess croak carp);
27      use CGI;      use CGI;
28        use Cwd;
29      use FIG_Config;      use FIG_Config;
30      use PageBuilder;      use PageBuilder;
31      use Digest::MD5;      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    
40  =head1 Tracing and Debugging Helpers  =head1 Tracing and Debugging Helpers
41    
42  =head2 Introduction  =head2 Tracing
43    
44  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
45  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.
46  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,
47  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
48  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
49  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
50  is less likely to be seen. A higher trace level passed to B<TSetup> means more trace messages will  is less likely to be seen, while a higher trace level passed to B<TSetup> means more trace messages will
51  appear. To generate a trace message, use the following syntax.  appear.
52    
53    =head3 Putting Trace Messages in Your Code
54    
55  C<< Trace($message) if T(errors => 4); >>  To generate a trace message, use the following syntax.
56    
57        Trace($message) if T(errors => 4);
58    
59  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>
60  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
61    
62  C<< Trace($message) if T(main => 4); >>      Trace($message) if T(main => 4);
63    
64  will trace if the trace level is 4 or more.  will trace if the trace level is 4 or more.
65    
# Line 37  Line 67 
67  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
68  active and the trace level is 2 or more.  active and the trace level is 2 or more.
69    
70  C<< Trace($message) if T(2); >>      Trace($message) if T(2);
71    
72    In scripts, where no package name is available, the category defaults to C<main>.
73    
74  To set up tracing, you call the L</TSetup> method. The method takes as input a trace level, a list  =head3 Custom Tracing
75  of category names, and a set of options. The trace level and list of category names are  
76    Many programs have customized tracing configured using the L</TSetup> method. This is no longer
77    the preferred method, but a knowledge of how custom tracing works can make the more modern
78    L</Emergency Tracing> easier to understand.
79    
80    To set up custom tracing, you call the L</TSetup> method. The method takes as input a trace level,
81    a list of category names, and a destination. The trace level and list of category names are
82  specified as a space-delimited string. Thus  specified as a space-delimited string. Thus
83    
84  C<< TSetup('3 errors Sprout ERDB', 'HTML'); >>      TSetup('3 errors Sprout ERDB', 'TEXT');
85    
86  sets the trace level to 3, activates the C<errors>, C<Sprout>, and C<ERDB> categories, and  sets the trace level to 3, activates the C<errors>, C<Sprout>, and C<ERDB> categories, and
87  specifies that messages should be output as HTML paragraphs.  specifies that messages should be sent to the standard output.
88    
89  To turn on tracing for ALL categories, use an asterisk. The call below sets every category to  To turn on tracing for ALL categories, use an asterisk. The call below sets every category to
90  level 3 and writes the output to the standard error output. This sort of thing might be  level 3 and writes the output to the standard error output. This sort of thing might be
91  useful in a CGI environment.  useful in a CGI environment.
92    
93  C<< TSetup('3 *', 'WARN'); >>      TSetup('3 *', 'WARN');
94    
95  In addition to HTML and file output for trace messages, you can specify that the trace messages  In addition standard error and file output for trace messages, you can specify that the trace messages
96  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
97  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
98  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
99  it easier to debug page formatting problems.  it easier to debug page formatting problems.
100    
101  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
102    a file at the same time. To trace to a file, specify the filename with an output character in front
103    of it.
104    
105        TSetup('4 SQL', ">$fileName");
106    
107    To trace to the standard output and a file at the same time, put a C<+> in front of the angle
108    bracket.
109    
110        TSetup('3 *', "+>$fileName");
111    
112  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>.
113  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.
114  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
115  being used out in the field.  being used out in the field.
116    
117    =head3 Trace Levels
118    
119  There is no hard and fast rule on how to use trace levels. The following is therefore only  There is no hard and fast rule on how to use trace levels. The following is therefore only
120  a suggestion.  a suggestion.
121    
122  =over 4  =over 4
123    
124  =item 0 Error  =item Error 0
125    
126  Message indicates an error that may lead to incorrect results or that has stopped the  Message indicates an error that may lead to incorrect results or that has stopped the
127  application entirely.  application entirely.
128    
129  =item 1 Warning  =item Warning 1
130    
131  Message indicates something that is unexpected but that probably did not interfere  Message indicates something that is unexpected but that probably did not interfere
132  with program execution.  with program execution.
133    
134  =item 2 Notice  =item Notice 2
135    
136  Message indicates the beginning or end of a major task.  Message indicates the beginning or end of a major task.
137    
138  =item 3 Information  =item Information 3
139    
140  Message indicates a subtask. In the FIG system, a subtask generally relates to a single  Message indicates a subtask. In the FIG system, a subtask generally relates to a single
141  genome. This would be a big loop that is not expected to execute more than 500 times or so.  genome. This would be a big loop that is not expected to execute more than 500 times or so.
142    
143  =item 4 Detail  =item Detail 4
144    
145  Message indicates a low-level loop iteration.  Message indicates a low-level loop iteration.
146    
147  =back  =back
148    
149    The format of trace messages is important because some utilities analyze trace files.
150    There are three fields-- the time stamp, the category name, and the text.
151    The time stamp is between square brackets and the category name between angle brackets.
152    After the category name there is a colon (C<:>) followed by the message text.
153    If the square brackets or angle brackets are missing, then the trace management
154    utilities assume that they are encountering a set of pre-formatted lines.
155    
156    Note, however, that this formatting is done automatically by the tracing functions. You
157    only need to know about it if you want to parse a trace file.
158    
159    =head3 Emergency Tracing
160    
161    Sometimes, you need a way for tracing to happen automatically without putting parameters
162    in a form or on the command line. Emergency tracing does this. You invoke emergency tracing
163    from the debug form, which is accessed from the [[DebugConsole]]. Emergency tracing requires
164    that you specify a tracing key. For command-line tools, the key is
165    taken from the C<TRACING> environment variable. For web services, the key is taken from
166    a cookie. Either way, the key tells the tracing facility who you are, so that you control
167    the tracing in your environment without stepping on other users.
168    
169    The key can be anything you want. If you don't have a key, the C<SetPassword> page will
170    generate one for you.
171    
172    You can activate and de-activate emergency tracing from the debugging control panel, as
173    well as display the trace file itself.
174    
175    To enable emergency tracing in your code, call
176    
177        ETracing($cgi)
178    
179    from a web script and
180    
181        ETracing()
182    
183    from a command-line script.
184    
185    The web script will look for the tracing key in the cookies, and the command-line
186    script will look for it in the C<TRACING> environment variable. If you are
187    using the L</StandardSetup> method or a [[WebApplication]], emergency tracing
188    will be configured automatically.
189    
190  =cut  =cut
191    
192  # Declare the configuration variables.  # Declare the configuration variables.
193    
194  my $Destination = "NONE";   # Description of where to send the trace output.  my $Destination = "WARN";   # Description of where to send the trace output.
195  my $TeeFlag = 0;            # TRUE if output is going to a file and to the  my $TeeFlag = 0;            # TRUE if output is going to a file and to the
196                              # standard output                              # standard output
197  my %Categories = ( main => 1 );  my %Categories = ( main => 1 );
198                              # hash of active category names                              # hash of active category names
199    my @LevelNames = qw(error warn notice info detail);
200  my $TraceLevel = 0;         # trace level; a higher trace level produces more  my $TraceLevel = 0;         # trace level; a higher trace level produces more
201                              # messages                              # messages
202  my @Queue = ();             # queued list of trace messages.  my @Queue = ();             # queued list of trace messages.
203  my $LastCategory = "main";  # name of the last category interrogated  my $LastCategory = "main";  # name of the last category interrogated
204    my $LastLevel = 0;          # level of the last test call
205  my $SetupCount = 0;         # number of times TSetup called  my $SetupCount = 0;         # number of times TSetup called
206  my $AllTrace = 0;           # TRUE if we are tracing all categories.  my $AllTrace = 0;           # TRUE if we are tracing all categories.
207    
208  =head2 Public Methods  =head2 Tracing Methods
209    
210    =head3 Setups
211    
212        my $count = Tracer::Setups();
213    
214    Return the number of times L</TSetup> has been called.
215    
216    This method allows for the creation of conditional tracing setups where, for example, we
217    may want to set up tracing if nobody else has done it before us.
218    
219    =cut
220    
221    sub Setups {
222        return $SetupCount;
223    }
224    
225  =head3 TSetup  =head3 TSetup
226    
227  C<< TSetup($categoryList, $target); >>      TSetup($categoryList, $target);
228    
229  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
230  and interrogated by the L</Trace> and L</T> methods.  and interrogated by the L</Trace> and L</T> methods.
# Line 157  Line 264 
264      # Presume category-based tracing until we learn otherwise.      # Presume category-based tracing until we learn otherwise.
265      $AllTrace = 0;      $AllTrace = 0;
266      # Build the category hash. Note that if we find a "*", we turn on non-category      # Build the category hash. Note that if we find a "*", we turn on non-category
267      # tracing.      # tracing. We must also clear away any pre-existing data.
268        %Categories = ( main => 1 );
269      for my $category (@categoryData) {      for my $category (@categoryData) {
270          if ($category eq '*') {          if ($category eq '*') {
271              $AllTrace = 1;              $AllTrace = 1;
# Line 175  Line 283 
283          }          }
284          if ($target =~ m/^>[^>]/) {          if ($target =~ m/^>[^>]/) {
285              open TRACEFILE, $target;              open TRACEFILE, $target;
286              print TRACEFILE Now() . " Tracing initialized.\n";              print TRACEFILE "[" . Now() . "] [Tracer] Tracing initialized.\n";
287              close TRACEFILE;              close TRACEFILE;
288              $Destination = ">$target";              $Destination = ">$target";
289          } else {          } else {
# Line 188  Line 296 
296      $SetupCount++;      $SetupCount++;
297  }  }
298    
299  =head3 Setups  =head3 SetLevel
   
 C<< my $count = Tracer::Setups(); >>  
   
 Return the number of times L</TSetup> has been called.  
   
 This method allows for the creation of conditional tracing setups where, for example, we  
 may want to set up tracing if nobody else has done it before us.  
   
 =cut  
300    
301  sub Setups {      Tracer::SetLevel($newLevel);
     return $SetupCount;  
 }  
302    
303  =head3 Open  Modify the trace level. A higher trace level will cause more messages to appear.
304    
305  C<< my $handle = Open($fileHandle, $fileSpec, $message); >>  =over 4
306    
307  Open a file.  =item newLevel
308    
309  The I<$fileSpec> is essentially the second argument of the PERL C<open>  Proposed new trace level.
 function. The mode is specified using Unix-like shell information. So, for  
 example,  
310    
311      Open(\*LOGFILE, '>>/usr/spool/news/twitlog', "Could not open twit log.");  =back
312    
313  would open for output appended to the specified file, and  =cut
314    
315      Open(\*DATASTREAM, "| sort -u >$outputFile", "Could not open $outputFile.");  sub SetLevel {
316        $TraceLevel = $_[0];
317    }
318    
319  would open a pipe that sorts the records written and removes duplicates. Note  =head3 ParseDate
 the use of file handle syntax in the Open call. To use anonymous file handles,  
 code as follows.  
320    
321      my $logFile = Open(undef, '>>/usr/spool/news/twitlog', "Could not open twit log.");      my $time = Tracer::ParseDate($dateString);
322    
323  The I<$message> parameter is used if the open fails. If it is set to C<0>, then  Convert a date into a PERL time number. This method expects a date-like string
324  the open returns TRUE if successful and FALSE if an error occurred. Otherwise, a  and parses it into a number. The string must be vaguely date-like or it will
325  failed open will throw an exception and the third parameter will be used to construct  return an undefined value. Our requirement is that a month and day be
326  an error message. If the parameter is omitted, a standard message is constructed  present and that three pieces of the date string (time of day, month and day,
327  using the file spec.  year) be separated by likely delimiters, such as spaces, commas, and such-like.
328    
329      Could not open "/usr/spool/news/twitlog"  If a time of day is present, it must be in military time with two digits for
330    everything but the hour.
331    
332  Note that the mode characters are automatically cleaned from the file name.  The year must be exactly four digits.
 The actual error message from the file system will be captured and appended to the  
 message in any case.  
333    
334      Could not open "/usr/spool/news/twitlog": file not found.  Additional stuff can be in the string. We presume it's time zones or weekdays or something
335    equally innocuous. This means, however, that a sufficiently long sentence with date-like
336    parts in it may be interpreted as a date. Hopefully this will not be a problem.
337    
338  In some versions of PERL the only error message we get is a number, which  It should be guaranteed that this method will parse the output of the L</Now> function.
 corresponds to the C++ C<errno> value.  
339    
340      Could not open "/usr/spool/news/twitlog": 6.  The parameters are as follows.
341    
342  =over 4  =over 4
343    
344  =item fileHandle  =item dateString
   
 File handle. If this parameter is C<undef>, a file handle will be generated  
 and returned as the value of this method.  
   
 =item fileSpec  
   
 File name and mode, as per the PERL C<open> function.  
   
 =item message (optional)  
345    
346  Error message to use if the open fails. If omitted, a standard error message  The date string to convert.
 will be generated. In either case, the error information from the file system  
 is appended to the message. To specify a conditional open that does not throw  
 an error if it fails, use C<0>.  
347    
348  =item RETURN  =item RETURN
349    
350  Returns the name of the file handle assigned to the file, or C<undef> if the  Returns a PERL time, that is, a number of seconds since the epoch, or C<undef> if
351  open failed.  the date string is invalid. A valid date string must contain a month and day.
352    
353  =back  =back
354    
355  =cut  =cut
356    
357  sub Open {  # Universal month conversion table.
358    use constant MONTHS => {    Jan =>  0, January   =>  0, '01' =>  0,  '1' =>  0,
359                                Feb =>  1, February  =>  1, '02' =>  1,  '2' =>  1,
360                                Mar =>  2, March     =>  2, '03' =>  2,  '3' =>  2,
361                                Apr =>  3, April     =>  3, '04' =>  3,  '4' =>  3,
362                                May =>  4, May       =>  4, '05' =>  4,  '5' =>  4,
363                                Jun =>  5, June      =>  5, '06' =>  5,  '6' =>  5,
364                                Jul =>  6, July      =>  6, '07' =>  6,  '7' =>  6,
365                                Aug =>  7, August    =>  7, '08' =>  7,  '8' =>  7,
366                                Sep =>  8, September =>  8, '09' =>  8,  '9' =>  8,
367                                Oct =>  9, October  =>   9, '10' =>  9,
368                                Nov => 10, November =>  10, '11' => 10,
369                                Dec => 11, December =>  11, '12' => 11
370                            };
371    
372    sub ParseDate {
373      # Get the parameters.      # Get the parameters.
374      my ($fileHandle, $fileSpec, $message) = @_;      my ($dateString) = @_;
375      # Attempt to open the file.      # Declare the return variable.
376      my $rv = open $fileHandle, $fileSpec;      my $retVal;
377      # If the open failed, generate an error message.      # Find the month and day of month. There are two ways that can happen. We check for the
378      if (! $rv) {      # numeric style first. That way, if the user's done something like "Sun 12/22", then we
379          # Save the system error message.      # won't be fooled into thinking the month is Sunday.
380          my $sysMessage = $!;      if ($dateString =~ m#\b(\d{1,2})/(\d{1,2})\b# || $dateString =~ m#\b(\w+)\s(\d{1,2})\b#) {
381          # See if we need a default message.          my ($mon, $mday) = (MONTHS->{$1}, $2);
382          if (!$message) {          # Insist that the month and day are valid.
383              # Clean any obvious mode characters and leading spaces from the          if (defined($mon) && $2 >= 1 && $2 <= 31) {
384              # filename.              # Find the time.
385              my ($fileName) = FindNamePart($fileSpec);              my ($hour, $min, $sec) = (0, 0, 0);
386              $message = "Could not open \"$fileName\"";              if ($dateString =~ /\b(\d{1,2}):(\d{2}):(\d{2})\b/) {
387                    ($hour, $min, $sec) = ($1, $2, $3);
388                }
389                # Find the year.
390                my $year;
391                if ($dateString =~ /\b(\d{4})\b/) {
392                    $year = $1;
393                } else {
394                    # Get the default year, which is this one. Note we must convert it to
395                    # the four-digit value expected by "timelocal".
396                    (undef, undef, undef, undef, undef, $year) = localtime();
397                    $year += 1900;
398          }          }
399          # Terminate with an error using the supplied message and the              $retVal = timelocal($sec, $min, $hour, $mday, $mon, $year);
         # error message from the file system.  
         Confess("$message: $!");  
400      }      }
401      # Return the file handle.      }
402      return $fileHandle;      # Return the result.
403        return $retVal;
404  }  }
405    
406  =head3 FindNamePart  =head3 LogErrors
   
 C<< my ($fileName, $start, $len) = Tracer::FindNamePart($fileSpec); >>  
   
 Extract the portion of a file specification that contains the file name.  
   
 A file specification is the string passed to an C<open> call. It specifies the file  
 mode and name. In a truly complex situation, it can specify a pipe sequence. This  
 method assumes that the file name is whatever follows the first angle bracket  
 sequence.  So, for example, in the following strings the file name is  
 C</usr/fig/myfile.txt>.  
407    
408      >>/usr/fig/myfile.txt      Tracer::LogErrors($fileName);
     </usr/fig/myfile.txt  
     | sort -u > /usr/fig/myfile.txt  
409    
410  If the method cannot find a file name using its normal methods, it will return the  Route the standard error output to a log file.
 whole incoming string.  
411    
412  =over 4  =over 4
413    
414  =item fileSpec  =item fileName
   
 File specification string from which the file name is to be extracted.  
   
 =item RETURN  
415    
416  Returns a three-element list. The first element contains the file name portion of  Name of the file to receive the error output.
 the specified string, or the whole string if a file name cannot be found via normal  
 methods. The second element contains the start position of the file name portion and  
 the third element contains the length.  
417    
418  =back  =back
419    
420  =cut  =cut
 #: Return Type $;  
 sub FindNamePart {  
     # Get the parameters.  
     my ($fileSpec) = @_;  
     # Default to the whole input string.  
     my ($retVal, $pos, $len) = ($fileSpec, 0, length $fileSpec);  
     # Parse out the file name if we can.  
     if ($fileSpec =~ m/(<|>>?)(.+?)(\s*)$/) {  
         $retVal = $2;  
         $len = length $retVal;  
         $pos = (length $fileSpec) - (length $3) - $len;  
     }  
     # Return the result.  
     return ($retVal, $pos, $len);  
 }  
   
 =head3 OpenDir  
   
 C<< my @files = OpenDir($dirName, $filtered); >>  
   
 Open a directory and return all the file names. This function essentially performs  
 the functions of an C<opendir> and C<readdir>. If the I<$filtered> parameter is  
 set to TRUE, all filenames beginning with a period (C<.>) will be filtered out of  
 the return list. If the directory does not open, an exception is thrown. So,  
 for example,  
   
     my @files = OpenDir("/Volumes/fig/contigs", 1);  
   
 is effectively the same as  
421    
422      opendir(TMP, "/Volumes/fig/contigs") || Confess("Could not open /Volumes/fig/contigs.");  sub LogErrors {
423      my @files = grep { $_ !~ /^\./ } readdir(TMP);      # Get the file name.
424        my ($fileName) = @_;
425        # Open the file as the standard error output.
426        open STDERR, '>', $fileName;
427    }
428    
429  Similarly, the following code  =head3 Trace
430    
431      my @files = grep { $_ =~ /^\d/ } OpenDir("/Volumes/fig/orgs");      Trace($message);
432    
433  Returns the names of all files in C</Volumes/fig/orgs> that begin with digits and  Write a trace message to the target location specified in L</TSetup>. If there has not been
434  automatically throws an error if the directory fails to open.  any prior call to B<TSetup>.
435    
436  =over 4  =over 4
437    
438  =item dirName  =item message
   
 Name of the directory to open.  
   
 =item filtered  
439    
440  TRUE if files whose names begin with a period (C<.>) should be automatically removed  Message to write.
 from the list, else FALSE.  
441    
442  =back  =back
443    
444  =cut  =cut
445  #: Return Type @;  
446  sub OpenDir {  sub Trace {
447      # Get the parameters.      # Get the parameters.
448      my ($dirName, $filtered) = @_;      my ($message) = @_;
449      # Declare the return variable.      # Strip off any line terminators at the end of the message. We will add
450      my @retVal;      # new-line stuff ourselves.
451      # Open the directory.      my $stripped = Strip($message);
452      if (opendir(my $dirHandle, $dirName)) {      # Compute the caller information.
453          # The directory opened successfully. Get the appropriate list according to the      my ($callPackage, $callFile, $callLine) = caller();
454          # strictures of the filter parameter.      my $callFileTitle = basename($callFile);
455          if ($filtered) {      # Check the caller.
456              @retVal = grep { $_ !~ /^\./ } readdir $dirHandle;      if ($callFileTitle ne "Tracer\.pm") {
457          } else {          # The caller isn't us, so add the caller info to the message.
458              @retVal = readdir $dirHandle;          $stripped = "[$callFileTitle $callLine] $stripped";
459        }
460        # Get the timestamp.
461        my $timeStamp = Now();
462        # Build the prefix.
463        my $level = $LevelNames[$LastLevel] || "($LastLevel)";
464        my $prefix = "[$timeStamp] [$level] ";
465        # Format the message.
466        my $formatted = "$prefix $stripped";
467        # Process according to the destination.
468        if ($Destination eq "TEXT") {
469            # Write the message to the standard output.
470            print "$formatted\n";
471        } elsif ($Destination eq "ERROR") {
472            # Write the message to the error output. Here, we want our prefix fields.
473            print STDERR "$formatted\n";
474        } elsif ($Destination eq "WARN") {
475            # Emit the message to the standard error output. It is presumed that the
476            # error logger will add its own prefix fields
477            print STDERR "$stripped\n";
478        } elsif ($Destination eq "QUEUE") {
479            # Push the message into the queue.
480            push @Queue, "$formatted";
481        } elsif ($Destination eq "HTML") {
482            # Convert the message to HTML and write it to the standard output.
483            my $escapedMessage = CGI::escapeHTML($stripped);
484            print "<p>$timeStamp $LastCategory $LastLevel: $escapedMessage</p>\n";
485        } elsif ($Destination =~ m/^>>/) {
486            # Write the trace message to an output file.
487            open(TRACING, $Destination) || die "Tracing open for \"$Destination\" failed: $!";
488            print TRACING "$formatted\n";
489            close TRACING;
490            # If the Tee flag is on, echo it to the standard output.
491            if ($TeeFlag) {
492                print "$formatted\n";
493          }          }
     } else {  
         # Here the directory would not open.  
         Confess("Could not open directory $dirName.");  
494      }      }
     # Return the result.  
     return @retVal;  
495  }  }
496    
497  =head3 SetLevel  =head3 T
498    
499  C<< Tracer::SetLevel($newLevel); >>      my $switch = T($category, $traceLevel);
500    
501  Modify the trace level. A higher trace level will cause more messages to appear.      or
502    
503  =over 4      my $switch = T($traceLevel);
504    
505  =item newLevel  Return TRUE if the trace level is at or above a specified value and the specified category
506    is active, else FALSE. If no category is specified, the caller's package name is used.
507    
508  Proposed new trace level.  =over 4
509    
510  =back  =item category
511    
512  =cut  Category to which the message belongs. If not specified, the caller's package name is
513    used.
514    
515  sub SetLevel {  =item traceLevel
     $TraceLevel = $_[0];  
 }  
516    
517  =head3 Now  Relevant tracing level.
518    
519    =item RETURN
520    
521    TRUE if a message at the specified trace level would appear in the trace, else FALSE.
522    
523    =back
524    
525    =cut
526    
527    sub T {
528        # Declare the return variable.
529        my $retVal = 0;
530        # Only proceed if tracing is turned on.
531        if ($Destination ne "NONE") {
532            # Get the parameters.
533            my ($category, $traceLevel) = @_;
534            if (!defined $traceLevel) {
535                # Here we have no category, so we need to get the calling package.
536                # The calling package is normally the first parameter. If it is
537                # omitted, the first parameter will be the tracelevel. So, the
538                # first thing we do is shift the so-called category into the
539                # $traceLevel variable where it belongs.
540                $traceLevel = $category;
541                my ($package, $fileName, $line) = caller;
542                # If there is no calling package, we default to "main".
543                if (!$package) {
544                    $category = "main";
545                } else {
546                    my @cats = split /::/, $package;
547                    $category = $cats[$#cats];
548                }
549            }
550            # Save the category name and level.
551            $LastCategory = $category;
552            $LastLevel = $traceLevel;
553            # Convert it to lower case before we hash it.
554            $category = lc $category;
555            # Use the category and tracelevel to compute the result.
556            if (ref $traceLevel) {
557                Confess("Bad trace level.");
558            } elsif (ref $TraceLevel) {
559                Confess("Bad trace config.");
560            }
561            $retVal = ($traceLevel <= $TraceLevel && ($AllTrace || exists $Categories{$category}));
562        }
563        # Return the computed result.
564        return $retVal;
565    }
566    
567    =head3 QTrace
568    
569        my $data = QTrace($format);
570    
571    Return the queued trace data in the specified format.
572    
573    =over 4
574    
575    =item format
576    
577    C<html> to format the data as an HTML list, C<text> to format it as straight text.
578    
579    =back
580    
581    =cut
582    
583    sub QTrace {
584        # Get the parameter.
585        my ($format) = @_;
586        # Create the return variable.
587        my $retVal = "";
588        # Only proceed if there is an actual queue.
589        if (@Queue) {
590            # Process according to the format.
591            if ($format =~ m/^HTML$/i) {
592                # Convert the queue into an HTML list.
593                $retVal = "<ul>\n";
594                for my $line (@Queue) {
595                    my $escapedLine = CGI::escapeHTML($line);
596                    $retVal .= "<li>$escapedLine</li>\n";
597                }
598                $retVal .= "</ul>\n";
599            } elsif ($format =~ m/^TEXT$/i) {
600                # Convert the queue into a list of text lines.
601                $retVal = join("\n", @Queue) . "\n";
602            }
603            # Clear the queue.
604            @Queue = ();
605        }
606        # Return the formatted list.
607        return $retVal;
608    }
609    
610    =head3 Confess
611    
612        Confess($message);
613    
614    Trace the call stack and abort the program with the specified message. When used with
615    the OR operator and the L</Assert> method, B<Confess> can function as a debugging assert.
616    So, for example
617    
618        Assert($recNum >= 0) || Confess("Invalid record number $recNum.");
619    
620    Will abort the program with a stack trace if the value of C<$recNum> is negative.
621    
622    =over 4
623    
624    =item message
625    
626    Message to include in the trace.
627    
628    =back
629    
630    =cut
631    
632    sub Confess {
633        # Get the parameters.
634        my ($message) = @_;
635        # Set up the category and level.
636        $LastCategory = "(confess)";
637        $LastLevel = 0;
638        if (! defined($FIG_Config::no_tool_hdr)) {
639            # Here we have a tool header. Display its length so that the user can adjust the line numbers.
640            my $toolHeaderFile = "$FIG_Config::fig_disk/dist/releases/current/$FIG_Config::arch/tool_hdr";
641            # Only proceed if the tool header file is actually present.
642            if (-f $toolHeaderFile) {
643                my $fh;
644                if (open $fh, "<$toolHeaderFile") {
645                    my @lines = <$fh>;
646                    Trace("Tool header has " . scalar(@lines) . " lines.");
647                }
648            }
649        }
650        # Trace the call stack.
651        Cluck($message);
652        # Abort the program.
653        croak(">>> $message");
654    }
655    
656    =head3 Assert
657    
658        Assert($condition1, $condition2, ... $conditionN);
659    
660    Return TRUE if all the conditions are true. This method can be used in conjunction with
661    the OR operator and the L</Confess> method as a debugging assert.
662    So, for example
663    
664        Assert($recNum >= 0) || Confess("Invalid record number $recNum.");
665    
666    Will abort the program with a stack trace if the value of C<$recNum> is negative.
667    
668    =cut
669    sub Assert {
670        my $retVal = 1;
671        LOOP: for my $condition (@_) {
672            if (! $condition) {
673                $retVal = 0;
674                last LOOP;
675            }
676        }
677        return $retVal;
678    }
679    
680    =head3 Cluck
681    
682        Cluck($message);
683    
684    Trace the call stack. Note that for best results, you should qualify the call with a
685    trace condition. For example,
686    
687        Cluck("Starting record parse.") if T(3);
688    
689    will only trace the stack if the trace level for the package is 3 or more.
690    
691    =over 4
692    
693    =item message
694    
695    Message to include in the trace.
696    
697    =back
698    
699    =cut
700    
701    sub Cluck {
702        # Get the parameters.
703        my ($message) = @_;
704        # Trace what's happening.
705        Trace("Stack trace for event: $message");
706        my $confession = longmess($message);
707        # Convert the confession to a series of trace messages.
708        for my $line (split /\s*\n/, $confession) {
709            # Only proceed if this call trace is for a method outside Tracer itself.
710            if ($line !~ /Tracer\.pm/) {
711                # Replace the leading tab with a series of spaces.
712                $line =~ s/\t/    /;
713                # Trace the line.
714                Trace($line);
715            }
716        }
717    }
718    
719    =head3 ScriptSetup (deprecated)
720    
721        my ($cgi, $varHash) = ScriptSetup($noTrace);
722    
723    Perform standard tracing and debugging setup for scripts. The value returned is
724    the CGI object followed by a pre-built variable hash. At the end of the script,
725    the client should call L</ScriptFinish> to output the web page.
726    
727    This method calls L</ETracing> to configure tracing, which allows the tracing
728    to be configured via the emergency tracing form on the debugging control panel.
729    Tracing will then be turned on automatically for all programs that use the L</ETracing>
730    method, which includes every program that uses this method or L</StandardSetup>.
731    
732    =over 4
733    
734    =item noTrace (optional)
735    
736    If specified, tracing will be suppressed. This is useful if the script wants to set up
737    tracing manually.
738    
739    =item RETURN
740    
741    Returns a two-element list consisting of a CGI query object and a variable hash for
742    the output page.
743    
744    =back
745    
746    =cut
747    
748    sub ScriptSetup {
749        # Get the parameters.
750        my ($noTrace) = @_;
751        # Get the CGI query object.
752        my $cgi = CGI->new();
753        # Set up tracing if it's not suppressed.
754        ETracing($cgi) unless $noTrace;
755        # Create the variable hash.
756        my $varHash = { results => '' };
757        # Return the query object and variable hash.
758        return ($cgi, $varHash);
759    }
760    
761    =head3 ETracing
762    
763        ETracing($parameter);
764    
765    Set up emergency tracing. Emergency tracing is tracing that is turned
766    on automatically for any program that calls this method. The emergency
767    tracing parameters are stored in a a file identified by a tracing key.
768    If this method is called with a CGI object, then the tracing key is
769    taken from a cookie. If it is called with no parameters, then the tracing
770    key is taken from an environment variable. If it is called with a string,
771    the tracing key is that string.
772    
773    =over 4
774    
775    =item parameter
776    
777    A parameter from which the tracing key is computed. If it is a scalar,
778    that scalar is used as the tracing key. If it is a CGI object, the
779    tracing key is taken from the C<IP> cookie. If it is omitted, the
780    tracing key is taken from the C<TRACING> environment variable. If it
781    is a CGI object and emergency tracing is not on, the C<Trace> and
782    C<TF> parameters will be used to determine the type of tracing.
783    
784    =back
785    
786    =cut
787    
788    sub ETracing {
789        # Get the parameter.
790        my ($parameter) = @_;
791        # Check for CGI mode.
792        my $cgi = (ref $parameter eq 'CGI' ? $parameter : undef);
793        # Default to no tracing except errors.
794        my ($tracing, $dest) = ("0", "WARN");
795        # Check for emergency tracing.
796        my $tkey = EmergencyKey($parameter);
797        my $emergencyFile = EmergencyFileName($tkey);
798        if (-e $emergencyFile) {
799            # We have the file. Read in the data.
800            my @tracing = GetFile($emergencyFile);
801            # Pull off the time limit.
802            my $expire = shift @tracing;
803            # Convert it to seconds.
804            $expire *= 3600;
805            # Check the file data.
806            my $stat = stat($emergencyFile);
807            my ($now) = gettimeofday;
808            if ($now - $stat->mtime > $expire) {
809                # Delete the expired file.
810                unlink $emergencyFile;
811            } else {
812                # Emergency tracing is on. Pull off the destination and
813                # the trace level;
814                $dest = shift @tracing;
815                my $level = shift @tracing;
816                # Convert the destination to a real tracing destination.
817                # temp directory.
818                $dest = EmergencyTracingDest($tkey, $dest);
819                # Insure Tracer is specified.
820                my %moduleHash = map { $_ => 1 } @tracing;
821                $moduleHash{Tracer} = 1;
822                # Set the trace parameter.
823                $tracing = join(" ", $level, sort keys %moduleHash);
824            }
825        } elsif (defined $cgi) {
826            # There's no emergency tracing, but we have a CGI object, so check
827            # for tracing from the form parameters.
828            if ($cgi->param('Trace')) {
829                # Here the user has requested tracing via a form.
830                $dest = ($cgi->param('TF') ? ">$FIG_Config::temp/Trace$$.log" : "QUEUE");
831                $tracing = $cgi->param('Trace') . " Tracer";
832            }
833        }
834        # Setup the tracing we've determined from all the stuff above.
835        TSetup($tracing, $dest);
836        # Check to see if we're a web script.
837        if (defined $cgi) {
838            # Yes we are. Trace the form and environment data.
839            TraceParms($cgi);
840            # Check for RAW mode. In raw mode, we print a fake header so that we see everything
841            # emitted by the script in its raw form.
842            if (T(Raw => 3)) {
843                print CGI::header(-type => 'text/plain', -tracing => 'Raw');
844            }
845        }
846    }
847    
848    =head3 EmergencyFileName
849    
850        my $fileName = Tracer::EmergencyFileName($tkey);
851    
852    Return the emergency tracing file name. This is the file that specifies
853    the tracing information.
854    
855    =over 4
856    
857    =item tkey
858    
859    Tracing key for the current program.
860    
861    =item RETURN
862    
863    Returns the name of the file to contain the emergency tracing information.
864    
865    =back
866    
867    =cut
868    
869    sub EmergencyFileName {
870        # Get the parameters.
871        my ($tkey) = @_;
872        # Compute the emergency tracing file name.
873        return "$FIG_Config::temp/Emergency$tkey.txt";
874    }
875    
876    =head3 EmergencyFileTarget
877    
878        my $fileName = Tracer::EmergencyFileTarget($tkey);
879    
880    Return the emergency tracing target file name. This is the file that receives
881    the tracing output for file-based tracing.
882    
883    =over 4
884    
885    =item tkey
886    
887    Tracing key for the current program.
888    
889    =item RETURN
890    
891    Returns the name of the file to contain the trace output.
892    
893    =back
894    
895    =cut
896    
897    sub EmergencyFileTarget {
898        # Get the parameters.
899        my ($tkey) = @_;
900        # Compute the emergency tracing file name.
901        return "$FIG_Config::temp/trace$tkey.log";
902    }
903    
904    =head3 EmergencyTracingDest
905    
906        my $dest = Tracer::EmergencyTracingDest($tkey, $myDest);
907    
908    This method converts an emergency tracing destination to a real
909    tracing destination. The main difference is that if the
910    destination is C<FILE> or C<APPEND>, we convert it to file
911    output. If the destination is C<DUAL>, we convert it to file
912    and standard output.
913    
914    =over 4
915    
916    =item tkey
917    
918    Tracing key for this environment.
919    
920    =item myDest
921    
922    Destination from the emergency tracing file.
923    
924    =item RETURN
925    
926    Returns a destination that can be passed into L</TSetup>.
927    
928    =back
929    
930    =cut
931    
932    sub EmergencyTracingDest {
933        # Get the parameters.
934        my ($tkey, $myDest) = @_;
935        # Declare the return variable.
936        my $retVal = $myDest;
937        # Process according to the destination value.
938        if ($myDest eq 'FILE') {
939            $retVal = ">" . EmergencyFileTarget($tkey);
940        } elsif ($myDest eq 'APPEND') {
941            $retVal = ">>" . EmergencyFileTarget($tkey);
942        } elsif ($myDest eq 'DUAL') {
943            $retVal = "+>" . EmergencyFileTarget($tkey);
944        } elsif ($myDest eq 'WARN') {
945            $retVal = "WARN";
946        }
947        # Return the result.
948        return $retVal;
949    }
950    
951    =head3 Emergency
952    
953        Emergency($key, $hours, $dest, $level, @modules);
954    
955    Turn on emergency tracing. This method is normally invoked over the web from
956    a debugging console, but it can also be called by the C<trace.pl> script.
957    The caller specifies the duration of the emergency in hours, the desired tracing
958    destination, the trace level, and a list of the trace modules to activate.
959    For the length of the duration, when a program in an environment with the
960    specified tracing key active invokes a Sprout CGI script, tracing will be
961    turned on automatically. See L</TSetup> for more about tracing setup and
962    L</ETracing> for more about emergency tracing.
963    
964    =over 4
965    
966    =item tkey
967    
968    The tracing key. This is used to identify the control file and the trace file.
969    
970    =item hours
971    
972    Number of hours to keep emergency tracing alive.
973    
974    =item dest
975    
976    Tracing destination. If no path information is specified for a file
977    destination, it is put in the FIG temporary directory.
978    
979    =item level
980    
981    Tracing level. A higher level means more trace messages.
982    
983    =item modules
984    
985    A list of the tracing modules to activate.
986    
987    =back
988    
989    =cut
990    
991    sub Emergency {
992        # Get the parameters.
993        my ($tkey, $hours, $dest, $level, @modules) = @_;
994        # Create the emergency file.
995        my $specFile = EmergencyFileName($tkey);
996        my $outHandle = Open(undef, ">$specFile");
997        print $outHandle join("\n", $hours, $dest, $level, @modules, "");
998    }
999    
1000    =head3 EmergencyKey
1001    
1002        my $tkey = EmergencyKey($parameter);
1003    
1004    Return the Key to be used for emergency tracing. This could be an IP address,
1005     a session ID, or a user name, depending on the environment.
1006    
1007    =over 4
1008    
1009    =item parameter
1010    
1011    Parameter defining the method for finding the tracing key. If it is a scalar,
1012    then it is presumed to be the tracing key itself. If it is a CGI object, then
1013    the tracing key is taken from the C<IP> cookie. Otherwise, the tracing key is
1014    taken from the C<TRACING> environment variable.
1015    
1016    =item RETURN
1017    
1018    Returns the key to be used for labels in emergency tracing.
1019    
1020    =back
1021    
1022    =cut
1023    
1024    sub EmergencyKey {
1025        # Get the parameters.
1026        my ($parameter) = @_;
1027        # Declare the return variable.
1028        my $retVal;
1029        # Determine the parameter type.
1030        if (! defined $parameter) {
1031            # Here we're supposed to check the environment.
1032            $retVal = $ENV{TRACING};
1033        } else {
1034            my $ptype = ref $parameter;
1035            if ($ptype eq 'CGI') {
1036                # Here we were invoked from a web page. Look for a cookie.
1037                $retVal = $parameter->cookie('IP');
1038            } elsif (! $ptype) {
1039                # Here the key was passed in.
1040                $retVal = $parameter;
1041            }
1042        }
1043        # If no luck finding a key, use the PID.
1044        if (! defined $retVal) {
1045            $retVal = $$;
1046        }
1047        # Return the result.
1048        return $retVal;
1049    }
1050    
1051    
1052    =head3 TraceParms
1053    
1054        Tracer::TraceParms($cgi);
1055    
1056    Trace the CGI parameters at trace level CGI => 3 and the environment variables
1057    at level CGI => 4. A self-referencing URL is traced at level CGI => 2.
1058    
1059    =over 4
1060    
1061    =item cgi
1062    
1063    CGI query object containing the parameters to trace.
1064    
1065    =back
1066    
1067    =cut
1068    
1069    sub TraceParms {
1070        # Get the parameters.
1071        my ($cgi) = @_;
1072        if (T(CGI => 2)) {
1073            # Here we trace the GET-style URL for the script.
1074            Trace("[URL] " . $cgi->url(-relative => 1, -query => 1));
1075        }
1076        if (T(CGI => 3)) {
1077            # Here we want to trace the parameter data.
1078            my @names = $cgi->param;
1079            for my $parmName (sort @names) {
1080                # Note we skip the Trace parameters, which are for our use only.
1081                if ($parmName ne 'Trace' && $parmName ne 'TF') {
1082                    my @values = $cgi->param($parmName);
1083                    Trace("[CGI] $parmName = " . join(", ", @values));
1084                }
1085            }
1086            # Display the request method.
1087            my $method = $cgi->request_method();
1088            Trace("Method: $method");
1089        }
1090        if (T(CGI => 4)) {
1091            # Here we want the environment data too.
1092            for my $envName (sort keys %ENV) {
1093                Trace("[ENV] $envName = $ENV{$envName}");
1094            }
1095        }
1096    }
1097    
1098    =head3 TraceImages
1099    
1100        Tracer::TraceImages($htmlString);
1101    
1102    Trace information about all of an html document's images. The tracing
1103    will be for type "IMG" at level 3. The image's source string
1104    will be displayed. This is generally either the URL of the image or
1105    raw data for the image itself. If the source is too long, only the first 300
1106    characters will be shown at trace level 3. The entire source will be shown,
1107    however, at trace level 4. This method is not very smart, and might catch
1108    Javascript code, but it is still useful when debugging the arcane
1109    behavior of images in multiple browser environments.
1110    
1111    =over 4
1112    
1113    =item htmlString
1114    
1115    HTML text for an outgoing web page.
1116    
1117    =back
1118    
1119    =cut
1120    
1121    sub TraceImages {
1122        # Only proceed if we're at the proper trace level.
1123        if (T(IMG => 3)) {
1124            # For performance reasons we're manipulating $_[0] instead of retrieving the string
1125            # into a variable called "$htmlString". This is because we expect html strings to be
1126            # long, and don't want to copy them any more than we have to.
1127            Trace(length($_[0]) . " characters in web page.");
1128            # Loop through the HTML, culling image tags.
1129            while ($_[0] =~ /<img\s+[^>]+?src="([^"]+)"/sgi) {
1130                # Extract the source string and determine whether or not it's too long.
1131                my $srcString = $1;
1132                my $pos = pos($_[0]) - length($srcString);
1133                my $excess = length($srcString) - 300;
1134                # We'll put the display string in here.
1135                my $srcDisplay = $srcString;
1136                # If it's a data string, split it at the comma.
1137                $srcDisplay =~ s/^(data[^,]+,)/$1\n/;
1138                # If there's no excess or we're at trace level 4, we're done. At level 3 with
1139                # a long string, however, we only show the first 300 characters.
1140                if ($excess > 0 && ! T(IMG => 4)) {
1141                    $srcDisplay = substr($srcDisplay,0,300) . "\nplus $excess characters.";
1142                }
1143                # Output the trace message.
1144                Trace("Image tag at position $pos:\n$srcDisplay");
1145            }
1146        }
1147    }
1148    
1149    
1150    =head3 ScriptFinish (deprecated)
1151    
1152        ScriptFinish($webData, $varHash);
1153    
1154    Output a web page at the end of a script. Either the string to be output or the
1155    name of a template file can be specified. If the second parameter is omitted,
1156    it is assumed we have a string to be output; otherwise, it is assumed we have the
1157    name of a template file. The template should have the variable C<DebugData>
1158    specified in any form that invokes a standard script. If debugging mode is turned
1159    on, a form field will be put in that allows the user to enter tracing data.
1160    Trace messages will be placed immediately before the terminal C<BODY> tag in
1161    the output, formatted as a list.
1162    
1163    A typical standard script would loook like the following.
1164    
1165        BEGIN {
1166            # Print the HTML header.
1167            print "CONTENT-TYPE: text/html\n\n";
1168        }
1169        use Tracer;
1170        use CGI;
1171        use FIG;
1172        # ... more uses ...
1173    
1174        my ($cgi, $varHash) = ScriptSetup();
1175        eval {
1176            # ... get data from $cgi, put it in $varHash ...
1177        };
1178        if ($@) {
1179            Trace("Script Error: $@") if T(0);
1180        }
1181        ScriptFinish("Html/MyTemplate.html", $varHash);
1182    
1183    The idea here is that even if the script fails, you'll see trace messages and
1184    useful output.
1185    
1186    =over 4
1187    
1188    =item webData
1189    
1190    A string containing either the full web page to be written to the output or the
1191    name of a template file from which the page is to be constructed. If the name
1192    of a template file is specified, then the second parameter must be present;
1193    otherwise, it must be absent.
1194    
1195    =item varHash (optional)
1196    
1197    If specified, then a reference to a hash mapping variable names for a template
1198    to their values. The template file will be read into memory, and variable markers
1199    will be replaced by data in this hash reference.
1200    
1201    =back
1202    
1203    =cut
1204    
1205    sub ScriptFinish {
1206        # Get the parameters.
1207        my ($webData, $varHash) = @_;
1208        # Check for a template file situation.
1209        my $outputString;
1210        if (defined $varHash) {
1211            # Here we have a template file. We need to determine the template type.
1212            my $template;
1213            if ($FIG_Config::template_url && $webData =~ /\.php$/) {
1214                $template = "$FIG_Config::template_url/$webData";
1215            } else {
1216                $template = "<<$webData";
1217            }
1218            $outputString = PageBuilder::Build($template, $varHash, "Html");
1219        } else {
1220            # Here the user gave us a raw string.
1221            $outputString = $webData;
1222        }
1223        # Check for trace messages.
1224        if ($Destination ne "NONE" && $TraceLevel > 0) {
1225            # We have trace messages, so we want to put them at the end of the body. This
1226            # is either at the end of the whole string or at the beginning of the BODY
1227            # end-tag.
1228            my $pos = length $outputString;
1229            if ($outputString =~ m#</body>#gi) {
1230                $pos = (pos $outputString) - 7;
1231            }
1232            # If the trace messages were queued, we unroll them. Otherwise, we display the
1233            # destination.
1234            my $traceHtml;
1235            if ($Destination eq "QUEUE") {
1236                $traceHtml = QTrace('Html');
1237            } elsif ($Destination =~ /^>>(.+)$/) {
1238                # Here the tracing output it to a file. We code it as a hyperlink so the user
1239                # can copy the file name into the clipboard easily.
1240                my $actualDest = $1;
1241                $traceHtml = "<p>Tracing output to $actualDest.</p>\n";
1242            } else {
1243                # Here we have one of the special destinations.
1244                $traceHtml = "<P>Tracing output type is $Destination.</p>\n";
1245            }
1246            substr $outputString, $pos, 0, $traceHtml;
1247        }
1248        # Write the output string.
1249        print $outputString;
1250    }
1251    
1252    =head2 Command-Line Utility Methods
1253    
1254    =head3 SendSMS
1255    
1256        my $msgID = Tracer::SendSMS($phoneNumber, $msg);
1257    
1258    Send a text message to a phone number using Clickatell. The FIG_Config file must contain the
1259    user name, password, and API ID for the relevant account in the hash reference variable
1260    I<$FIG_Config::phone>, using the keys C<user>, C<password>, and C<api_id>. For
1261    example, if the user name is C<BruceTheHumanPet>, the password is C<silly>, and the API ID
1262    is C<2561022>, then the FIG_Config file must contain
1263    
1264        $phone =  { user => 'BruceTheHumanPet',
1265                    password => 'silly',
1266                    api_id => '2561022' };
1267    
1268    The original purpose of this method was to insure Bruce would be notified immediately when the
1269    Sprout Load terminates. Care should be taken if you do not wish Bruce to be notified immediately
1270    when you call this method.
1271    
1272    The message ID will be returned if successful, and C<undef> if an error occurs.
1273    
1274    =over 4
1275    
1276    =item phoneNumber
1277    
1278    Phone number to receive the message, in international format. A United States phone number
1279    would be prefixed by "1". A British phone number would be prefixed by "44".
1280    
1281    =item msg
1282    
1283    Message to send to the specified phone.
1284    
1285    =item RETURN
1286    
1287    Returns the message ID if successful, and C<undef> if the message could not be sent.
1288    
1289    =back
1290    
1291    =cut
1292    
1293    sub SendSMS {
1294        # Get the parameters.
1295        my ($phoneNumber, $msg) = @_;
1296        # Declare the return variable. If we do not change it, C<undef> will be returned.
1297        my $retVal;
1298        # Only proceed if we have phone support.
1299        if (! defined $FIG_Config::phone) {
1300            Trace("Phone support not present in FIG_Config.") if T(1);
1301        } else {
1302            # Get the phone data.
1303            my $parms = $FIG_Config::phone;
1304            # Get the Clickatell URL.
1305            my $url = "http://api.clickatell.com/http/";
1306            # Create the user agent.
1307            my $ua = LWP::UserAgent->new;
1308            # Request a Clickatell session.
1309            my $resp = $ua->post("$url/sendmsg", { user => $parms->{user},
1310                                         password => $parms->{password},
1311                                         api_id => $parms->{api_id},
1312                                         to => $phoneNumber,
1313                                         text => $msg});
1314            # Check for an error.
1315            if (! $resp->is_success) {
1316                Trace("Alert failed.") if T(1);
1317            } else {
1318                # Get the message ID.
1319                my $rstring = $resp->content;
1320                if ($rstring =~ /^ID:\s+(.*)$/) {
1321                    $retVal = $1;
1322                } else {
1323                    Trace("Phone attempt failed with $rstring") if T(1);
1324                }
1325            }
1326        }
1327        # Return the result.
1328        return $retVal;
1329    }
1330    
1331    =head3 StandardSetup
1332    
1333        my ($options, @parameters) = StandardSetup(\@categories, \%options, $parmHelp, @ARGV);
1334    
1335    This method performs standard command-line parsing and tracing setup. The return
1336    values are a hash of the command-line options and a list of the positional
1337    parameters. Tracing is automatically set up and the command-line options are
1338    validated.
1339    
1340    This is a complex method that does a lot of grunt work. The parameters can
1341    be more easily understood, however, once they are examined individually.
1342    
1343    The I<categories> parameter is the most obtuse. It is a reference to a list of
1344    special-purpose tracing categories. Most tracing categories are PERL package
1345    names. So, for example, if you wanted to turn on tracing inside the B<Sprout>,
1346    B<ERDB>, and B<SproutLoad> packages, you would specify the categories
1347    
1348        ["Sprout", "SproutLoad", "ERDB"]
1349    
1350    This would cause trace messages in the specified three packages to appear in
1351    the output. There are two special tracing categories that are automatically
1352    handled by this method. In other words, if you used L</TSetup> you would need
1353    to include these categories manually, but if you use this method they are turned
1354    on automatically.
1355    
1356    =over 4
1357    
1358    =item SQL
1359    
1360    Traces SQL commands and activity.
1361    
1362    =item Tracer
1363    
1364    Traces error messages and call stacks.
1365    
1366    =back
1367    
1368    C<SQL> is only turned on if the C<-sql> option is specified in the command line.
1369    The trace level is specified using the C<-trace> command-line option. For example,
1370    the following command line for C<TransactFeatures> turns on SQL tracing and runs
1371    all tracing at level 3.
1372    
1373        TransactFeatures -trace=3 -sql register ../xacts IDs.tbl
1374    
1375    Standard tracing is output to the standard output and echoed to the file
1376    C<trace>I<$$>C<.log> in the FIG temporary directory, where I<$$> is the
1377    process ID. You can also specify the C<user> parameter to put a user ID
1378    instead of a process ID in the trace file name. So, for example
1379    
1380    The default trace level is 2. To get all messages, specify a trace level of 4.
1381    For a genome-by-genome update, use 3.
1382    
1383        TransactFeatures -trace=3 -sql -user=Bruce register ../xacts IDs.tbl
1384    
1385    would send the trace output to C<traceBruce.log> in the temporary directory.
1386    
1387    The I<options> parameter is a reference to a hash containing the command-line
1388    options, their default values, and an explanation of what they mean. Command-line
1389    options may be in the form of switches or keywords. In the case of a switch, the
1390    option value is 1 if it is specified and 0 if it is not specified. In the case
1391    of a keyword, the value is separated from the option name by an equal sign. You
1392    can see this last in the command-line example above.
1393    
1394    You can specify a different default trace level by setting C<$options->{trace}>
1395    prior to calling this method.
1396    
1397    An example at this point would help. Consider, for example, the command-line utility
1398    C<TransactFeatures>. It accepts a list of positional parameters plus the options
1399    C<safe>, C<noAlias>, C<start>, and C<tblFiles>. To start up this command, we execute
1400    the following code.
1401    
1402        my ($options, @parameters) = Tracer::StandardSetup(["DocUtils"],
1403                            { safe => [0, "use database transactions"],
1404                              noAlias => [0, "do not expect aliases in CHANGE transactions"],
1405                              start => [' ', "start with this genome"],
1406                              tblFiles => [0, "output TBL files containing the corrected IDs"] },
1407                            "<command> <transactionDirectory> <IDfile>",
1408                          @ARGV);
1409    
1410    
1411    The call to C<ParseCommand> specifies the default values for the options and
1412    stores the actual options in a hash that is returned as C<$options>. The
1413    positional parameters are returned in C<@parameters>.
1414    
1415    The following is a sample command line for C<TransactFeatures>.
1416    
1417        TransactFeatures -trace=2 -noAlias register ../xacts IDs.tbl
1418    
1419    Single and double hyphens are equivalent. So, you could also code the
1420    above command as
1421    
1422        TransactFeatures --trace=2 --noAlias register ../xacts IDs.tbl
1423    
1424    In this case, C<register>, C<../xacts>, and C<IDs.tbl> are the positional
1425    parameters, and would find themselves in I<@parameters> after executing the
1426    above code fragment. The tracing would be set to level 2, and the categories
1427    would be C<Tracer>, and <DocUtils>. C<Tracer> is standard,
1428    and C<DocUtils> was included because it came in within the first parameter
1429    to this method. The I<$options> hash would be
1430    
1431        { trace => 2, sql => 0, safe => 0,
1432          noAlias => 1, start => ' ', tblFiles => 0 }
1433    
1434    Use of C<StandardSetup> in this way provides a simple way of performing
1435    standard tracing setup and command-line parsing. Note that the caller is
1436    not even aware of the command-line switches C<-trace> and C<-sql>, which
1437    are used by this method to control the tracing. If additional tracing features
1438    need to be added in the future, they can be processed by this method without
1439    upsetting the command-line utilities.
1440    
1441    If the C<background> option is specified on the command line, then the
1442    standard and error outputs will be directed to files in the temporary
1443    directory, using the same suffix as the trace file. So, if the command
1444    line specified
1445    
1446        -user=Bruce -background
1447    
1448    then the trace output would go to C<traceBruce.log>, the standard output to
1449    C<outBruce.log>, and the error output to C<errBruce.log>. This is designed to
1450    simplify starting a command in the background.
1451    
1452    The user name is also used as the tracing key for L</Emergency Tracing>.
1453    Specifying a value of C<E> for the trace level causes emergency tracing to
1454    be used instead of custom tracing. If the user name is not specified,
1455    the tracing key is taken from the C<Tracing> environment variable. If there
1456    is no value for that variable, the tracing key will be computed from the PID.
1457    
1458    Finally, if the special option C<-help> is specified, the option
1459    names will be traced at level 0 and the program will exit without processing.
1460    This provides a limited help capability. For example, if the user enters
1461    
1462        TransactFeatures -help
1463    
1464    he would see the following output.
1465    
1466        TransactFeatures [options] <command> <transactionDirectory> <IDfile>
1467            -trace    tracing level (default E)
1468            -sql      trace SQL commands
1469            -safe     use database transactions
1470            -noAlias  do not expect aliases in CHANGE transactions
1471            -start    start with this genome
1472            -tblFiles output TBL files containing the corrected IDs
1473    
1474    The caller has the option of modifying the tracing scheme by placing a value
1475    for C<trace> in the incoming options hash. The default value can be overridden,
1476    or the tracing to the standard output can be turned off by suffixing a minus
1477    sign to the trace level. So, for example,
1478    
1479        { trace => [0, "tracing level (default 0)"],
1480           ...
1481    
1482    would set the default trace level to 0 instead of E, while
1483    
1484        { trace => ["2-", "tracing level (default 2)"],
1485           ...
1486    
1487    would set the default to 2, but trace only to the log file, not to the
1488    standard output.
1489    
1490    The parameters to this method are as follows.
1491    
1492    =over 4
1493    
1494    =item categories
1495    
1496    Reference to a list of tracing category names. These should be names of
1497    packages whose internal workings will need to be debugged to get the
1498    command working.
1499    
1500    =item options
1501    
1502    Reference to a hash containing the legal options for the current command mapped
1503    to their default values and descriptions. The user can override the defaults
1504    by specifying the options as command-line switches prefixed by a hyphen.
1505    Tracing-related options may be added to this hash. If the C<-h> option is
1506    specified on the command line, the option descriptions will be used to
1507    explain the options. To turn off tracing to the standard output, add a
1508    minus sign to the value for C<trace> (see above).
1509    
1510    =item parmHelp
1511    
1512    A string that vaguely describes the positional parameters. This is used
1513    if the user specifies the C<-h> option.
1514    
1515    =item argv
1516    
1517    List of command line parameters, including the option switches, which must
1518    precede the positional parameters and be prefixed by a hyphen.
1519    
1520    =item RETURN
1521    
1522    Returns a list. The first element of the list is the reference to a hash that
1523    maps the command-line option switches to their values. These will either be the
1524    default values or overrides specified on the command line. The remaining
1525    elements of the list are the position parameters, in order.
1526    
1527    =back
1528    
1529    =cut
1530    
1531    sub StandardSetup {
1532        # Get the parameters.
1533        my ($categories, $options, $parmHelp, @argv) = @_;
1534        # Get the default tracing key.
1535        my $tkey = EmergencyKey();
1536        # Add the tracing options.
1537        if (! exists $options->{trace}) {
1538            $options->{trace} = ['2', "tracing level (E for emergency tracing)"];
1539        }
1540        $options->{sql} = [0, "turn on SQL tracing"];
1541        $options->{help} = [0, "display command-line options"];
1542        $options->{user} = [$tkey, "tracing key"];
1543        $options->{background} = [0, "spool standard and error output"];
1544        # Create a parsing hash from the options hash. The parsing hash
1545        # contains the default values rather than the default value
1546        # and the description. While we're at it, we'll memorize the
1547        # length of the longest option name.
1548        my $longestName = 0;
1549        my %parseOptions = ();
1550        for my $key (keys %{$options}) {
1551            if (length $key > $longestName) {
1552                $longestName = length $key;
1553            }
1554            $parseOptions{$key} = $options->{$key}->[0];
1555        }
1556        # Parse the command line.
1557        my ($retOptions, @retParameters) = ParseCommand(\%parseOptions, @argv);
1558        # Get the logfile suffix.
1559        my $suffix = $retOptions->{user};
1560        # Check for background mode.
1561        if ($retOptions->{background}) {
1562            my $outFileName = "$FIG_Config::temp/out$suffix.log";
1563            my $errFileName = "$FIG_Config::temp/err$suffix.log";
1564            open STDOUT, ">$outFileName";
1565            open STDERR, ">$errFileName";
1566            # Check for phone support. If we have phone support and a phone number,
1567            # we want to turn it on.
1568            if ($ENV{PHONE} && defined($FIG_Config::phone)) {
1569                $retOptions->{phone} = $ENV{PHONE};
1570            }
1571        }
1572        # Now we want to set up tracing. First, we need to know if the user
1573        # wants emergency tracing.
1574        if ($retOptions->{trace} eq 'E') {
1575            ETracing($retOptions->{user});
1576        } else {
1577            # Here the tracing is controlled from the command line.
1578            my @cats = @{$categories};
1579            if ($retOptions->{sql}) {
1580                push @cats, "SQL";
1581            }
1582            # Add the default categories.
1583            push @cats, "Tracer";
1584            # Next, we create the category string by joining the categories.
1585            my $cats = join(" ", @cats);
1586            # Check to determine whether or not the caller wants to turn off tracing
1587            # to the standard output.
1588            my $traceLevel = $retOptions->{trace};
1589            my $textOKFlag = 1;
1590            if ($traceLevel =~ /^(.)-/) {
1591                $traceLevel = $1;
1592                $textOKFlag = 0;
1593            }
1594            # Now we set up the trace mode.
1595            my $traceMode;
1596            # Verify that we can open a file in the FIG temporary directory.
1597            my $traceFileName = "$FIG_Config::temp/trace$suffix.log";
1598            if (open TESTTRACE, ">$traceFileName") {
1599                # Here we can trace to a file.
1600                $traceMode = ">$traceFileName";
1601                if ($textOKFlag) {
1602                    # Echo to standard output if the text-OK flag is set.
1603                    $traceMode = "+$traceMode";
1604                }
1605                # Close the test file.
1606                close TESTTRACE;
1607            } else {
1608                # Here we can't trace to a file. We trace to the standard output if it's
1609                # okay, and the error log otherwise.
1610                if ($textOKFlag) {
1611                    $traceMode = "TEXT";
1612                } else {
1613                    $traceMode = "WARN";
1614                }
1615            }
1616            # Now set up the tracing.
1617            TSetup("$traceLevel $cats", $traceMode);
1618        }
1619        # Check for the "help" option. If it is specified, dump the command-line
1620        # options and exit the program.
1621        if ($retOptions->{help}) {
1622            $0 =~ m#[/\\](\w+)(\.pl)?$#i;
1623            print "$1 [options] $parmHelp\n";
1624            for my $key (sort keys %{$options}) {
1625                my $name = Pad($key, $longestName, 0, ' ');
1626                my $desc = $options->{$key}->[1];
1627                if ($options->{$key}->[0]) {
1628                    $desc .= " (default " . $options->{$key}->[0] . ")";
1629                }
1630                print "  $name $desc\n";
1631            }
1632            exit(0);
1633        }
1634        # Trace the options, if applicable.
1635        if (T(3)) {
1636            my @parms = grep { $retOptions->{$_} } keys %{$retOptions};
1637            Trace("Selected options: " . join(", ", sort @parms) . ".");
1638        }
1639        # Return the parsed parameters.
1640        return ($retOptions, @retParameters);
1641    }
1642    
1643    =head3 ReadOptions
1644    
1645        my %options = Tracer::ReadOptions($fileName);
1646    
1647    Read a set of options from a file. Each option is encoded in a line of text that has the
1648    format
1649    
1650    I<optionName>C<=>I<optionValue>C<; >I<comment>
1651    
1652    The option name must consist entirely of letters, digits, and the punctuation characters
1653    C<.> and C<_>, and is case sensitive. Blank lines and lines in which the first nonblank
1654    character is a semi-colon will be ignored. The return hash will map each option name to
1655    the corresponding option value.
1656    
1657    =over 4
1658    
1659    =item fileName
1660    
1661    Name of the file containing the option data.
1662    
1663    =item RETURN
1664    
1665    Returns a hash mapping the option names specified in the file to their corresponding option
1666    value.
1667    
1668    =back
1669    
1670    =cut
1671    
1672    sub ReadOptions {
1673        # Get the parameters.
1674        my ($fileName) = @_;
1675        # Open the file.
1676        (open CONFIGFILE, "<$fileName") || Confess("Could not open option file $fileName.");
1677        # Count the number of records read.
1678        my ($records, $comments) = 0;
1679        # Create the return hash.
1680        my %retVal = ();
1681        # Loop through the file, accumulating key-value pairs.
1682        while (my $line = <CONFIGFILE>) {
1683            # Denote we've read a line.
1684            $records++;
1685            # Determine the line type.
1686            if ($line =~ /^\s*[\n\r]/) {
1687                # A blank line is a comment.
1688                $comments++;
1689            } elsif ($line =~ /^\s*([A-Za-z0-9_\.]+)=([^;]*);/) {
1690                # Here we have an option assignment.
1691                retVal{$1} = $2;
1692            } elsif ($line =~ /^\s*;/) {
1693                # Here we have a text comment.
1694                $comments++;
1695            } else {
1696                # Here we have an invalid line.
1697                Trace("Invalid option statement in record $records.") if T(0);
1698            }
1699        }
1700        # Return the hash created.
1701        return %retVal;
1702    }
1703    
1704    =head3 GetOptions
1705    
1706        Tracer::GetOptions(\%defaults, \%options);
1707    
1708    Merge a specified set of options into a table of defaults. This method takes two hash references
1709    as input and uses the data from the second to update the first. If the second does not exist,
1710    there will be no effect. An error will be thrown if one of the entries in the second hash does not
1711    exist in the first.
1712    
1713    Consider the following example.
1714    
1715        my $optionTable = GetOptions({ dbType => 'mySQL', trace => 0 }, $options);
1716    
1717    In this example, the variable B<$options> is expected to contain at most two options-- B<dbType> and
1718    B<trace>. The default database type is C<mySQL> and the default trace level is C<0>. If the value of
1719    B<$options> is C<< {dbType => 'Oracle'} >>, then the database type will be changed to C<Oracle> and
1720    the trace level will remain at 0. If B<$options> is undefined, then the database type and trace level
1721    will remain C<mySQL> and C<0>. If, on the other hand, B<$options> is defined as
1722    
1723        {databaseType => 'Oracle'}
1724    
1725    an error will occur because the B<databaseType> option does not exist.
1726    
1727    =over 4
1728    
1729    =item defaults
1730    
1731    Table of default option values.
1732    
1733    =item options
1734    
1735    Table of overrides, if any.
1736    
1737    =item RETURN
1738    
1739    Returns a reference to the default table passed in as the first parameter.
1740    
1741    =back
1742    
1743    =cut
1744    
1745    sub GetOptions {
1746        # Get the parameters.
1747        my ($defaults, $options) = @_;
1748        # Check for overrides.
1749        if ($options) {
1750            # Loop through the overrides.
1751            while (my ($option, $setting) = each %{$options}) {
1752                # Insure this override exists.
1753                if (!exists $defaults->{$option}) {
1754                    croak "Unrecognized option $option encountered.";
1755                } else {
1756                    # Apply the override.
1757                    $defaults->{$option} = $setting;
1758                }
1759            }
1760        }
1761        # Return the merged table.
1762        return $defaults;
1763    }
1764    
1765    =head3 MergeOptions
1766    
1767        Tracer::MergeOptions(\%table, \%defaults);
1768    
1769    Merge default values into a hash table. This method looks at the key-value pairs in the
1770    second (default) hash, and if a matching key is not found in the first hash, the default
1771    pair is copied in. The process is similar to L</GetOptions>, but there is no error-
1772    checking and no return value.
1773    
1774    =over 4
1775    
1776    =item table
1777    
1778    Hash table to be updated with the default values.
1779    
1780    =item defaults
1781    
1782    Default values to be merged into the first hash table if they are not already present.
1783    
1784    =back
1785    
1786    =cut
1787    
1788    sub MergeOptions {
1789        # Get the parameters.
1790        my ($table, $defaults) = @_;
1791        # Loop through the defaults.
1792        while (my ($key, $value) = each %{$defaults}) {
1793            if (!exists $table->{$key}) {
1794                $table->{$key} = $value;
1795            }
1796        }
1797    }
1798    
1799    =head3 ParseCommand
1800    
1801        my ($options, @arguments) = Tracer::ParseCommand(\%optionTable, @inputList);
1802    
1803    Parse a command line consisting of a list of parameters. The initial parameters may be option
1804    specifiers of the form C<->I<option> or C<->I<option>C<=>I<value>. The options are stripped
1805    off and merged into a table of default options. The remainder of the command line is
1806    returned as a list of positional arguments. For example, consider the following invocation.
1807    
1808        my ($options, @arguments) = ParseCommand({ errors => 0, logFile => 'trace.log'}, @words);
1809    
1810    In this case, the list @words will be treated as a command line and there are two options available,
1811    B<errors> and B<logFile>. If @words has the following format
1812    
1813        -logFile=error.log apple orange rutabaga
1814    
1815    then at the end of the invocation, C<$options> will be
1816    
1817        { errors => 0, logFile => 'error.log' }
1818    
1819    and C<@arguments> will contain
1820    
1821        apple orange rutabaga
1822    
1823    The parser allows for some escape sequences. See L</UnEscape> for a description. There is no
1824    support for quote characters. Options can be specified with single or double hyphens.
1825    
1826    =over 4
1827    
1828    =item optionTable
1829    
1830    Table of default options.
1831    
1832    =item inputList
1833    
1834    List of words on the command line.
1835    
1836    =item RETURN
1837    
1838    Returns a reference to the option table and a list of the positional arguments.
1839    
1840    =back
1841    
1842    =cut
1843    
1844    sub ParseCommand {
1845        # Get the parameters.
1846        my ($optionTable, @inputList) = @_;
1847        # Process any options in the input list.
1848        my %overrides = ();
1849        while ((@inputList > 0) && ($inputList[0] =~ /^--?/)) {
1850            # Get the current option.
1851            my $arg = shift @inputList;
1852            # Pull out the option name.
1853            $arg =~ /^--?([^=]*)/g;
1854            my $name = $1;
1855            # Check for an option value.
1856            if ($arg =~ /\G=(.*)$/g) {
1857                # Here we have a value for the option.
1858                $overrides{$name} = UnEscape($1);
1859            } else {
1860                # Here there is no value, so we use 1.
1861                $overrides{$name} = 1;
1862            }
1863        }
1864        # Merge the options into the defaults.
1865        GetOptions($optionTable, \%overrides);
1866        # Translate the remaining parameters.
1867        my @retVal = ();
1868        for my $inputParm (@inputList) {
1869            push @retVal, UnEscape($inputParm);
1870        }
1871        # Return the results.
1872        return ($optionTable, @retVal);
1873    }
1874    
1875    
1876    =head2 File Utility Methods
1877    
1878    =head3 GetFile
1879    
1880        my @fileContents = Tracer::GetFile($fileName);
1881    
1882        or
1883    
1884        my $fileContents = Tracer::GetFile($fileName);
1885    
1886    Return the entire contents of a file. In list context, line-ends are removed and
1887    each line is a list element. In scalar context, line-ends are replaced by C<\n>.
1888    
1889    =over 4
1890    
1891    =item fileName
1892    
1893    Name of the file to read.
1894    
1895    =item RETURN
1896    
1897    In a list context, returns the entire file as a list with the line terminators removed.
1898    In a scalar context, returns the entire file as a string. If an error occurs opening
1899    the file, an empty list will be returned.
1900    
1901    =back
1902    
1903    =cut
1904    
1905    sub GetFile {
1906        # Get the parameters.
1907        my ($fileName) = @_;
1908        # Declare the return variable.
1909        my @retVal = ();
1910        # Open the file for input.
1911        my $handle = Open(undef, "<$fileName");
1912        # Read the whole file into the return variable, stripping off any terminator
1913        # characters.
1914        my $lineCount = 0;
1915        while (my $line = <$handle>) {
1916            $lineCount++;
1917            $line = Strip($line);
1918            push @retVal, $line;
1919        }
1920        # Close it.
1921        close $handle;
1922        my $actualLines = @retVal;
1923        Trace("$actualLines lines read from file $fileName.") if T(File => 2);
1924        # Return the file's contents in the desired format.
1925        if (wantarray) {
1926            return @retVal;
1927        } else {
1928            return join "\n", @retVal;
1929        }
1930    }
1931    
1932    =head3 PutFile
1933    
1934        Tracer::PutFile($fileName, \@lines);
1935    
1936    Write out a file from a list of lines of text.
1937    
1938    =over 4
1939    
1940    =item fileName
1941    
1942    Name of the output file.
1943    
1944    =item lines
1945    
1946    Reference to a list of text lines. The lines will be written to the file in order, with trailing
1947    new-line characters. Alternatively, may be a string, in which case the string will be written without
1948    modification.
1949    
1950    =back
1951    
1952    =cut
1953    
1954    sub PutFile {
1955        # Get the parameters.
1956        my ($fileName, $lines) = @_;
1957        # Open the output file.
1958        my $handle = Open(undef, ">$fileName");
1959        # Count the lines written.
1960        if (ref $lines ne 'ARRAY') {
1961            # Here we have a scalar, so we write it raw.
1962            print $handle $lines;
1963            Trace("Scalar put to file $fileName.") if T(File => 3);
1964        } else {
1965            # Write the lines one at a time.
1966            my $count = 0;
1967            for my $line (@{$lines}) {
1968                print $handle "$line\n";
1969                $count++;
1970            }
1971            Trace("$count lines put to file $fileName.") if T(File => 3);
1972        }
1973        # Close the output file.
1974        close $handle;
1975    }
1976    
1977    =head3 ParseRecord
1978    
1979        my @fields = Tracer::ParseRecord($line);
1980    
1981    Parse a tab-delimited data line. The data line is split into field values. Embedded tab
1982    and new-line characters in the data line must be represented as C<\t> and C<\n>, respectively.
1983    These will automatically be converted.
1984    
1985    =over 4
1986    
1987    =item line
1988    
1989    Line of data containing the tab-delimited fields.
1990    
1991    =item RETURN
1992    
1993    Returns a list of the fields found in the data line.
1994    
1995    =back
1996    
1997    =cut
1998    
1999    sub ParseRecord {
2000        # Get the parameter.
2001        my ($line) = @_;
2002        # Remove the trailing new-line, if any.
2003        chomp $line;
2004        # Split the line read into pieces using the tab character.
2005        my @retVal = split /\t/, $line;
2006        # Trim and fix the escapes in each piece.
2007        for my $value (@retVal) {
2008            # Trim leading whitespace.
2009            $value =~ s/^\s+//;
2010            # Trim trailing whitespace.
2011            $value =~ s/\s+$//;
2012            # Delete the carriage returns.
2013            $value =~ s/\r//g;
2014            # Convert the escapes into their real values.
2015            $value =~ s/\\t/"\t"/ge;
2016            $value =~ s/\\n/"\n"/ge;
2017        }
2018        # Return the result.
2019        return @retVal;
2020    }
2021    
2022    =head3 Merge
2023    
2024        my @mergedList = Tracer::Merge(@inputList);
2025    
2026    Sort a list of strings and remove duplicates.
2027    
2028    =over 4
2029    
2030    =item inputList
2031    
2032    List of scalars to sort and merge.
2033    
2034    =item RETURN
2035    
2036    Returns a list containing the same elements sorted in ascending order with duplicates
2037    removed.
2038    
2039    =back
2040    
2041    =cut
2042    
2043    sub Merge {
2044        # Get the input list in sort order.
2045        my @inputList = sort @_;
2046        # Only proceed if the list has at least two elements.
2047        if (@inputList > 1) {
2048            # Now we want to move through the list splicing out duplicates.
2049            my $i = 0;
2050            while ($i < @inputList) {
2051                # Get the current entry.
2052                my $thisEntry = $inputList[$i];
2053                # Find out how many elements duplicate the current entry.
2054                my $j = $i + 1;
2055                my $dup1 = $i + 1;
2056                while ($j < @inputList && $inputList[$j] eq $thisEntry) { $j++; };
2057                # If the number is nonzero, splice out the duplicates found.
2058                if ($j > $dup1) {
2059                    splice @inputList, $dup1, $j - $dup1;
2060                }
2061                # Now the element at position $dup1 is different from the element before it
2062                # at position $i. We push $i forward one position and start again.
2063                $i++;
2064            }
2065        }
2066        # Return the merged list.
2067        return @inputList;
2068    }
2069    
2070    =head3 Open
2071    
2072        my $handle = Open($fileHandle, $fileSpec, $message);
2073    
2074    Open a file.
2075    
2076    The I<$fileSpec> is essentially the second argument of the PERL C<open>
2077    function. The mode is specified using Unix-like shell information. So, for
2078    example,
2079    
2080        Open(\*LOGFILE, '>>/usr/spool/news/twitlog', "Could not open twit log.");
2081    
2082    would open for output appended to the specified file, and
2083    
2084        Open(\*DATASTREAM, "| sort -u >$outputFile", "Could not open $outputFile.");
2085    
2086    would open a pipe that sorts the records written and removes duplicates. Note
2087    the use of file handle syntax in the Open call. To use anonymous file handles,
2088    code as follows.
2089    
2090        my $logFile = Open(undef, '>>/usr/spool/news/twitlog', "Could not open twit log.");
2091    
2092    The I<$message> parameter is used if the open fails. If it is set to C<0>, then
2093    the open returns TRUE if successful and FALSE if an error occurred. Otherwise, a
2094    failed open will throw an exception and the third parameter will be used to construct
2095    an error message. If the parameter is omitted, a standard message is constructed
2096    using the file spec.
2097    
2098        Could not open "/usr/spool/news/twitlog"
2099    
2100    Note that the mode characters are automatically cleaned from the file name.
2101    The actual error message from the file system will be captured and appended to the
2102    message in any case.
2103    
2104        Could not open "/usr/spool/news/twitlog": file not found.
2105    
2106    In some versions of PERL the only error message we get is a number, which
2107    corresponds to the C++ C<errno> value.
2108    
2109        Could not open "/usr/spool/news/twitlog": 6.
2110    
2111    =over 4
2112    
2113    =item fileHandle
2114    
2115    File handle. If this parameter is C<undef>, a file handle will be generated
2116    and returned as the value of this method.
2117    
2118    =item fileSpec
2119    
2120    File name and mode, as per the PERL C<open> function.
2121    
2122    =item message (optional)
2123    
2124    Error message to use if the open fails. If omitted, a standard error message
2125    will be generated. In either case, the error information from the file system
2126    is appended to the message. To specify a conditional open that does not throw
2127    an error if it fails, use C<0>.
2128    
2129    =item RETURN
2130    
2131    Returns the name of the file handle assigned to the file, or C<undef> if the
2132    open failed.
2133    
2134    =back
2135    
2136    =cut
2137    
2138    sub Open {
2139        # Get the parameters.
2140        my ($fileHandle, $fileSpec, $message) = @_;
2141        # Attempt to open the file.
2142        my $rv = open $fileHandle, $fileSpec;
2143        # If the open failed, generate an error message.
2144        if (! $rv) {
2145            # Save the system error message.
2146            my $sysMessage = $!;
2147            # See if we need a default message.
2148            if (!$message) {
2149                # Clean any obvious mode characters and leading spaces from the
2150                # filename.
2151                my ($fileName) = FindNamePart($fileSpec);
2152                $message = "Could not open \"$fileName\"";
2153            }
2154            # Terminate with an error using the supplied message and the
2155            # error message from the file system.
2156            Confess("$message: $!");
2157        }
2158        # Return the file handle.
2159        return $fileHandle;
2160    }
2161    
2162    =head3 FindNamePart
2163    
2164        my ($fileName, $start, $len) = Tracer::FindNamePart($fileSpec);
2165    
2166    Extract the portion of a file specification that contains the file name.
2167    
2168    A file specification is the string passed to an C<open> call. It specifies the file
2169    mode and name. In a truly complex situation, it can specify a pipe sequence. This
2170    method assumes that the file name is whatever follows the first angle bracket
2171    sequence.  So, for example, in the following strings the file name is
2172    C</usr/fig/myfile.txt>.
2173    
2174        >>/usr/fig/myfile.txt
2175        </usr/fig/myfile.txt
2176        | sort -u > /usr/fig/myfile.txt
2177    
2178    If the method cannot find a file name using its normal methods, it will return the
2179    whole incoming string.
2180    
2181    =over 4
2182    
2183    =item fileSpec
2184    
2185    File specification string from which the file name is to be extracted.
2186    
2187    =item RETURN
2188    
2189    Returns a three-element list. The first element contains the file name portion of
2190    the specified string, or the whole string if a file name cannot be found via normal
2191    methods. The second element contains the start position of the file name portion and
2192    the third element contains the length.
2193    
2194    =back
2195    
2196    =cut
2197    #: Return Type $;
2198    sub FindNamePart {
2199        # Get the parameters.
2200        my ($fileSpec) = @_;
2201        # Default to the whole input string.
2202        my ($retVal, $pos, $len) = ($fileSpec, 0, length $fileSpec);
2203        # Parse out the file name if we can.
2204        if ($fileSpec =~ m/(<|>>?)(.+?)(\s*)$/) {
2205            $retVal = $2;
2206            $len = length $retVal;
2207            $pos = (length $fileSpec) - (length $3) - $len;
2208        }
2209        # Return the result.
2210        return ($retVal, $pos, $len);
2211    }
2212    
2213    =head3 OpenDir
2214    
2215        my @files = OpenDir($dirName, $filtered, $flag);
2216    
2217    Open a directory and return all the file names. This function essentially performs
2218    the functions of an C<opendir> and C<readdir>. If the I<$filtered> parameter is
2219    set to TRUE, all filenames beginning with a period (C<.>), dollar sign (C<$>),
2220    or pound sign (C<#>) and all filenames ending with a tilde C<~>) will be
2221    filtered out of the return list. If the directory does not open and I<$flag> is not
2222    set, an exception is thrown. So, for example,
2223    
2224        my @files = OpenDir("/Volumes/fig/contigs", 1);
2225    
2226  C<< my $string = Tracer::Now(); >>  is effectively the same as
2227    
2228  Return a displayable time stamp containing the local time.      opendir(TMP, "/Volumes/fig/contigs") || Confess("Could not open /Volumes/fig/contigs.");
2229        my @files = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir(TMP);
2230    
2231  =cut  Similarly, the following code
2232    
2233  sub Now {      my @files = grep { $_ =~ /^\d/ } OpenDir("/Volumes/fig/orgs", 0, 1);
     my ($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 $retVal;  
 }  
2234    
2235  # Pad a number to 2 digits.  Returns the names of all files in C</Volumes/fig/orgs> that begin with digits and
2236  sub _p2 {  automatically returns an empty list if the directory fails to open.
     my ($value) = @_;  
     $value = "0$value" if ($value < 10);  
     return $value;  
 }  
2237    
2238  =head3 LogErrors  =over 4
2239    
2240  C<< Tracer::LogErrors($fileName); >>  =item dirName
2241    
2242  Route the standard error output to a log file.  Name of the directory to open.
2243    
2244  =over 4  =item filtered
2245    
2246  =item fileName  TRUE if files whose names begin with a period (C<.>) should be automatically removed
2247    from the list, else FALSE.
2248    
2249  Name of the file to receive the error output.  =item flag
2250    
2251    TRUE if a failure to open is okay, else FALSE
2252    
2253  =back  =back
2254    
2255  =cut  =cut
2256    #: Return Type @;
2257  sub LogErrors {  sub OpenDir {
2258      # Get the file name.      # Get the parameters.
2259      my ($fileName) = @_;      my ($dirName, $filtered, $flag) = @_;
2260      # Open the file as the standard error output.      # Declare the return variable.
2261      open STDERR, '>', $fileName;      my @retVal = ();
2262        # Open the directory.
2263        if (opendir(my $dirHandle, $dirName)) {
2264            # The directory opened successfully. Get the appropriate list according to the
2265            # strictures of the filter parameter.
2266            if ($filtered) {
2267                @retVal = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir $dirHandle;
2268            } else {
2269                @retVal = readdir $dirHandle;
2270            }
2271        } elsif (! $flag) {
2272            # Here the directory would not open and it's considered an error.
2273            Confess("Could not open directory $dirName.");
2274        }
2275        # Return the result.
2276        return @retVal;
2277  }  }
2278    
 =head3 ReadOptions  
   
 C<< my %options = Tracer::ReadOptions($fileName); >>  
2279    
2280  Read a set of options from a file. Each option is encoded in a line of text that has the  =head3 Insure
 format  
2281    
2282  I<optionName>C<=>I<optionValue>C<; >I<comment>      Insure($dirName, $chmod);
2283    
2284  The option name must consist entirely of letters, digits, and the punctuation characters  Insure a directory is present.
 C<.> and C<_>, and is case sensitive. Blank lines and lines in which the first nonblank  
 character is a semi-colon will be ignored. The return hash will map each option name to  
 the corresponding option value.  
2285    
2286  =over 4  =over 4
2287    
2288  =item fileName  =item dirName
2289    
2290  Name of the file containing the option data.  Name of the directory to check. If it does not exist, it will be created.
2291    
2292  =item RETURN  =item chmod (optional)
2293    
2294  Returns a hash mapping the option names specified in the file to their corresponding option  Security privileges to be given to the directory if it is created.
 value.  
2295    
2296  =back  =back
2297    
2298  =cut  =cut
2299    
2300  sub ReadOptions {  sub Insure {
2301      # Get the parameters.      my ($dirName, $chmod) = @_;
2302      my ($fileName) = @_;      if (! -d $dirName) {
2303      # Open the file.          Trace("Creating $dirName directory.") if T(2);
2304      (open CONFIGFILE, "<$fileName") || Confess("Could not open option file $fileName.");          eval {
2305      # Count the number of records read.              mkpath $dirName;
2306      my ($records, $comments) = 0;              # If we have permissions specified, set them here.
2307      # Create the return hash.              if (defined($chmod)) {
2308      my %retVal = ();                  chmod $chmod, $dirName;
2309      # Loop through the file, accumulating key-value pairs.              }
2310      while (my $line = <CONFIGFILE>) {          };
2311          # Denote we've read a line.          if ($@) {
2312          $records++;              Confess("Error creating $dirName: $@");
         # Determine the line type.  
         if ($line =~ /^\s*[\n\r]/) {  
             # A blank line is a comment.  
             $comments++;  
         } elsif ($line =~ /^\s*([A-Za-z0-9_\.]+)=([^;]*);/) {  
             # Here we have an option assignment.  
             retVal{$1} = $2;  
         } elsif ($line =~ /^\s*;/) {  
             # Here we have a text comment.  
             $comments++;  
         } else {  
             # Here we have an invalid line.  
             Trace("Invalid option statement in record $records.") if T(0);  
2313          }          }
2314      }      }
     # Return the hash created.  
     return %retVal;  
2315  }  }
2316    
2317  =head3 GetOptions  =head3 ChDir
2318    
2319  C<< Tracer::GetOptions(\%defaults, \%options); >>      ChDir($dirName);
2320    
2321  Merge a specified set of options into a table of defaults. This method takes two hash references  Change to the specified directory.
 as input and uses the data from the second to update the first. If the second does not exist,  
 there will be no effect. An error will be thrown if one of the entries in the second hash does not  
 exist in the first.  
2322    
2323  Consider the following example.  =over 4
2324    
2325  C<< my $optionTable = GetOptions({ dbType => 'mySQL', trace => 0 }, $options); >>  =item dirName
2326    
2327  In this example, the variable B<$options> is expected to contain at most two options-- B<dbType> and  Name of the directory to which we want to change.
 B<trace>. The default database type is C<mySQL> and the default trace level is C<0>. If the value of  
 B<$options> is C<< {dbType => 'Oracle'} >>, then the database type will be changed to C<Oracle> and  
 the trace level will remain at 0. If B<$options> is undefined, then the database type and trace level  
 will remain C<mySQL> and C<0>. If, on the other hand, B<$options> is defined as  
2328    
2329  C<< {databaseType => 'Oracle'} >>  =back
2330    
2331  an error will occur because the B<databaseType> option does not exist.  =cut
2332    
2333    sub ChDir {
2334        my ($dirName) = @_;
2335        if (! -d $dirName) {
2336            Confess("Cannot change to directory $dirName: no such directory.");
2337        } else {
2338            Trace("Changing to directory $dirName.") if T(File => 4);
2339            my $okFlag = chdir $dirName;
2340            if (! $okFlag) {
2341                Confess("Error switching to directory $dirName.");
2342            }
2343        }
2344    }
2345    
2346    =head3 SetPermissions
2347    
2348        Tracer::SetPermissions($dirName, $group, $mask, %otherMasks);
2349    
2350    Set the permissions for a directory and all the files and folders inside it.
2351    In addition, the group ownership will be changed to the specified value.
2352    
2353    This method is more vulnerable than most to permission and compatability
2354    problems, so it does internal error recovery.
2355    
2356  =over 4  =over 4
2357    
2358  =item defaults  =item dirName
2359    
2360  Table of default option values.  Name of the directory to process.
2361    
2362  =item options  =item group
2363    
2364  Table of overrides, if any.  Name of the group to be assigned.
2365    
2366  =item RETURN  =item mask
2367    
2368  Returns a reference to the default table passed in as the first parameter.  Permission mask. Bits that are C<1> in this mask will be ORed into the
2369    permission bits of any file or directory that does not already have them
2370    set to 1.
2371    
2372    =item otherMasks
2373    
2374    Map of search patterns to permission masks. If a directory name matches
2375    one of the patterns, that directory and all its members and subdirectories
2376    will be assigned the new pattern. For example, the following would
2377    assign 01664 to most files, but would use 01777 for directories named C<tmp>.
2378    
2379        Tracer::SetPermissions($dirName, 'fig', 01664, '^tmp$' => 01777);
2380    
2381    The list is ordered, so the following would use 0777 for C<tmp1> and
2382    0666 for C<tmp>, C<tmp2>, or C<tmp3>.
2383    
2384        Tracer::SetPermissions($dirName, 'fig', 01664, '^tmp1' => 0777,
2385                                                       '^tmp' => 0666);
2386    
2387    Note that the pattern matches are all case-insensitive, and only directory
2388    names are matched, not file names.
2389    
2390  =back  =back
2391    
2392  =cut  =cut
2393    
2394  sub GetOptions {  sub SetPermissions {
2395      # Get the parameters.      # Get the parameters.
2396      my ($defaults, $options) = @_;      my ($dirName, $group, $mask, @otherMasks) = @_;
2397      # Check for overrides.      # Set up for error recovery.
2398      if ($options) {      eval {
2399          # Loop through the overrides.          # Switch to the specified directory.
2400          while (my ($option, $setting) = each %{$options}) {          ChDir($dirName);
2401              # Insure this override exists.          # Get the group ID.
2402              if (!exists $defaults->{$option}) {          my $gid = getgrnam($group);
2403                  croak "Unrecognized option $option encountered.";          # Get the mask for tracing.
2404            my $traceMask = sprintf("%04o", $mask) . "($mask)";
2405            Trace("Fixing permissions for directory $dirName using group $group($gid) and mask $traceMask.") if T(File => 2);
2406            my $fixCount = 0;
2407            my $lookCount = 0;
2408            # @dirs will be a stack of directories to be processed.
2409            my @dirs = (getcwd());
2410            while (scalar(@dirs) > 0) {
2411                # Get the current directory.
2412                my $dir = pop @dirs;
2413                # Check for a match to one of the specified directory names. To do
2414                # that, we need to pull the individual part of the name off of the
2415                # whole path.
2416                my $simpleName = $dir;
2417                if ($dir =~ m!/([^/]+)$!) {
2418                    $simpleName = $1;
2419                }
2420                Trace("Simple directory name for $dir is $simpleName.") if T(File => 4);
2421                # Search for a match.
2422                my $match = 0;
2423                my $i;
2424                for ($i = 0; $i < $#otherMasks && ! $match; $i += 2) {
2425                    my $pattern = $otherMasks[$i];
2426                    if ($simpleName =~ /$pattern/i) {
2427                        $match = 1;
2428                    }
2429                }
2430                # Check for a match. Note we use $i-1 because the loop added 2
2431                # before terminating due to the match.
2432                if ($match && $otherMasks[$i-1] != $mask) {
2433                    # This directory matches one of the incoming patterns, and it's
2434                    # a different mask, so we process it recursively with that mask.
2435                    SetPermissions($dir, $group, $otherMasks[$i-1], @otherMasks);
2436              } else {              } else {
2437                  # Apply the override.                  # Here we can process normally. Get all of the non-hidden members.
2438                  $defaults->{$option} = $setting;                  my @submems = OpenDir($dir, 1);
2439                    for my $submem (@submems) {
2440                        # Get the full name.
2441                        my $thisMem = "$dir/$submem";
2442                        Trace("Checking member $thisMem.") if T(4);
2443                        $lookCount++;
2444                        if ($lookCount % 1000 == 0) {
2445                            Trace("$lookCount members examined. Current is $thisMem. Mask is $traceMask") if T(File => 3);
2446              }              }
2447                        # Fix the group.
2448                        chown -1, $gid, $thisMem;
2449                        # Insure this member is not a symlink.
2450                        if (! -l $thisMem) {
2451                            # Get its info.
2452                            my $fileInfo = stat $thisMem;
2453                            # Only proceed if we got the info. Otherwise, it's a hard link
2454                            # and we want to skip it anyway.
2455                            if ($fileInfo) {
2456                                my $fileMode = $fileInfo->mode;
2457                                if (($fileMode & $mask) != $mask) {
2458                                    # Fix this member.
2459                                    $fileMode |= $mask;
2460                                    chmod $fileMode, $thisMem;
2461                                    $fixCount++;
2462          }          }
2463                                # If it's a subdirectory, stack it.
2464                                if (-d $thisMem) {
2465                                    push @dirs, $thisMem;
2466                                }
2467                            }
2468                        }
2469                    }
2470                }
2471            }
2472            Trace("$lookCount files and directories processed, $fixCount fixed.") if T(File => 2);
2473        };
2474        # Check for an error.
2475        if ($@) {
2476            Confess("SetPermissions error: $@");
2477      }      }
     # Return the merged table.  
     return $defaults;  
2478  }  }
2479    
2480  =head3 MergeOptions  =head3 GetLine
2481    
2482  C<< Tracer::MergeOptions(\%table, \%defaults); >>      my @data = Tracer::GetLine($handle);
2483    
2484  Merge default values into a hash table. This method looks at the key-value pairs in the  Read a line of data from a tab-delimited 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.  
2485    
2486  =over 4  =over 4
2487    
2488  =item table  =item handle
2489    
2490  Hash table to be updated with the default values.  Open file handle from which to read.
2491    
2492  =item defaults  =item RETURN
2493    
2494  Default values to be merged into the first hash table if they are not already present.  Returns a list of the fields in the record read. The fields are presumed to be
2495    tab-delimited. If we are at the end of the file, then an empty list will be
2496    returned. If an empty line is read, a single list item consisting of a null
2497    string will be returned.
2498    
2499  =back  =back
2500    
2501  =cut  =cut
2502    
2503  sub MergeOptions {  sub GetLine {
2504      # Get the parameters.      # Get the parameters.
2505      my ($table, $defaults) = @_;      my ($handle) = @_;
2506      # Loop through the defaults.      # Declare the return variable.
2507      while (my ($key, $value) = each %{$defaults}) {      my @retVal = ();
2508          if (!exists $table->{$key}) {      Trace("File position is " . tell($handle) . ". EOF flag is " . eof($handle) . ".") if T(File => 4);
2509              $table->{$key} = $value;      # Read from the file.
2510        my $line = <$handle>;
2511        # Only proceed if we found something.
2512        if (defined $line) {
2513            # Remove the new-line. We are a bit over-cautious here because the file may be coming in via an
2514            # upload control and have a nonstandard EOL combination.
2515            $line =~ s/(\r|\n)+$//;
2516            # Here we do some fancy tracing to help in debugging complicated EOL marks.
2517            if (T(File => 4)) {
2518                my $escapedLine = $line;
2519                $escapedLine =~ s/\n/\\n/g;
2520                $escapedLine =~ s/\r/\\r/g;
2521                $escapedLine =~ s/\t/\\t/g;
2522                Trace("Line read: -->$escapedLine<--");
2523            }
2524            # If the line is empty, return a single empty string; otherwise, parse
2525            # it into fields.
2526            if ($line eq "") {
2527                push @retVal, "";
2528            } else {
2529                push @retVal, split /\t/,$line;
2530          }          }
2531        } else {
2532            # Trace the reason the read failed.
2533            Trace("End of file: $!") if T(File => 3);
2534      }      }
2535        # Return the result.
2536        return @retVal;
2537  }  }
2538    
2539  =head3 Trace  =head3 PutLine
2540    
2541  C<< Trace($message); >>      Tracer::PutLine($handle, \@fields, $eol);
2542    
2543  Write a trace message to the target location specified in L</TSetup>. If there has not been  Write a line of data to a tab-delimited file. The specified field values will be
2544  any prior call to B<TSetup>.  output in tab-separated form, with a trailing new-line.
2545    
2546  =over 4  =over 4
2547    
2548  =item message  =item handle
2549    
2550  Message to write.  Output file handle.
2551    
2552    =item fields
2553    
2554    List of field values.
2555    
2556    =item eol (optional)
2557    
2558    End-of-line character (default is "\n").
2559    
2560  =back  =back
2561    
2562  =cut  =cut
2563    
2564  sub Trace {  sub PutLine {
2565      # Get the parameters.      # Get the parameters.
2566      my ($message) = @_;      my ($handle, $fields, $eol) = @_;
2567      # Get the timestamp.      # Write the data.
2568      my $timeStamp = Now();      print $handle join("\t", @{$fields}) . ($eol || "\n");
     # Format the message. Note we strip off any line terminators at the end.  
     my $formatted = "$timeStamp <$LastCategory>: " . Strip($message);  
     # Process according to the destination.  
     if ($Destination eq "TEXT") {  
         # Write the message to the standard output.  
         print "$formatted\n";  
     } elsif ($Destination eq "ERROR") {  
         # Write the message to the error output.  
         print STDERR "$formatted\n";  
     } elsif ($Destination eq "QUEUE") {  
         # Push the message into the queue.  
         push @Queue, "$formatted";  
     } elsif ($Destination eq "HTML") {  
         # Convert the message to HTML and write it to the standard output.  
         my $escapedMessage = CGI::escapeHTML($message);  
         print "<p>$formatted</p>\n";  
     } elsif ($Destination eq "WARN") {  
        # Emit the message as a warning.  
        warn $message;  
     } elsif ($Destination =~ m/^>>/) {  
         # Write the trace message to an output file.  
         (open TRACING, $Destination) || die "Tracing open for \"$Destination\" failed: $!";  
         print TRACING "$formatted\n";  
         close TRACING;  
         # If the Tee flag is on, echo it to the standard output.  
         if ($TeeFlag) {  
             print "$formatted\n";  
         }  
     }  
2569  }  }
2570    
 =head3 T  
   
 C<< my $switch = T($category, $traceLevel); >>  
2571    
2572      or  =head3 PrintLine
2573    
2574  C<< my $switch = T($traceLevel); >>      Tracer::PrintLine($line);
2575    
2576  Return TRUE if the trace level is at or above a specified value and the specified category  Print a line of text with a trailing new-line.
 is active, else FALSE. If no category is specified, the caller's package name is used.  
2577    
2578  =over 4  =over 4
2579    
2580  =item category  =item line
   
 Category to which the message belongs. If not specified, the caller's package name is  
 used.  
   
 =item traceLevel  
   
 Relevant tracing level.  
   
 =item RETURN  
2581    
2582  TRUE if a message at the specified trace level would appear in the trace, else FALSE.  Line of text to print.
2583    
2584  =back  =back
2585    
2586  =cut  =cut
2587    
2588  sub T {  sub PrintLine {
2589      # Declare the return variable.      # Get the parameters.
2590      my $retVal = 0;      my ($line) = @_;
2591      # Only proceed if tracing is turned on.      # Print the line.
2592      if ($Destination ne "NONE") {      print "$line\n";
         # Get the parameters.  
         my ($category, $traceLevel) = @_;  
         if (!defined $traceLevel) {  
             # Here we have no category, so we need to get the calling package.  
             # The calling package is normally the first parameter. If it is  
             # omitted, the first parameter will be the tracelevel. So, the  
             # first thing we do is shift the so-called category into the  
             # $traceLevel variable where it belongs.  
             $traceLevel = $category;  
             my ($package, $fileName, $line) = caller;  
             # If there is no calling package, we default to "main".  
             if (!$package) {  
                 $category = "main";  
             } else {  
                 $category = $package;  
             }  
         }  
         # Save the category name.  
         $LastCategory = $category;  
         # Convert it to lower case before we hash it.  
         $category = lc $category;  
         # Use the category and tracelevel to compute the result.  
         $retVal = ($traceLevel <= $TraceLevel && ($AllTrace || exists $Categories{$category}));  
     }  
     # Return the computed result.  
     return $retVal;  
2593  }  }
2594    
 =head3 ParseCommand  
2595    
2596  C<< my ($options, @arguments) = Tracer::ParseCommand(\%optionTable, @inputList); >>  =head2 Other Useful Methods
2597    
2598  Parse a command line consisting of a list of parameters. The initial parameters may be option  =head3 ParseParm
 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.  
2599    
2600  C<< my ($options, @arguments) = ParseCommand({ errors => 0, logFile => 'trace.log'}, @words); >>      my $listValue = Tracer::ParseParm($string);
2601    
2602  In this case, the list @words will be treated as a command line. There are two options available,  Convert a parameter into a list reference. If the parameter is undefined,
2603  B<errors> and B<logFile>. If @words has the following format  an undefined value will be returned. Otherwise, it will be parsed as a
2604    comma-separated list of values.
2605    
2606  C<< -logFile=error.log apple orange rutabaga >>  =over 4
2607    
2608  then at the end of the invocation, C<$options> will be  =item string
2609    
2610  C<< { errors => 0, logFile => 'error.log' } >>  Incoming string.
2611    
2612  and C<@arguments> will contain  =item RETURN
2613    
2614  C<< apple orange rutabaga >>  Returns a reference to a list of values, or C<undef> if the incoming value
2615    was undefined.
2616    
2617  The parser allows for some escape sequences. See L</UnEscape> for a description. There is no  =back
 support for quote characters.  
2618    
2619  =over 4  =cut
2620    
2621  =item optionTable  sub ParseParm {
2622        # Get the parameters.
2623        my ($string) = @_;
2624        # Declare the return variable.
2625        my $retVal;
2626        # Check for data.
2627        if (defined $string) {
2628            # We have some, so split it into a list.
2629            $retVal = [ split /\s*,\s*/, $string];
2630        }
2631        # Return the result.
2632        return $retVal;
2633    }
2634    
2635  Table of default options.  =head3 Now
2636    
2637  =item inputList      my $string = Tracer::Now();
2638    
2639  List of words on the command line.  Return a displayable time stamp containing the local time. Whatever format this
2640    method produces must be parseable by L</ParseDate>.
2641    
2642    =cut
2643    
2644    sub Now {
2645        return DisplayTime(time);
2646    }
2647    
2648    =head3 DisplayTime
2649    
2650        my $string = Tracer::DisplayTime($time);
2651    
2652    Convert a time value to a displayable time stamp. Whatever format this
2653    method produces must be parseable by L</ParseDate>.
2654    
2655    =over 4
2656    
2657    =item time
2658    
2659    Time to display, in seconds since the epoch, or C<undef> if the time is unknown.
2660    
2661  =item RETURN  =item RETURN
2662    
2663  Returns a reference to the option table and a list of the positional arguments.  Returns a displayable time, or C<(n/a)> if the incoming time is undefined.
2664    
2665  =back  =back
2666    
2667  =cut  =cut
2668    
2669  sub ParseCommand {  sub DisplayTime {
2670      # Get the parameters.      my ($time) = @_;
2671      my ($optionTable, @inputList) = @_;      my $retVal = "(n/a)";
2672      # Process any options in the input list.      if (defined $time) {
2673      my %overrides = ();          my ($sec,$min,$hour,$mday,$mon,$year,$wday,$yday,$isdst) = localtime($time);
2674      while ((@inputList > 0) && ($inputList[0] =~ /^-/)) {          $retVal = _p2($mon+1) . "/" . _p2($mday) . "/" . ($year + 1900) . " " .
2675          # Get the current option.                    _p2($hour) . ":" . _p2($min) . ":" . _p2($sec);
         my $arg = shift @inputList;  
         # Pull out the option name.  
         $arg =~ /^-([^=]*)/g;  
         my $name = $1;  
         # Check for an option value.  
         if ($arg =~ /\G=(.*)$/g) {  
             # Here we have a value for the option.  
             $overrides{$name} = UnEscape($1);  
         } else {  
             # Here there is no value, so we use 1.  
             $overrides{$name} = 1;  
         }  
2676      }      }
2677      # Merge the options into the defaults.      return $retVal;
     GetOptions($optionTable, \%overrides);  
     # Translate the remaining parameters.  
     my @retVal = ();  
     for my $inputParm (@inputList) {  
         push @retVal, UnEscape($inputParm);  
2678      }      }
2679      # Return the results.  
2680      return ($optionTable, @retVal);  # Pad a number to 2 digits.
2681    sub _p2 {
2682        my ($value) = @_;
2683        $value = "0$value" if ($value < 10);
2684        return $value;
2685  }  }
2686    
2687  =head3 Escape  =head3 Escape
2688    
2689  C<< my $codedString = Tracer::Escape($realString); >>      my $codedString = Tracer::Escape($realString);
2690    
2691  Escape a string for use in a command length. Spaces will be replaced by C<\b>,  Escape a string for use in a command. Tabs will be replaced by C<\t>, new-lines
2692  tabs replaced by C<\t>, new-lines replaced by C<\n>, and backslashes will be  replaced by C<\n>, carriage returns will be deleted, and backslashes will be doubled. The
2693  doubled. The effect is to exactly reverse the effect of L</UnEscape>.  result is to reverse the effect of L</UnEscape>.
2694    
2695  =over 4  =over 4
2696    
# Line 850  Line 2714 
2714      # Loop through the parameter string, looking for sequences to escape.      # Loop through the parameter string, looking for sequences to escape.
2715      while (length $realString > 0) {      while (length $realString > 0) {
2716          # Look for the first sequence to escape.          # Look for the first sequence to escape.
2717          if ($realString =~ /^(.*?)([ \n\t\\])/) {          if ($realString =~ /^(.*?)([\n\t\r\\])/) {
2718              # Here we found it. The text preceding the sequence is in $1. The sequence              # Here we found it. The text preceding the sequence is in $1. The sequence
2719              # itself is in $2. First, move the clear text to the return variable.              # itself is in $2. First, move the clear text to the return variable.
2720              $retVal .= $1;              $retVal .= $1;
2721              # Strip the processed section off the real string.              # Strip the processed section off the real string.
2722              $realString = substr $realString, (length $2) + (length $1);              $realString = substr $realString, (length $2) + (length $1);
2723              # Encode the escape sequence.              # Get the matched character.
2724              my $char = $2;              my $char = $2;
2725              $char =~ tr/ \t\n/btn/;              # If we have a CR, we are done.
2726                if ($char ne "\r") {
2727                    # It's not a CR, so encode the escape sequence.
2728                    $char =~ tr/\t\n/tn/;
2729              $retVal .= "\\" . $char;              $retVal .= "\\" . $char;
2730                }
2731          } else {          } else {
2732              # Here there are no more escape sequences. The rest of the string is              # Here there are no more escape sequences. The rest of the string is
2733              # transferred unmodified.              # transferred unmodified.
# Line 873  Line 2741 
2741    
2742  =head3 UnEscape  =head3 UnEscape
2743    
2744  C<< my $realString = Tracer::UnEscape($codedString); >>      my $realString = Tracer::UnEscape($codedString);
2745    
2746  Replace escape sequences with their actual equivalents. C<\b> will be replaced by a space,  Replace escape sequences with their actual equivalents. C<\t> will be replaced by
2747  C<\t> by a tab, C<\n> by a new-line character, and C<\\> by a back-slash.  a tab, C<\n> by a new-line character, and C<\\> by a backslash. C<\r> codes will
2748    be deleted.
2749    
2750  =over 4  =over 4
2751    
# Line 896  Line 2765 
2765  sub UnEscape {  sub UnEscape {
2766      # Get the parameter.      # Get the parameter.
2767      my ($codedString) = @_;      my ($codedString) = @_;
     Tracer("Coded string is \"$codedString\".") if T(4);  
2768      # Initialize the return variable.      # Initialize the return variable.
2769      my $retVal = "";      my $retVal = "";
2770      # Only proceed if the incoming string is nonempty.      # Only proceed if the incoming string is nonempty.
2771      if (defined $codedString) {      if (defined $codedString) {
2772          # Loop through the parameter string, looking for escape sequences. We can't do          # Loop through the parameter string, looking for escape sequences. We can't do
2773          # translating because it causes problems with the escaped slash. ("\\b" becomes          # translating because it causes problems with the escaped slash. ("\\t" becomes
2774          # "\ " no matter what we do.)          # "\<tab>" no matter what we do.)
2775          while (length $codedString > 0) {          while (length $codedString > 0) {
2776              # Look for the first escape sequence.              # Look for the first escape sequence.
2777              if ($codedString =~ /^(.*?)\\(\\|b|n|t)/) {              if ($codedString =~ /^(.*?)\\(\\|n|t|r)/) {
2778                  # Here we found it. The text preceding the sequence is in $1. The sequence                  # Here we found it. The text preceding the sequence is in $1. The sequence
2779                  # itself is in $2. First, move the clear text to the return variable.                  # itself is in $2. First, move the clear text to the return variable.
2780                  $retVal .= $1;                  $retVal .= $1;
2781                  $codedString = substr $codedString, (2 + length $1);                  $codedString = substr $codedString, (2 + length $1);
2782                  # Decode the escape sequence.                  # Get the escape value.
2783                  my $char = $2;                  my $char = $2;
2784                  $char =~ tr/\\btn/\\ \t\n/;                  # If we have a "\r", we are done.
2785                    if ($char ne 'r') {
2786                        # Here it's not an 'r', so we convert it.
2787                        $char =~ tr/\\tn/\\\t\n/;
2788                  $retVal .= $char;                  $retVal .= $char;
2789                    }
2790              } else {              } else {
2791                  # Here there are no more escape sequences. The rest of the string is                  # Here there are no more escape sequences. The rest of the string is
2792                  # transferred unmodified.                  # transferred unmodified.
# Line 922  Line 2794 
2794                  $codedString = "";                  $codedString = "";
2795              }              }
2796          }          }
2797      }      }
2798      # Return the result.      # Return the result.
     return $retVal;  
 }  
   
 =head3 ParseRecord  
   
 C<< my @fields = Tracer::ParseRecord($line); >>  
   
 Parse a tab-delimited data line. The data line is split into field values. Embedded tab  
 and new-line characters in the data line must be represented as C<\t> and C<\n>, respectively.  
 These will automatically be converted.  
   
 =over 4  
   
 =item line  
   
 Line of data containing the tab-delimited fields.  
   
 =item RETURN  
   
 Returns a list of the fields found in the data line.  
   
 =back  
   
 =cut  
   
 sub ParseRecord {  
     # Get the parameter.  
     my ($line) = @_;  
     # Remove the trailing new-line, if any.  
     chomp $line;  
     # Split the line read into pieces using the tab character.  
     my @retVal = split /\t/, $line;  
     # Trim and fix the escapes in each piece.  
     for my $value (@retVal) {  
         # Trim leading whitespace.  
         $value =~ s/^\s+//;  
         # Trim trailing whitespace.  
         $value =~ s/\s+$//;  
         # Delete the carriage returns.  
         $value =~ s/\r//g;  
         # Convert the escapes into their real values.  
         $value =~ s/\\t/"\t"/ge;  
         $value =~ s/\\n/"\n"/ge;  
     }  
     # Return the result.  
     return @retVal;  
 }  
   
 =head3 Merge  
   
 C<< my @mergedList = Tracer::Merge(@inputList); >>  
   
 Sort a list of strings and remove duplicates.  
   
 =over 4  
   
 =item inputList  
   
 List of scalars to sort and merge.  
   
 =item RETURN  
   
 Returns a list containing the same elements sorted in ascending order with duplicates  
 removed.  
   
 =back  
   
 =cut  
   
 sub Merge {  
     # Get the input list in sort order.  
     my @inputList = sort @_;  
     # Only proceed if the list has at least two elements.  
     if (@inputList > 1) {  
         # Now we want to move through the list splicing out duplicates.  
         my $i = 0;  
         while ($i < @inputList) {  
             # Get the current entry.  
             my $thisEntry = $inputList[$i];  
             # Find out how many elements duplicate the current entry.  
             my $j = $i + 1;  
             my $dup1 = $i + 1;  
             while ($j < @inputList && $inputList[$j] eq $thisEntry) { $j++; };  
             # If the number is nonzero, splice out the duplicates found.  
             if ($j > $dup1) {  
                 splice @inputList, $dup1, $j - $dup1;  
             }  
             # Now the element at position $dup1 is different from the element before it  
             # at position $i. We push $i forward one position and start again.  
             $i++;  
         }  
     }  
     # Return the merged list.  
     return @inputList;  
 }  
   
 =head3 GetFile  
   
 C<< my @fileContents = Tracer::GetFile($fileName); >>  
   
 Return the entire contents of a file.  
   
 =over 4  
   
 =item fileName  
   
 Name of the file to read.  
   
 =item RETURN  
   
 In a list context, returns the entire file as a list with the line terminators removed.  
 In a scalar context, returns the entire file as a string.  
   
 =back  
   
 =cut  
   
 sub GetFile {  
     # Get the parameters.  
     my ($fileName) = @_;  
     # Declare the return variable.  
     my @retVal = ();  
     # Open the file for input.  
     my $ok = open INPUTFILE, "<$fileName";  
     if (!$ok) {  
         # If we had an error, trace it. We will automatically return a null value.  
         Trace("Could not open \"$fileName\" for input: $!") if T(0);  
     } else {  
         # Read the whole file into the return variable, stripping off any terminator  
         # characters.  
         my $lineCount = 0;  
         while (my $line = <INPUTFILE>) {  
             $lineCount++;  
             $line = Strip($line);  
             push @retVal, $line;  
         }  
         # Close it.  
         close INPUTFILE;  
         my $actualLines = @retVal;  
     }  
     # Return the file's contents in the desired format.  
     if (wantarray) {  
         return @retVal;  
     } else {  
         return join "\n", @retVal;  
     }  
 }  
   
 =head3 QTrace  
   
 C<< my $data = QTrace($format); >>  
   
 Return the queued trace data in the specified format.  
   
 =over 4  
   
 =item format  
   
 C<html> to format the data as an HTML list, C<text> to format it as straight text.  
   
 =back  
   
 =cut  
   
 sub QTrace {  
     # Get the parameter.  
     my ($format) = @_;  
     # Create the return variable.  
     my $retVal = "";  
     # Only proceed if there is an actual queue.  
     if (@Queue) {  
         # Process according to the format.  
         if ($format =~ m/^HTML$/i) {  
             # Convert the queue into an HTML list.  
             $retVal = "<ul>\n";  
             for my $line (@Queue) {  
                 my $escapedLine = CGI::escapeHTML($line);  
                 $retVal .= "<li>$escapedLine</li>\n";  
             }  
             $retVal .= "</ul>\n";  
         } elsif ($format =~ m/^TEXT$/i) {  
             # Convert the queue into a list of text lines.  
             $retVal = join("\n", @Queue) . "\n";  
         }  
         # Clear the queue.  
         @Queue = ();  
     }  
     # Return the formatted list.  
2799      return $retVal;      return $retVal;
2800  }  }
2801    
2802  =head3 Confess  =head3 Percent
2803    
2804  C<< Confess($message); >>      my $percent = Tracer::Percent($number, $base);
2805    
2806  Trace the call stack and abort the program with the specified message. When used with  Returns the percent of the base represented by the given number. If the base
2807  the OR operator and the L</Assert> method, B<Confess> can function as a debugging assert.  is zero, returns zero.
2808  So, for example  
2809    =over 4
2810    
2811  C<< Assert($recNum >= 0) || Confess("Invalid record number $recNum."); >>  =item number
2812    
2813  Will abort the program with a stack trace if the value of C<$recNum> is negative.  Percent numerator.
2814    
2815  =over 4  =item base
2816    
2817  =item message  Percent base.
2818    
2819  Message to include in the trace.  =item RETURN
2820    
2821    Returns the percentage of the base represented by the numerator.
2822    
2823  =back  =back
2824    
2825  =cut  =cut
2826    
2827  sub Confess {  sub Percent {
2828      # Get the parameters.      # Get the parameters.
2829      my ($message) = @_;      my ($number, $base) = @_;
2830      # Trace the call stack.      # Declare the return variable.
2831      Cluck($message);      my $retVal = 0;
2832      # Abort the program.      # Compute the percent.
2833      croak(">>> $message");      if ($base != 0) {
2834            $retVal = $number * 100 / $base;
2835        }
2836        # Return the result.
2837        return $retVal;
2838  }  }
2839    
2840  =head3 Assert  =head3 Constrain
   
 C<< Assert($condition1, $condition2, ... $conditionN); >>  
   
 Return TRUE if all the conditions are true. This method can be used in conjunction with  
 the OR operator and the L</Confess> method, B<Assert> can function as a debugging assert.  
 So, for example  
2841    
2842  C<< Assert($recNum >= 0) || Confess("Invalid record number $recNum."); >>      my $constrained = Constrain($value, $min, $max);
2843    
2844  Will abort the program with a stack trace if the value of C<$recNum> is negative.  Modify a numeric value to bring it to a point in between a maximum and a minimum.
2845    
2846  =cut  =over 4
 sub Assert {  
     my $retVal = 1;  
     LOOP: for my $condition (@_) {  
         if (! $condition) {  
             $retVal = 0;  
             last LOOP;  
         }  
     }  
     return $retVal;  
 }  
2847    
2848  =head3 Cluck  =item value
2849    
2850  C<< Cluck($message); >>  Value to constrain.
2851    
2852  Trace the call stack. Note that for best results, you should qualify the call with a  =item min (optional)
 trace condition. For example,  
2853    
2854  C<< Cluck("Starting record parse.") if T(3); >>  Minimum permissible value. If this parameter is undefined, no minimum constraint will be applied.
2855    
2856  will only trace the stack if the trace level for the package is 3 or more.  =item max (optional)
2857    
2858  =over 4  Maximum permissible value. If this parameter is undefined, no maximum constraint will be applied.
2859    
2860  =item message  =item RETURN
2861    
2862  Message to include in the trace.  Returns the incoming value, constrained according to the other parameters.
2863    
2864  =back  =back
2865    
2866  =cut  =cut
2867    
2868  sub Cluck {  sub Constrain {
2869      # Get the parameters.      # Get the parameters.
2870      my ($message) = @_;      my ($value, $min, $max) = @_;
2871      # Trace what's happening.      # Declare the return variable.
2872      Trace("Stack trace for event: $message");      my $retVal = $value;
2873      my $confession = longmess($message);      # Apply the minimum constraint.
2874      # Convert the confession to a series of trace messages. Note we skip any      if (defined $min && $retVal < $min) {
2875      # messages relating to calls into Tracer.          $retVal = $min;
2876      for my $line (split /\s*\n/, $confession) {      }
2877          Trace($line) if ($line !~ /Tracer\.pm/);      # Apply the maximum constraint.
2878        if (defined $max && $retVal > $max) {
2879            $retVal = $max;
2880      }      }
2881        # Return the result.
2882        return $retVal;
2883  }  }
2884    
2885  =head3 Min  =head3 Min
2886    
2887  C<< my $min = Min($value1, $value2, ... $valueN); >>      my $min = Min($value1, $value2, ... $valueN);
2888    
2889  Return the minimum argument. The arguments are treated as numbers.  Return the minimum argument. The arguments are treated as numbers.
2890    
# Line 1239  Line 2917 
2917    
2918  =head3 Max  =head3 Max
2919    
2920  C<< my $max = Max($value1, $value2, ... $valueN); >>      my $max = Max($value1, $value2, ... $valueN);
2921    
2922  Return the maximum argument. The arguments are treated as numbers.  Return the maximum argument. The arguments are treated as numbers.
2923    
# Line 1270  Line 2948 
2948      return $retVal;      return $retVal;
2949  }  }
2950    
 =head3 AddToListMap  
   
 C<< Tracer::AddToListMap(\%hash, $key, $value); >>  
   
 Add a key-value pair to a hash of lists. If no value exists for the key, a singleton list  
 is created for the key. Otherwise, the new value is pushed onto the list.  
   
 =over 4  
   
 =item hash  
   
 Reference to the target hash.  
   
 =item key  
   
 Key for which the value is to be added.  
   
 =item value  
   
 Value to add to the key's value list.  
   
 =back  
   
 =cut  
   
 sub AddToListMap {  
     # Get the parameters.  
     my ($hash, $key, $value) = @_;  
     # Process according to whether or not the key already has a value.  
     if (! exists $hash->{$key}) {  
         $hash->{$key} = [$value];  
     } else {  
         push @{$hash->{$key}}, $value;  
     }  
 }  
   
 =head3 DebugMode  
   
 C<< if (Tracer::DebugMode) { ...code... } >>  
   
 Return TRUE if debug mode has been turned on, else output an error  
 page and return FALSE.  
   
 Certain CGI scripts are too dangerous to exist in the production  
 environment. This method provides a simple way to prevent them  
 from working unless they are explicitly turned on by creating a password  
 cookie via the B<SetPassword> script.  If debugging mode  
 is not turned on, an error web page will be output directing the  
 user to enter in the correct password.  
   
 =cut  
   
 sub DebugMode {  
     # Declare the return variable.  
     my $retVal = 0;  
     # Check the debug configuration.  
     my $password = CGI::cookie("DebugMode");  
     my $encrypted = Digest::MD5::md5_hex($password);  
     if ($encrypted eq "252dec43280e0c0d6a75ffcec486e61d") {  
         $retVal = 1;  
     } else {  
         # Here debug mode is off, so we generate an error page.  
         my $pageString = PageBuilder::Build("<Html/ErrorPage.html", {}, "Html");  
         print $pageString;  
     }  
     # Return the determination indicator.  
     return $retVal;  
 }  
2951    
2952  =head3 Strip  =head3 Strip
2953    
2954  C<< my $string = Tracer::Strip($line); >>      my $string = Tracer::Strip($line);
2955    
2956  Strip all line terminators off a string. This is necessary when dealing with files  Strip all line terminators off a string. This is necessary when dealing with files
2957  that may have been transferred back and forth several times among different  that may have been transferred back and forth several times among different
# Line 1364  Line 2974 
2974  sub Strip {  sub Strip {
2975      # Get a copy of the parameter string.      # Get a copy of the parameter string.
2976      my ($string) = @_;      my ($string) = @_;
2977      my $retVal = $string;      my $retVal = (defined $string ? $string : "");
2978      # Strip the line terminator characters.      # Strip the line terminator characters.
2979      $retVal =~ s/(\r|\n)+$//g;      $retVal =~ s/(\r|\n)+$//g;
2980      # Return the result.      # Return the result.
# Line 1373  Line 2983 
2983    
2984  =head3 Pad  =head3 Pad
2985    
2986  C<< my $paddedString = Tracer::Pad($string, $len, $left, $padChar); >>      my $paddedString = Tracer::Pad($string, $len, $left, $padChar);
2987    
2988  Pad a string to a specified length. The pad character will be a  Pad a string to a specified length. The pad character will be a
2989  space, and the padding will be on the right side unless specified  space, and the padding will be on the right side unless specified
# Line 1432  Line 3042 
3042      return $retVal;      return $retVal;
3043  }  }
3044    
3045    =head3 EOF
3046    
3047    This is a constant that is lexically greater than any useful string.
3048    
3049    =cut
3050    
3051    sub EOF {
3052        return "\xFF\xFF\xFF\xFF\xFF";
3053    }
3054    
3055  =head3 TICK  =head3 TICK
3056    
3057  C<< my @results = TICK($commandString); >>      my @results = TICK($commandString);
3058    
3059  Perform a back-tick operation on a command. If this is a Windows environment, any leading  Perform a back-tick operation on a command. If this is a Windows environment, any leading
3060  dot-slash (C<./> will be removed. So, for example, if you were doing  dot-slash (C<./> will be removed. So, for example, if you were doing
# Line 1473  Line 3093 
3093      return `$commandString`;      return `$commandString`;
3094  }  }
3095    
3096    
3097    =head3 CommaFormat
3098    
3099        my $formatted = Tracer::CommaFormat($number);
3100    
3101    Insert commas into a number.
3102    
3103    =over 4
3104    
3105    =item number
3106    
3107    A sequence of digits.
3108    
3109    =item RETURN
3110    
3111    Returns the same digits with commas strategically inserted.
3112    
3113    =back
3114    
3115    =cut
3116    
3117    sub CommaFormat {
3118        # Get the parameters.
3119        my ($number) = @_;
3120        # Pad the length up to a multiple of three.
3121        my $padded = "$number";
3122        $padded = " " . $padded while length($padded) % 3 != 0;
3123        # This is a fancy PERL trick. The parentheses in the SPLIT pattern
3124        # cause the delimiters to be included in the output stream. The
3125        # GREP removes the empty strings in between the delimiters.
3126        my $retVal = join(",", grep { $_ ne '' } split(/(...)/, $padded));
3127        # Clean out the spaces.
3128        $retVal =~ s/ //g;
3129        # Return the result.
3130        return $retVal;
3131    }
3132    
3133    
3134    =head3 CompareLists
3135    
3136        my ($inserted, $deleted) = Tracer::CompareLists(\@newList, \@oldList, $keyIndex);
3137    
3138    Compare two lists of tuples, and return a hash analyzing the differences. The lists
3139    are presumed to be sorted alphabetically by the value in the $keyIndex column.
3140    The return value contains a list of items that are only in the new list
3141    (inserted) and only in the old list (deleted).
3142    
3143    =over 4
3144    
3145    =item newList
3146    
3147    Reference to a list of new tuples.
3148    
3149    =item oldList
3150    
3151    Reference to a list of old tuples.
3152    
3153    =item keyIndex (optional)
3154    
3155    Index into each tuple of its key field. The default is 0.
3156    
3157    =item RETURN
3158    
3159    Returns a 2-tuple consisting of a reference to the list of items that are only in the new
3160    list (inserted) followed by a reference to the list of items that are only in the old
3161    list (deleted).
3162    
3163    =back
3164    
3165    =cut
3166    
3167    sub CompareLists {
3168        # Get the parameters.
3169        my ($newList, $oldList, $keyIndex) = @_;
3170        if (! defined $keyIndex) {
3171            $keyIndex = 0;
3172        }
3173        # Declare the return variables.
3174        my ($inserted, $deleted) = ([], []);
3175        # Loop through the two lists simultaneously.
3176        my ($newI, $oldI) = (0, 0);
3177        my ($newN, $oldN) = (scalar @{$newList}, scalar @{$oldList});
3178        while ($newI < $newN || $oldI < $oldN) {
3179            # Get the current object in each list. Note that if one
3180            # of the lists is past the end, we'll get undef.
3181            my $newItem = $newList->[$newI];
3182            my $oldItem = $oldList->[$oldI];
3183            if (! defined($newItem) || defined($oldItem) && $newItem->[$keyIndex] gt $oldItem->[$keyIndex]) {
3184                # The old item is not in the new list, so mark it deleted.
3185                push @{$deleted}, $oldItem;
3186                $oldI++;
3187            } elsif (! defined($oldItem) || $oldItem->[$keyIndex] gt $newItem->[$keyIndex]) {
3188                # The new item is not in the old list, so mark it inserted.
3189                push @{$inserted}, $newItem;
3190                $newI++;
3191            } else {
3192                # The item is in both lists, so push forward.
3193                $oldI++;
3194                $newI++;
3195            }
3196        }
3197        # Return the result.
3198        return ($inserted, $deleted);
3199    }
3200    
3201    =head3 GenerateURL
3202    
3203        my $queryUrl = Tracer::GenerateURL($page, %parameters);
3204    
3205    Generate a GET-style URL for the specified page with the specified parameter
3206    names and values. The values will be URL-escaped automatically. So, for
3207    example
3208    
3209        Tracer::GenerateURL("form.cgi", type => 1, string => "\"high pass\" or highway")
3210    
3211    would return
3212    
3213        form.cgi?type=1;string=%22high%20pass%22%20or%20highway
3214    
3215    =over 4
3216    
3217    =item page
3218    
3219    Page URL.
3220    
3221    =item parameters
3222    
3223    Hash mapping parameter names to parameter values.
3224    
3225    =item RETURN
3226    
3227    Returns a GET-style URL that goes to the specified page and passes in the
3228    specified parameters and values.
3229    
3230    =back
3231    
3232    =cut
3233    
3234    sub GenerateURL {
3235        # Get the parameters.
3236        my ($page, %parameters) = @_;
3237        # Prime the return variable with the page URL.
3238        my $retVal = $page;
3239        # Loop through the parameters, creating parameter elements in a list.
3240        my @parmList = map { "$_=" . uri_escape($parameters{$_}) } keys %parameters;
3241        # If the list is nonempty, tack it on.
3242        if (@parmList) {
3243            $retVal .= "?" . join(";", @parmList);
3244        }
3245        # Return the result.
3246        return $retVal;
3247    }
3248    
3249    =head3 ApplyURL
3250    
3251        Tracer::ApplyURL($table, $target, $url);
3252    
3253    Run through a two-dimensional table (or more accurately, a list of lists), converting the
3254    I<$target> column to HTML text having a hyperlink to a URL in the I<$url> column. The
3255    URL column will be deleted by this process and the target column will be HTML-escaped.
3256    
3257    This provides a simple way to process the results of a database query into something
3258    displayable by combining a URL with text.
3259    
3260    =over 4
3261    
3262    =item table
3263    
3264    Reference to a list of lists. The elements in the containing list will be updated by
3265    this method.
3266    
3267    =item target
3268    
3269    The index of the column to be converted into HTML.
3270    
3271    =item url
3272    
3273    The index of the column containing the URL. Note that the URL must have a recognizable
3274    C<http:> at the beginning.
3275    
3276    =back
3277    
3278    =cut
3279    
3280    sub ApplyURL {
3281        # Get the parameters.
3282        my ($table, $target, $url) = @_;
3283        # Loop through the table.
3284        for my $row (@{$table}) {
3285            # Apply the URL to the target cell.
3286            $row->[$target] = CombineURL($row->[$target], $row->[$url]);
3287            # Delete the URL from the row.
3288            delete $row->[$url];
3289        }
3290    }
3291    
3292    =head3 CombineURL
3293    
3294        my $combinedHtml = Tracer::CombineURL($text, $url);
3295    
3296    This method will convert the specified text into HTML hyperlinked to the specified
3297    URL. The hyperlinking will only take place if the URL looks legitimate: that is, it
3298    is defined and begins with an C<http:> header.
3299    
3300    =over 4
3301    
3302    =item text
3303    
3304    Text to return. This will be HTML-escaped automatically.
3305    
3306    =item url
3307    
3308    A URL to be hyperlinked to the text. If it does not look like a URL, then the text
3309    will be returned without any hyperlinking.
3310    
3311    =item RETURN
3312    
3313    Returns the original text, HTML-escaped, with the URL hyperlinked to it. If the URL
3314    doesn't look right, the HTML-escaped text will be returned without any further
3315    modification.
3316    
3317    =back
3318    
3319    =cut
3320    
3321    sub CombineURL {
3322        # Get the parameters.
3323        my ($text, $url) = @_;
3324        # Declare the return variable.
3325        my $retVal = CGI::escapeHTML($text);
3326        # Verify the URL.
3327        if (defined($url) && $url =~ m!http://!i) {
3328            # It's good, so we apply it to the text.
3329            $retVal = "<a href=\"$url\">$retVal</a>";
3330        }
3331        # Return the result.
3332        return $retVal;
3333    }
3334    
3335    =head3 Cmp
3336    
3337        my $cmp = Tracer::Cmp($a, $b);
3338    
3339    This method performs a universal sort comparison. Each value coming in is
3340    separated into a leading text part and a trailing number part. The text
3341    part is string compared, and if both parts are equal, then the number
3342    parts are compared numerically. A stream of just numbers or a stream of
3343    just strings will sort correctly, and a mixed stream will sort with the
3344    numbers first. Strings with a label and a number will sort in the
3345    expected manner instead of lexically.
3346    
3347    =over 4
3348    
3349    =item a
3350    
3351    First item to compare.
3352    
3353    =item b
3354    
3355    Second item to compare.
3356    
3357    =item RETURN
3358    
3359    Returns a negative number if the first item should sort first (is less), a positive
3360    number if the first item should sort second (is greater), and a zero if the items are
3361    equal.
3362    
3363    =back
3364    
3365    =cut
3366    
3367    sub Cmp {
3368        # Get the parameters.
3369        my ($a, $b) = @_;
3370        # Declare the return value.
3371        my $retVal;
3372        # Check for nulls.
3373        if (! defined($a)) {
3374            $retVal = (! defined($b) ? 0 : -1);
3375        } elsif (! defined($b)) {
3376            $retVal = 1;
3377        } else {
3378            # Here we have two real values. Parse the two strings.
3379            $a =~ /^(\D*)(\d*)$/;
3380            my $aParsed = [$1, $2];
3381            $b =~ /^(\D*)(\d*)$/;
3382            my $bParsed = [$1, $2];
3383            # Compare the string parts.
3384            $retVal = $aParsed->[0] cmp $bParsed->[0];
3385            if (! $retVal) {
3386                $retVal = $aParsed->[1] <=> $bParsed->[1];
3387            }
3388        }
3389        # Return the result.
3390        return $retVal;
3391    }
3392    
3393    
3394    =head3 TrackingCode
3395    
3396        my $html = Tracer::TrackingCode();
3397    
3398    Returns the HTML code for doing web page traffic monitoring. If the
3399    current environment is a test system, then it returns a null string;
3400    otherwise, it returns a bunch of javascript containing code for turning
3401    on SiteMeter and Google Analytics.
3402    
3403    =cut
3404    
3405    sub TrackingCode {
3406        # Declare the return variable.
3407        my $retVal = "<!-- tracking off -->";
3408        # Determine if we're in production.
3409        if ($FIG_Config::site_meter) {
3410            $retVal = <<END_HTML
3411            <!-- Site Meter -->
3412            <script type="text/javascript" src="http://s20.sitemeter.com/js/counter.js?site=s20nmpdr">
3413            </script>
3414            <noscript>
3415            <a href="http://s20.sitemeter.com/stats.asp?site=s20nmpdr" target="_top">
3416            <img src="http://s20.sitemeter.com/meter.asp?site=s20nmpdr" alt="Site Meter" border="0"/></a>
3417            </noscript>
3418            <!-- Copyright (c)2006 Site Meter -->
3419    END_HTML
3420        }
3421        return $retVal;
3422    }
3423    
3424    
3425  1;  1;

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