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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);      @EXPORT = qw(Trace T TSetup QTrace Confess Cluck Min Max Assert Open OpenDir TICK StandardSetup EmergencyKey ETracing Constrain Insure ChDir Emergency Warn);
24          @EXPORT_OK = qw(GetFile GetOptions Merge MergeOptions ParseCommand ParseRecord UnEscape);      @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;
30        use PageBuilder;
31        use Digest::MD5;
32        use File::Basename;
33        use File::Path;
34        use File::stat;
35        use LWP::UserAgent;
36        use Time::HiRes 'gettimeofday';
37        use URI::Escape;
38        use Time::Local;
39        use POSIX qw(strftime);
40        use Time::Zone;
41        use Fcntl qw(:DEFAULT :flock);
42    
43    
44  =head1 Tracing and Debugging Helpers  =head1 Tracing and Debugging Helpers
45    
46  =head2 Introduction  =head2 Tracing
47    
48  This package provides simple tracing for debugging and reporting purposes. To use it simply call the  This package provides simple tracing for debugging and reporting purposes. To use it simply call the
49  L</TSetup> method to set the options and call L</Trace> to write out trace messages. Each trace  L</TSetup> or L</ETracing> method to set the options and call L</Trace> to write out trace messages.
50  message has a I<trace level> and I<category> associated with it. In addition, the tracing package itself  L</TSetup> and L</ETracing> both establish a I<trace level> and a list of I<categories>. Similarly,
51  has a list of categories and a single trace level set by the B<TSetup> method. Only messages whose trace  each trace message has a I<trace level> and I<category> associated with it. Only messages whose trace
52  level is less than or equal to this package's trace level and whose category is activated will  level is less than or equal to the setup trace level and whose category is activated will
53  be written. Thus, a higher trace level on a message indicates that the message  be written. Thus, a higher trace level on a message indicates that the message
54  is less likely to be seen. A higher trace level passed to B<Setup> means more trace messages will  is less likely to be seen, while a higher trace level passed to B<TSetup> means more trace messages will
55  appear. To generate a trace message, use the following syntax.  appear.
56    
57    =head3 Putting Trace Messages in Your Code
58    
59    To generate a trace message, use the following syntax.
60    
61  C<< Trace($message) if T(errors => 4); >>      Trace($message) if T(errors => 4);
62    
63  This statement will produce a trace message if the trace level is 4 or more and the C<errors>  This statement will produce a trace message if the trace level is 4 or more and the C<errors>
64  category is active. Note that the special category C<main> is always active, so  category is active. There is a special category C<main> that is always active, so
65    
66  C<< Trace($message) if T(main => 4); >>      Trace($message) if T(main => 4);
67    
68  will trace if the trace level is 4 or more.  will trace if the trace level is 4 or more.
69    
# Line 34  Line 71 
71  following call is made in the B<Sprout> package, it will appear if the C<Sprout> category is  following call is made in the B<Sprout> package, it will appear if the C<Sprout> category is
72  active and the trace level is 2 or more.  active and the trace level is 2 or more.
73    
74  C<< Trace($message) if T(2); >>      Trace($message) if T(2);
75    
76  To set up tracing, you call the C</Setup> method. The method takes as input a trace level, a list  In scripts, where no package name is available, the category defaults to C<main>.
77  of category names, and a set of options. The trace level and list of category names are  
78    =head3 Custom Tracing
79    
80    Many programs have customized tracing configured using the L</TSetup> method. This is no longer
81    the preferred method, but a knowledge of how custom tracing works can make the more modern
82    L</Emergency Tracing> easier to understand.
83    
84    To set up custom tracing, you call the L</TSetup> method. The method takes as input a trace level,
85    a list of category names, and a destination. The trace level and list of category names are
86  specified as a space-delimited string. Thus  specified as a space-delimited string. Thus
87    
88  C<< TSetup('3 errors Sprout ERDB', 'HTML'); >>      TSetup('3 errors Sprout ERDB', 'TEXT');
89    
90    sets the trace level to 3, activates the C<errors>, C<Sprout>, and C<ERDB> categories, and
91    specifies that messages should be sent to the standard output.
92    
93  sets the trace level to 3, activated the C<errors>, C<Sprout>, and C<ERDB> categories, and  To turn on tracing for ALL categories, use an asterisk. The call below sets every category to
94  specifies that messages should be output as HTML paragraphs. The idea is to make it easier to  level 3 and writes the output to the standard error output. This sort of thing might be
95  input tracing configuration on a web form.  useful in a CGI environment.
96    
97  In addition to HTML and file output for trace messages, you can specify that the trace messages      TSetup('3 *', 'WARN');
98    
99    In addition standard error and file output for trace messages, you can specify that the trace messages
100  be queued. The messages can then be retrieved by calling the L</QTrace> method. This approach  be queued. The messages can then be retrieved by calling the L</QTrace> method. This approach
101  is useful if you are building a web page. Instead of having the trace messages interspersed with  is useful if you are building a web page. Instead of having the trace messages interspersed with
102  the page output, they can be gathered together and displayed at the end of the page. This makes  the page output, they can be gathered together and displayed at the end of the page. This makes
103  it easier to debug page formatting problems.  it easier to debug page formatting problems.
104    
105  Finally, you can specify that all trace messages be emitted as warnings.  Finally, you can specify that all trace messages be emitted to a file, or the standard output and
106    a file at the same time. To trace to a file, specify the filename with an output character in front
107    of it.
108    
109        TSetup('4 SQL', ">$fileName");
110    
111    To trace to the standard output and a file at the same time, put a C<+> in front of the angle
112    bracket.
113    
114        TSetup('3 *', "+>$fileName");
115    
116  The flexibility of tracing makes it superior to simple use of directives like C<die> and C<warn>.  The flexibility of tracing makes it superior to simple use of directives like C<die> and C<warn>.
117  Tracer calls can be left in the code with minimal overhead and then turned on only when needed.  Tracer calls can be left in the code with minimal overhead and then turned on only when needed.
118  Thus, debugging information is available and easily retrieved even when the application is  Thus, debugging information is available and easily retrieved even when the application is
119  being used out in the field.  being used out in the field.
120    
121    =head3 Trace Levels
122    
123    There is no hard and fast rule on how to use trace levels. The following is therefore only
124    a suggestion.
125    
126    =over 4
127    
128    =item Error 0
129    
130    Message indicates an error that may lead to incorrect results or that has stopped the
131    application entirely.
132    
133    =item Warning 1
134    
135    Message indicates something that is unexpected but that probably did not interfere
136    with program execution.
137    
138    =item Notice 2
139    
140    Message indicates the beginning or end of a major task.
141    
142    =item Information 3
143    
144    Message indicates a subtask. In the FIG system, a subtask generally relates to a single
145    genome. This would be a big loop that is not expected to execute more than 500 times or so.
146    
147    =item Detail 4
148    
149    Message indicates a low-level loop iteration.
150    
151    =back
152    
153    The format of trace messages is important because some utilities analyze trace files.
154    There are three fields-- the time stamp, the category name, and the text.
155    The time stamp is between square brackets and the category name between angle brackets.
156    After the category name there is a colon (C<:>) followed by the message text.
157    If the square brackets or angle brackets are missing, then the trace management
158    utilities assume that they are encountering a set of pre-formatted lines.
159    
160    Note, however, that this formatting is done automatically by the tracing functions. You
161    only need to know about it if you want to parse a trace file.
162    
163    =head3 Emergency Tracing
164    
165    Sometimes, you need a way for tracing to happen automatically without putting parameters
166    in a form or on the command line. Emergency tracing does this. You invoke emergency tracing
167    from the debug form, which is accessed from the [[DebugConsole]]. Emergency tracing requires
168    that you specify a tracing key. For command-line tools, the key is
169    taken from the C<TRACING> environment variable. For web services, the key is taken from
170    a cookie. Either way, the key tells the tracing facility who you are, so that you control
171    the tracing in your environment without stepping on other users.
172    
173    The key can be anything you want. If you don't have a key, the C<SetPassword> page will
174    generate one for you.
175    
176    You can activate and de-activate emergency tracing from the debugging control panel, as
177    well as display the trace file itself.
178    
179    To enable emergency tracing in your code, call
180    
181        ETracing($cgi)
182    
183    from a web script and
184    
185        ETracing()
186    
187    from a command-line script.
188    
189    The web script will look for the tracing key in the cookies, and the command-line
190    script will look for it in the C<TRACING> environment variable. If you are
191    using the L</StandardSetup> method or a [[WebApplication]], emergency tracing
192    will be configured automatically.
193    
194  =cut  =cut
195    
196  # Declare the configuration variables.  # Declare the configuration variables.
197    
198  my $Destination = "NONE";       # Description of where to send the trace output.  my $Destination = "WARN";   # Description of where to send the trace output.
199    my $TeeFlag = 0;            # TRUE if output is going to a file and to the
200                                # standard output
201  my %Categories = ( main => 1 );  my %Categories = ( main => 1 );
202                                                          # hash of active category names                                                          # hash of active category names
203    my @LevelNames = qw(error warn notice info detail);
204  my $TraceLevel = 0;                     # trace level; a higher trace level produces more  my $TraceLevel = 0;                     # trace level; a higher trace level produces more
205                                                          # messages                                                          # messages
206  my @Queue = ();                         # queued list of trace messages.  my @Queue = ();                         # queued list of trace messages.
207    my $LastCategory = "main";  # name of the last category interrogated
208    my $LastLevel = 0;          # level of the last test call
209    my $SetupCount = 0;         # number of times TSetup called
210    my $AllTrace = 0;           # TRUE if we are tracing all categories.
211    my $SavedCGI;               # CGI object passed to ETracing
212    my $CommandLine;            # Command line passed to StandardSetup
213    umask 2;                    # Fix the damn umask so everything is group-writable.
214    
215  =head2 Public Methods  =head2 Tracing Methods
216    
217    =head3 Setups
218    
219        my $count = Tracer::Setups();
220    
221    Return the number of times L</TSetup> has been called.
222    
223    This method allows for the creation of conditional tracing setups where, for example, we
224    may want to set up tracing if nobody else has done it before us.
225    
226    =cut
227    
228    sub Setups {
229        return $SetupCount;
230    }
231    
232  =head3 TSetup  =head3 TSetup
233    
234  C<< TSetup($categoryList, $target); >>      TSetup($categoryList, $target);
235    
236  This method is used to specify the trace options. The options are stored as package data  This method is used to specify the trace options. The options are stored as package data
237  and interrogated by the L</Trace> and L</T> methods.  and interrogated by the L</Trace> and L</T> methods.
# Line 90  Line 247 
247    
248  The destination for the trace output. To send the trace output to a file, specify the file  The destination for the trace output. To send the trace output to a file, specify the file
249  name preceded by a ">" symbol. If a double symbol is used (">>"), then the data is appended  name preceded by a ">" symbol. If a double symbol is used (">>"), then the data is appended
250  to the file. Otherwise the file is cleared before tracing begins. In addition to sending  to the file. Otherwise the file is cleared before tracing begins. Precede the first ">"
251  the trace messages to a file, you can specify a special destination. C<HTML> will cause  symbol with a C<+> to echo output to a file AND to the standard output. In addition to
252  tracing to the standard output with each line formatted as an HTML paragraph. C<TEXT>  sending the trace messages to a file, you can specify a special destination. C<HTML> will
253    cause tracing to the standard output with each line formatted as an HTML paragraph. C<TEXT>
254  will cause tracing to the standard output as ordinary text. C<ERROR> will cause trace  will cause tracing to the standard output as ordinary text. C<ERROR> will cause trace
255  messages to be sent to the standard error output as ordinary text. C<QUEUE> will cause trace  messages to be sent to the standard error output as ordinary text. C<QUEUE> will cause trace
256  messages to be stored in a queue for later retrieval by the L</QTrace> method. C<WARN> will  messages to be stored in a queue for later retrieval by the L</QTrace> method. C<WARN> will
# Line 110  Line 268 
268          my @categoryData = split /\s+/, $categoryList;          my @categoryData = split /\s+/, $categoryList;
269          # Extract the trace level.          # Extract the trace level.
270          $TraceLevel = shift @categoryData;          $TraceLevel = shift @categoryData;
271          # Build the category hash.      # Presume category-based tracing until we learn otherwise.
272        $AllTrace = 0;
273        # Build the category hash. Note that if we find a "*", we turn on non-category
274        # tracing. We must also clear away any pre-existing data.
275        %Categories = ( main => 1 );
276          for my $category (@categoryData) {          for my $category (@categoryData) {
277                  $Categories{$category} = 1;          if ($category eq '*') {
278                $AllTrace = 1;
279            } else {
280                $Categories{lc $category} = 1;
281            }
282          }          }
283          # Now we need to process the destination information. The most important special          # Now we need to process the destination information. The most important special
284          # case is the single ">", which requires we clear the file first. After doing      # case is when we're writing to a file. This is indicated by ">" (overwrite) and
285          # so, we tack on another ">" sign so that future trace messages are appended.      # ">>" (append). A leading "+" for either indicates that we are also writing to
286        # the standard output (tee mode).
287        if ($target =~ m/^\+?>>?/) {
288            if ($target =~ m/^\+/) {
289                $TeeFlag = 1;
290                $target = substr($target, 1);
291            }
292          if ($target =~ m/^>[^>]/) {          if ($target =~ m/^>[^>]/) {
293                # We need to initialize the file (which clears it).
294                  open TRACEFILE, $target;                  open TRACEFILE, $target;
295                  print TRACEFILE Now() . " Tracing initialized.\n";              print TRACEFILE "[" . Now() . "] [notice] [Tracer] Tracing initialized.\n";
296                  close TRACEFILE;                  close TRACEFILE;
297                # Set to append mode now that the file has been cleared.
298                  $Destination = ">$target";                  $Destination = ">$target";
299          } else {          } else {
300                $Destination = $target;
301            }
302        } else {
303                  $Destination = uc($target);                  $Destination = uc($target);
304          }          }
305        # Increment the setup counter.
306        $SetupCount++;
307  }  }
308    
309  =head3 SetLevel  =head3 SetLevel
310    
311  C<< Tracer::SetLevel($newLevel); >>      Tracer::SetLevel($newLevel);
312    
313  Modify the trace level. A higher trace level will cause more messages to appear.  Modify the trace level. A higher trace level will cause more messages to appear.
314    
# Line 147  Line 326 
326      $TraceLevel = $_[0];      $TraceLevel = $_[0];
327  }  }
328    
329  =head3 Now  =head3 ParseDate
   
 C<< my $string = Tracer::Now(); >>  
   
 Return a displayable time stamp containing the local time.  
   
 =cut  
   
 sub Now {  
         my ($sec,$min,$hour,$mday,$mon,$year,$wday,$yday,$isdst) = localtime(time);  
         my $retVal = _p2($mon+1) . "/" . _p2($mday) . "/" . ($year + 1900) . " " .  
                                  _p2($hour) . ":" . _p2($min) . ":" . _p2($sec);  
         return $retVal;  
 }  
   
 # Pad a number to 2 digits.  
 sub _p2 {  
         my ($value) = @_;  
         $value = "0$value" if ($value < 10);  
         return $value;  
 }  
   
 =head3 LogErrors  
   
 C<< Tracer::LogErrors($fileName); >>  
   
 Route the standard error output to a log file.  
   
 =over 4  
   
 =item fileName  
   
 Name of the file to receive the error output.  
   
 =back  
330    
331  =cut      my $time = Tracer::ParseDate($dateString);
332    
333  sub LogErrors {  Convert a date into a PERL time number. This method expects a date-like string
334          # Get the file name.  and parses it into a number. The string must be vaguely date-like or it will
335          my ($fileName) = @_;  return an undefined value. Our requirement is that a month and day be
336          # Open the file as the standard error output.  present and that three pieces of the date string (time of day, month and day,
337          open STDERR, '>', $fileName;  year) be separated by likely delimiters, such as spaces, commas, and such-like.
 }  
338    
339  =head3 ReadOptions  If a time of day is present, it must be in military time with two digits for
340    everything but the hour.
341    
342  C<< my %options = Tracer::ReadOptions($fileName); >>  The year must be exactly four digits.
343    
344  Read a set of options from a file. Each option is encoded in a line of text that has the  Additional stuff can be in the string. We presume it's time zones or weekdays or something
345  format  equally innocuous. This means, however, that a sufficiently long sentence with date-like
346    parts in it may be interpreted as a date. Hopefully this will not be a problem.
347    
348  I<optionName>C<=>I<optionValue>C<; >I<comment>  It should be guaranteed that this method will parse the output of the L</Now> function.
349    
350  The option name must consist entirely of letters, digits, and the punctuation characters  The parameters are as follows.
 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.  
351    
352  =over 4  =over 4
353    
354  =item fileName  =item dateString
355    
356  Name of the file containing the option data.  The date string to convert.
357    
358  =item RETURN  =item RETURN
359    
360  Returns a hash mapping the option names specified in the file to their corresponding option  Returns a PERL time, that is, a number of seconds since the epoch, or C<undef> if
361  value.  the date string is invalid. A valid date string must contain a month and day.
362    
363  =back  =back
364    
365  =cut  =cut
366    
367  sub ReadOptions {  # Universal month conversion table.
368          # Get the parameters.  use constant MONTHS => {    Jan =>  0, January   =>  0, '01' =>  0,  '1' =>  0,
369          my ($fileName) = @_;                              Feb =>  1, February  =>  1, '02' =>  1,  '2' =>  1,
370          # Open the file.                              Mar =>  2, March     =>  2, '03' =>  2,  '3' =>  2,
371          (open CONFIGFILE, "<$fileName") || Confess("Could not open option file $fileName.");                              Apr =>  3, April     =>  3, '04' =>  3,  '4' =>  3,
372          # Count the number of records read.                              May =>  4, May       =>  4, '05' =>  4,  '5' =>  4,
373          my ($records, $comments) = 0;                              Jun =>  5, June      =>  5, '06' =>  5,  '6' =>  5,
374          # Create the return hash.                              Jul =>  6, July      =>  6, '07' =>  6,  '7' =>  6,
375          my %retVal = ();                              Aug =>  7, August    =>  7, '08' =>  7,  '8' =>  7,
376          # Loop through the file, accumulating key-value pairs.                              Sep =>  8, September =>  8, '09' =>  8,  '9' =>  8,
377          while (my $line = <CONFIGFILE>) {                              Oct =>  9, October  =>   9, '10' =>  9,
378                  # Denote we've read a line.                              Nov => 10, November =>  10, '11' => 10,
379                  $records++;                              Dec => 11, December =>  11, '12' => 11
380                  # Determine the line type.                          };
                 if ($line =~ /^\s*[\n\r]/) {  
                         # A blank line is a comment.  
                         $comments++;  
                 } elsif ($line =~ /^\s*([A-Za-z0-9_\.]+)=([^;]*);/) {  
                         # Here we have an option assignment.  
                         retVal{$1} = $2;  
                 } elsif ($line =~ /^\s*;/) {  
                         # Here we have a text comment.  
                         $comments++;  
                 } else {  
                         # Here we have an invalid line.  
                         Trace("Invalid option statement in record $records.") if T(0);  
                 }  
         }  
         # Return the hash created.  
         return %retVal;  
 }  
   
 =head3 GetOptions  
   
 C<< Tracer::GetOptions(\%defaults, \%options); >>  
   
 Merge a specified set of options into a table of defaults. This method takes two hash references  
 as input and uses the data from the second to update the first. If the second does not exist,  
 there will be no effect. An error will be thrown if one of the entries in the second hash does not  
 exist in the first.  
   
 Consider the following example.  
   
 C<< my $optionTable = GetOptions({ dbType => 'mySQL', trace => 0 }, $options); >>  
   
 In this example, the variable B<$options> is expected to contain at most two options-- B<dbType> and  
 B<trace>. The default database type is C<mySQL> and the default trace level is C<0>. If the value of  
 B<$options> is C<< {dbType => 'Oracle'} >>, then the database type will be changed to C<Oracle> and  
 the trace level will remain at 0. If B<$options> is undefined, then the database type and trace level  
 will remain C<mySQL> and C<0>. If, on the other hand, B<$options> is defined as  
   
 C<< {databaseType => 'Oracle'} >>  
   
 an error will occur because the B<databaseType> option does not exist.  
   
 =over 4  
   
 =item defaults  
   
 Table of default option values.  
   
 =item options  
   
 Table of overrides, if any.  
   
 =item RETURN  
   
 Returns a reference to the default table passed in as the first parameter.  
   
 =back  
   
 =cut  
381    
382  sub GetOptions {  sub ParseDate {
383          # Get the parameters.          # Get the parameters.
384          my ($defaults, $options) = @_;      my ($dateString) = @_;
385          # Check for overrides.      # Declare the return variable.
386          if ($options) {      my $retVal;
387                  # Loop through the overrides.      # Find the month and day of month. There are two ways that can happen. We check for the
388                  while (my ($option, $setting) = each %{$options}) {      # numeric style first. That way, if the user's done something like "Sun 12/22", then we
389                          # Insure this override exists.      # won't be fooled into thinking the month is Sunday.
390                          if (!exists $defaults->{$option}) {      if ($dateString =~ m#\b(\d{1,2})/(\d{1,2})\b# || $dateString =~ m#\b(\w+)\s(\d{1,2})\b#) {
391                                  croak "Unrecognized option $option encountered.";          my ($mon, $mday) = (MONTHS->{$1}, $2);
392            # Insist that the month and day are valid.
393            if (defined($mon) && $2 >= 1 && $2 <= 31) {
394                # Find the time.
395                my ($hour, $min, $sec) = (0, 0, 0);
396                if ($dateString =~ /\b(\d{1,2}):(\d{2}):(\d{2})\b/) {
397                    ($hour, $min, $sec) = ($1, $2, $3);
398                }
399                # Find the year.
400                my $year;
401                if ($dateString =~ /\b(\d{4})\b/) {
402                    $year = $1;
403                          } else {                          } else {
404                                  # Apply the override.                  # Get the default year, which is this one. Note we must convert it to
405                                  $defaults->{$option} = $setting;                  # the four-digit value expected by "timelocal".
406                    (undef, undef, undef, undef, undef, $year) = localtime();
407                    $year += 1900;
408                          }                          }
409                $retVal = timelocal($sec, $min, $hour, $mday, $mon, $year);
410                  }                  }
411          }          }
412          # Return the merged table.      # Return the result.
413          return $defaults;      return $retVal;
414  }  }
415    
416  =head3 MergeOptions  =head3 LogErrors
417    
418  C<< Tracer::MergeOptions(\%table, \%defaults); >>      Tracer::LogErrors($fileName);
419    
420  Merge default values into a hash table. This method looks at the key-value pairs in the  Route the standard error output to a log file.
 second (default) hash, and if a matching key is not found in the first hash, the default  
 pair is copied in. The process is similar to L</GetOptions>, but there is no error-  
 checking and no return value.  
421    
422  =over 4  =over 4
423    
424  =item table  =item fileName
   
 Hash table to be updated with the default values.  
   
 =item defaults  
425    
426  Default values to be merged into the first hash table if they are not already present.  Name of the file to receive the error output.
427    
428  =back  =back
429    
430  =cut  =cut
431    
432  sub MergeOptions {  sub LogErrors {
433          # Get the parameters.      # Get the file name.
434          my ($table, $defaults) = @_;      my ($fileName) = @_;
435          # Loop through the defaults.      # Open the file as the standard error output.
436          while (my ($key, $value) = each %{$defaults}) {      open STDERR, '>', $fileName;
                 if (!exists $table->{$key}) {  
                         $table->{$key} = $value;  
                 }  
         }  
437  }  }
438    
439  =head3 Trace  =head3 Trace
440    
441  C<< Trace($message); >>      Trace($message);
442    
443  Write a trace message to the target location specified in L</TSetup>. If there has not been  Write a trace message to the target location specified in L</TSetup>. If there has not been
444  any prior call to B<TSetup>.  any prior call to B<TSetup>.
# Line 368  Line 456 
456  sub Trace {  sub Trace {
457          # Get the parameters.          # Get the parameters.
458          my ($message) = @_;          my ($message) = @_;
459        # Strip off any line terminators at the end of the message. We will add
460        # new-line stuff ourselves.
461        my $stripped = Strip($message);
462        # Compute the caller information.
463        my ($callPackage, $callFile, $callLine) = caller();
464        my $callFileTitle = basename($callFile);
465        # Check the caller.
466        my $callerInfo = ($callFileTitle ne "Tracer.pm" ? " [$callFileTitle $callLine]" : "");
467          # Get the timestamp.          # Get the timestamp.
468          my $timeStamp = Now();          my $timeStamp = Now();
469        # Build the prefix.
470        my $level = $LevelNames[$LastLevel] || "($LastLevel)";
471        my $prefix = "[$timeStamp] [$level] [$LastCategory]$callerInfo";
472          # Format the message.          # Format the message.
473          my $formatted = "$timeStamp $message";      my $formatted = "$prefix $stripped";
474          # Process according to the destination.          # Process according to the destination.
475          if ($Destination eq "TEXT") {          if ($Destination eq "TEXT") {
476                  # Write the message to the standard output.                  # Write the message to the standard output.
477                  print "$formatted\n";                  print "$formatted\n";
478          } elsif ($Destination eq "ERROR") {          } elsif ($Destination eq "ERROR") {
479                  # Write the message to the error output.          # Write the message to the error output. Here, we want our prefix fields.
480                  print STDERR "$formatted\n";                  print STDERR "$formatted\n";
481        } elsif ($Destination eq "WARN") {
482            # Emit the message to the standard error output. It is presumed that the
483            # error logger will add its own prefix fields, the notable exception being
484            # the caller info.
485            print STDERR "$callerInfo$stripped\n";
486          } elsif ($Destination eq "QUEUE") {          } elsif ($Destination eq "QUEUE") {
487                  # Push the message into the queue.                  # Push the message into the queue.
488                  push @Queue, "$formatted";                  push @Queue, "$formatted";
489          } elsif ($Destination eq "HTML") {          } elsif ($Destination eq "HTML") {
490                  # Convert the message to HTML and write it to the standard output.                  # Convert the message to HTML and write it to the standard output.
491                  my $escapedMessage = CGI::escapeHTML($message);          my $escapedMessage = CGI::escapeHTML($stripped);
492                  print "<p>$formatted</p>\n";          print "<p>$timeStamp $LastCategory $LastLevel: $escapedMessage</p>\n";
     } elsif ($Destination eq "WARN") {  
        # Emit the message as a warning.  
        warn $message;  
493          } elsif ($Destination =~ m/^>>/) {          } elsif ($Destination =~ m/^>>/) {
494                  # Write the trace message to an output file.                  # Write the trace message to an output file.
495                  open TRACING, $Destination;          open(TRACING, $Destination) || die "Tracing open for \"$Destination\" failed: $!";
496            # Lock the file.
497            flock TRACING, LOCK_EX;
498                  print TRACING "$formatted\n";                  print TRACING "$formatted\n";
499                  close TRACING;                  close TRACING;
500            # If the Tee flag is on, echo it to the standard output.
501            if ($TeeFlag) {
502                print "$formatted\n";
503            }
504          }          }
505  }  }
506    
507  =head3 T  =head3 T
508    
509  C<< my $switch = T($category, $traceLevel); >>      my $switch = T($category, $traceLevel);
510    
511          or          or
512    
513  C<< my $switch = T($traceLevel); >>      my $switch = T($traceLevel);
514    
515  Return TRUE if the trace level is at or above a specified value and the specified category  Return TRUE if the trace level is at or above a specified value and the specified category
516  is active, else FALSE. If no category is specified, the caller's package name is used.  is active, else FALSE. If no category is specified, the caller's package name is used.
# Line 436  Line 543 
543                  my ($category, $traceLevel) = @_;                  my ($category, $traceLevel) = @_;
544                  if (!defined $traceLevel) {                  if (!defined $traceLevel) {
545                          # Here we have no category, so we need to get the calling package.                          # Here we have no category, so we need to get the calling package.
546                # The calling package is normally the first parameter. If it is
547                # omitted, the first parameter will be the tracelevel. So, the
548                # first thing we do is shift the so-called category into the
549                # $traceLevel variable where it belongs.
550                          $traceLevel = $category;                          $traceLevel = $category;
551                          my ($package, $fileName, $line) = caller;                          my ($package, $fileName, $line) = caller;
552              # If there is no calling package, we default to "main".              # If there is no calling package, we default to "main".
553                          if (!$package) {                          if (!$package) {
554                  $category = "main";                  $category = "main";
555                          } else {                          } else {
556                                  $category = $package;                  my @cats = split /::/, $package;
557                    $category = $cats[$#cats];
558                          }                          }
559                  }                  }
560                  # Use the package and tracelevel to compute the result.          # Save the category name and level.
561                  $retVal = ($traceLevel <= $TraceLevel && exists $Categories{$category});          $LastCategory = $category;
562            $LastLevel = $traceLevel;
563            # Convert it to lower case before we hash it.
564            $category = lc $category;
565            # Validate the trace level.
566            if (ref $traceLevel) {
567                Confess("Bad trace level.");
568            } elsif (ref $TraceLevel) {
569                Confess("Bad trace config.");
570            }
571            # Make the check. Note that level 0 shows even if the category is turned off.
572            $retVal = ($traceLevel <= $TraceLevel && ($traceLevel == 0 || $AllTrace || exists $Categories{$category}));
573      }      }
574          # Return the computed result.          # Return the computed result.
575      return $retVal;      return $retVal;
576  }  }
577    
578  =head3 ParseCommand  =head3 QTrace
   
 C<< my ($options, @arguments) = Tracer::ParseCommand(\%optionTable, @inputList); >>  
   
 Parse a command line consisting of a list of parameters. The initial parameters may be option  
 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.  
   
 C<< my ($options, @arguments) = ParseCommand({ errors => 0, logFile => 'trace.log'}, @words); >>  
   
 In this case, the list @words will be treated as a command line. There are two options available,  
 B<errors> and B<logFile>. If @words has the following format  
   
 C<< -logFile=error.log apple orange rutabaga >>  
   
 then at the end of the invocation, C<$options> will be  
   
 C<< { errors => 0, logFile => 'error.log' } >>  
   
 and C<@arguments> will contain  
579    
580  C<< apple orange rutabaga >>      my $data = QTrace($format);
581    
582  The parser allows for some escape sequences. See L</UnEscape> for a description. There is no  Return the queued trace data in the specified format.
 support for quote characters.  
583    
584  =over 4  =over 4
585    
586  =item optionTable  =item format
   
 Table of default options.  
   
 =item inputList  
   
 List of words on the command line.  
   
 =item RETURN  
587    
588  Returns a reference to the option table and a list of the positional arguments.  C<html> to format the data as an HTML list, C<text> to format it as straight text.
589    
590  =back  =back
591    
592  =cut  =cut
593    
594  sub ParseCommand {  sub QTrace {
595          # Get the parameters.      # Get the parameter.
596          my ($optionTable, @inputList) = @_;      my ($format) = @_;
597          # Process any options in the input list.      # Create the return variable.
598        my $retVal = "";
599        # Only proceed if there is an actual queue.
600        if (@Queue) {
601            # Process according to the format.
602            if ($format =~ m/^HTML$/i) {
603                # Convert the queue into an HTML list.
604                $retVal = "<ul>\n";
605                for my $line (@Queue) {
606                    my $escapedLine = CGI::escapeHTML($line);
607                    $retVal .= "<li>$escapedLine</li>\n";
608                }
609                $retVal .= "</ul>\n";
610            } elsif ($format =~ m/^TEXT$/i) {
611                # Convert the queue into a list of text lines.
612                $retVal = join("\n", @Queue) . "\n";
613            }
614            # Clear the queue.
615            @Queue = ();
616        }
617        # Return the formatted list.
618        return $retVal;
619    }
620    
621    =head3 Confess
622    
623        Confess($message);
624    
625    Trace the call stack and abort the program with the specified message. When used with
626    the OR operator and the L</Assert> method, B<Confess> can function as a debugging assert.
627    So, for example
628    
629        Assert($recNum >= 0) || Confess("Invalid record number $recNum.");
630    
631    Will abort the program with a stack trace if the value of C<$recNum> is negative.
632    
633    =over 4
634    
635    =item message
636    
637    Message to include in the trace.
638    
639    =back
640    
641    =cut
642    
643    sub Confess {
644        # Get the parameters.
645        my ($message) = @_;
646        # Set up the category and level.
647        $LastCategory = "(confess)";
648        $LastLevel = 0;
649        if (! defined($FIG_Config::no_tool_hdr)) {
650            # Here we have a tool header. Display its length so that the user can adjust the line numbers.
651            my $toolHeaderFile = "$FIG_Config::fig_disk/dist/releases/current/$FIG_Config::arch/tool_hdr";
652            # Only proceed if the tool header file is actually present.
653            if (-f $toolHeaderFile) {
654                my $fh;
655                if (open $fh, "<$toolHeaderFile") {
656                    my @lines = <$fh>;
657                    Trace("Tool header has " . scalar(@lines) . " lines.");
658                }
659            }
660        }
661        # Trace the call stack.
662        Cluck($message);
663        # Abort the program.
664        croak(">>> $message");
665    }
666    
667    =head3 SaveCGI
668    
669        Tracer::SaveCGI($cgi);
670    
671    This method saves the CGI object but does not activate emergency tracing.
672    It is used to allow L</Warn> to work in situations where emergency
673    tracing is contra-indicated (e.g. the wiki).
674    
675    =over 4
676    
677    =item cgi
678    
679    Active CGI query object.
680    
681    =back
682    
683    =cut
684    
685    sub SaveCGI {
686        $SavedCGI = $_[0];
687    }
688    
689    =head3 Warn
690    
691        Warn($message, @options);
692    
693    This method traces an important message. If an RSS feed is configured
694    (via I<FIG_Config::error_feed>) and the tracing destination is C<WARN>,
695    then the message will be echoed to the feed. In general, a tracing
696    destination of C<WARN> indicates that the caller is running as a web
697    service in a production environment; however, this is not a requirement.
698    
699    To force warnings into the RSS feed even when the tracing destination
700    is not C<WARN>, simply specify the C<Feed> tracing module. This can be
701    configured automatically when L</StandardSetup> is used.
702    
703    The L</Cluck> method calls this one for its final message. Since
704    L</Confess> calls L</Cluck>, this means that any error which is caught
705    and confessed will put something in the feed. This insures that someone
706    will be alerted relatively quickly when a failure occurs.
707    
708    =over 4
709    
710    =item message
711    
712    Message to be traced.
713    
714    =item options
715    
716    A list containing zero or more options.
717    
718    =back
719    
720    The permissible options are as follows.
721    
722    =over 4
723    
724    =item noStack
725    
726    If specified, then the stack trace is not included in the output.
727    
728    =back
729    
730    =cut
731    
732    sub Warn {
733        # Get the parameters.
734        my $message = shift @_;
735        my %options = map { $_ => 1 } @_;
736        # Save $@;
737        my $savedError = $@;
738        # Trace the message.
739        Trace($message);
740        # This will contain the lock handle. If it's defined, it means we need to unlock.
741        my $lock;
742        # Check for feed forcing.
743        my $forceFeed = exists $Categories{feed};
744        # An error here would be disastrous. Note that if debug mode is specified,
745        # we do this stuff even in a test environment.
746        eval {
747            # Do we need to put this in the RSS feed?
748            if ($FIG_Config::error_feed && ($Destination eq 'WARN' || $forceFeed)) {
749                # Probably. We need to check first, however, to see if it's from an
750                # ignored IP. For non-CGI situations, we default the IP to the self-referent.
751                my $key = "127.0.0.1";
752                if (defined $SavedCGI) {
753                    # Get the IP address.
754                    $key = $ENV{HTTP_X_FORWARDED_FOR} || $ENV{REMOTE_ADDR};
755                }
756                # Is the IP address in the ignore list?
757                my $found = scalar(grep { $_ eq $key } @FIG_Config::error_ignore_ips);
758                if (! $found) {
759                    # No. We're good. We now need to compute the date, the link, and the title.
760                    # First, the date, in a very specific format.
761                    my $date = strftime("%a, %02e %b %H:%M:%S %Y ", localtime) .
762                        (tz_local_offset() / 30);
763                    # Environment data goes in here. We start with the date.
764                    my $environment = "$date.  ";
765                    # If we need to recap the message (because it's too long to be a title), we'll
766                    # put it in here.
767                    my $recap;
768                    # Copy the message and remove excess space.
769                    my $title = $message;
770                    $title =~ s/\s+/ /gs;
771                    # If it's too long, we have to split it up.
772                    if (length $title > 60) {
773                        # Put the full message in the environment string.
774                        $recap = $title;
775                        # Excerpt it as the title.
776                        $title = substr($title, 0, 50) . "...";
777                    }
778                    # If we have a CGI object, then this is a web error. Otherwise, it's
779                    # command-line.
780                    if (defined $SavedCGI) {
781                        # We're in a web service. The environment is the user's IP, and the link
782                        # is the URL that got us here.
783                        $environment .= "Event Reported at IP address $key process $$.";
784                        my $url = $SavedCGI->self_url();
785                        # We need the user agent string and (if available) the referrer.
786                        # The referrer will be the link.
787                        $environment .= " User Agent $ENV{HTTP_USER_AGENT}";
788                        if ($ENV{HTTP_REFERER}) {
789                            my $link = $ENV{HTTP_REFERER};
790                            $environment .= " referred from <a href=\"$link\">$link</a>.";
791                        } else {
792                            $environment .= " referrer unknown.";
793                        }
794                        # Close off the sentence with the original link.
795                        $environment .= " URL of event is <a href=\"$url\">$url</a>.";
796                    } else {
797                        # No CGI object, so we're a command-line tool. Use the tracing
798                        # key and the PID as the user identifier, and add the command.
799                        my $key = EmergencyKey();
800                        $environment .= "Event Reported by $key process $$.";
801                        if ($CommandLine) {
802                            # We're in a StandardSetup script, so we have the real command line.
803                            $environment .= "\n<pre>" . CGI::escapeHTML($CommandLine) . "</pre>\n";
804                        } elsif ($ENV{_}) {
805                            # We're in a BASH script, so the command has been stored in the _ variable.
806                            $environment .= "  Command = " . CGI::escapeHTML($ENV{_}) . "\n";
807                        }
808                    }
809                    # Build a GUID. We use the current time, the title, and the process ID,
810                    # then digest the result.
811                    my $guid = Digest::MD5::md5_base64(gettimeofday(), $title, $$);
812                    # Finally, the description. This is a stack trace plus various environmental stuff.
813                    # The trace is optional.
814                    my $stackTrace;
815                    if ($options{noStack}) {
816                        $stackTrace = "";
817                    } else {
818                        my @trace = LongMess();
819                        # Only proceed if we got something back.
820                        if (scalar(@trace) > 0) {
821                            $trace[0] =~ s/Tracer::Warn.+?called/Event occurred/;
822                            $stackTrace = "Stack trace:<pre>" . join("\n", @trace, "</pre>");
823                        }
824                    }
825                    # We got the stack trace. Now it's time to put it all together.
826                    # We have a goofy thing here in that we need to HTML-escape some sections of the description
827                    # twice. They will be escaped once here, and then once when written by XML::Simple. They are
828                    # unescaped once when processed by the RSS reader, and stuff in the description is treated as
829                    # HTML. So, anything escaped here is treated as a literal when viewed in the RSS reader, but
830                    # our <br>s and <pre>s are used to format the description.
831                    $recap = (defined $recap ? "<em>" . CGI::escapeHTML($recap) . "</em><br /><br />" : "");
832                    my $description = "$recap$environment  $stackTrace";
833                    # Okay, we have all the pieces. Create a hash of the new event.
834                    my $newItem = { title => $title,
835                                    description => $description,
836                                    category => $LastCategory,
837                                    pubDate => $date,
838                                    guid => $guid,
839                                  };
840                    # We need XML capability for this.
841                    require XML::Simple;
842                    # The RSS document goes in here.
843                    my $rss;
844                    # Get the name of the RSS file. It's in the FIG temporary directory.
845                    my $fileName = "$FIG_Config::temp/$FIG_Config::error_feed";
846                    # Open the config file and lock it.
847                    $lock = Open(undef, "<$FIG_Config::fig_disk/config/FIG_Config.pm");
848                    flock $lock, LOCK_EX;
849                    # Does it exist?
850                    if (-s $fileName) {
851                        # Slurp it in.
852                        $rss = XML::Simple::XMLin($fileName, ForceArray => ['item']);
853                    } else {
854                        my $size = -s $fileName;
855                        # Create an empty channel.
856                        $rss = {
857                            channel => {
858                                title => 'NMPDR Warning Feed',
859                                link => "$FIG_Config::temp_url/$FIG_Config::error_feed",
860                                description => "Important messages regarding the status of the NMPDR.",
861                                generator => "NMPDR Trace Facility",
862                                docs => "http://blogs.law.harvard.edu/tech/rss",
863                                item => []
864                            },
865                        };
866                    }
867                    # Get the channel object.
868                    my $channel = $rss->{channel};
869                    # Update the last-build date.
870                    $channel->{lastBuildDate} = $date;
871                    # Get the item array.
872                    my $items = $channel->{item};
873                    # Insure it has only 100 entries.
874                    while (scalar @{$items} > 100) {
875                        pop @{$items};
876                    }
877                    # Add our new item at the front.
878                    unshift @{$items}, $newItem;
879                    # Create the XML. Note we do not include the root or the declaration. XML Simple can't handle
880                    # the requirements for those.
881                    my $xml = XML::Simple::XMLout($channel, NoAttr => 1, RootName => 'channel', XmlDecl => '');
882                    # Here we put in the root and declaration. The problem is that the root has to have the version attribute
883                    # in it. So, we suppress the root and do it by hand, and that requires suppressing the declaration, too.
884                    $xml = "<?xml version=\"1.0\" encoding=\"utf-8\"?>\n<rss version=\"2.0\">$xml\n</rss>";
885                    # We don't use Open here because we can't afford an error.
886                    if (open XMLOUT, ">$fileName") {
887                        print XMLOUT $xml;
888                        close XMLOUT;
889                    }
890                }
891            }
892        };
893        if ($@) {
894            # If the feed failed, we need to know why. The error will be traced, but this method will not be involved
895            # (which is a good thing).
896            my $error = $@;
897            Trace("Feed Error: $error") if T(Feed => 0);
898        }
899        # Be sure to unlock.
900        if ($lock) {
901            flock $lock, LOCK_UN;
902            undef $lock;
903        }
904        # Restore the error message.
905        $@ = $savedError;
906    }
907    
908    
909    
910    
911    =head3 Assert
912    
913        Assert($condition1, $condition2, ... $conditionN);
914    
915    Return TRUE if all the conditions are true. This method can be used in conjunction with
916    the OR operator and the L</Confess> method as a debugging assert.
917    So, for example
918    
919        Assert($recNum >= 0) || Confess("Invalid record number $recNum.");
920    
921    Will abort the program with a stack trace if the value of C<$recNum> is negative.
922    
923    =cut
924    sub Assert {
925        my $retVal = 1;
926        LOOP: for my $condition (@_) {
927            if (! $condition) {
928                $retVal = 0;
929                last LOOP;
930            }
931        }
932        return $retVal;
933    }
934    
935    =head3 Cluck
936    
937        Cluck($message);
938    
939    Trace the call stack. Note that for best results, you should qualify the call with a
940    trace condition. For example,
941    
942        Cluck("Starting record parse.") if T(3);
943    
944    will only trace the stack if the trace level for the package is 3 or more.
945    
946    =over 4
947    
948    =item message
949    
950    Message to include in the trace.
951    
952    =back
953    
954    =cut
955    
956    sub Cluck {
957        # Get the parameters.
958        my ($message) = @_;
959        # Trace what's happening.
960        Trace("Stack trace for event: $message");
961        # Get the stack trace.
962        my @trace = LongMess();
963        # Convert the trace to a series of messages.
964        for my $line (@trace) {
965            # Replace the tab at the beginning with spaces.
966            $line =~ s/^\t/    /;
967            # Trace the line.
968            Trace($line);
969        }
970        # Issue a warning. This displays the event message and inserts it into the RSS error feed.
971        Warn($message);
972    }
973    
974    =head3 LongMess
975    
976        my @lines = Tracer::LongMess();
977    
978    Return a stack trace with all tracing methods removed. The return will be in the form of a list
979    of message strings.
980    
981    =cut
982    
983    sub LongMess {
984        # Declare the return variable.
985        my @retVal = ();
986        my $confession = longmess("");
987        for my $line (split /\s*\n/, $confession) {
988            unless ($line =~ /Tracer\.pm/) {
989                # Here we have a line worth keeping. Push it onto the result list.
990                push @retVal, $line;
991            }
992        }
993        # Return the result.
994        return @retVal;
995    }
996    
997    =head3 ETracing
998    
999        ETracing($parameter);
1000    
1001    Set up emergency tracing. Emergency tracing is tracing that is turned
1002    on automatically for any program that calls this method. The emergency
1003    tracing parameters are stored in a a file identified by a tracing key.
1004    If this method is called with a CGI object, then the tracing key is
1005    taken from a cookie. If it is called with no parameters, then the tracing
1006    key is taken from an environment variable. If it is called with a string,
1007    the tracing key is that string.
1008    
1009    =over 4
1010    
1011    =item parameter
1012    
1013    A parameter from which the tracing key is computed. If it is a scalar,
1014    that scalar is used as the tracing key. If it is a CGI object, the
1015    tracing key is taken from the C<IP> cookie. If it is omitted, the
1016    tracing key is taken from the C<TRACING> environment variable. If it
1017    is a CGI object and emergency tracing is not on, the C<Trace> and
1018    C<TF> parameters will be used to determine the type of tracing.
1019    
1020    =back
1021    
1022    =cut
1023    
1024    sub ETracing {
1025        # Get the parameter.
1026        my ($parameter) = @_;
1027        # Check for CGI mode.
1028        if (defined $parameter && ref $parameter eq 'CGI') {
1029            $SavedCGI = $parameter;
1030        } else {
1031            $SavedCGI = undef;
1032        }
1033        # Default to no tracing except errors.
1034        my ($tracing, $dest) = ("0", "WARN");
1035        # Check for emergency tracing.
1036        my $tkey = EmergencyKey($parameter);
1037        my $emergencyFile = EmergencyFileName($tkey);
1038        if (-e $emergencyFile) {
1039            # We have the file. Read in the data.
1040            my @tracing = GetFile($emergencyFile);
1041            # Pull off the time limit.
1042            my $expire = shift @tracing;
1043            # Convert it to seconds.
1044            $expire *= 3600;
1045            # Check the file data.
1046            my $stat = stat($emergencyFile);
1047            my ($now) = gettimeofday;
1048            if ($now - $stat->mtime > $expire) {
1049                # Delete the expired file.
1050                unlink $emergencyFile;
1051            } else {
1052                # Emergency tracing is on. Pull off the destination and
1053                # the trace level;
1054                $dest = shift @tracing;
1055                my $level = shift @tracing;
1056                # Convert the destination to a real tracing destination.
1057                # temp directory.
1058                $dest = EmergencyTracingDest($tkey, $dest);
1059                # Insure Tracer is specified.
1060                my %moduleHash = map { $_ => 1 } @tracing;
1061                $moduleHash{Tracer} = 1;
1062                # Set the trace parameter.
1063                $tracing = join(" ", $level, sort keys %moduleHash);
1064            }
1065        } elsif (defined $SavedCGI) {
1066            # There's no emergency tracing, but we have a CGI object, so check
1067            # for tracing from the form parameters.
1068            if ($SavedCGI->param('Trace')) {
1069                # Here the user has requested tracing via a form.
1070                $dest = ($SavedCGI->param('TF') ? ">$FIG_Config::temp/Trace$$.log" : "QUEUE");
1071                $tracing = $SavedCGI->param('Trace') . " Tracer";
1072            }
1073        }
1074        # Setup the tracing we've determined from all the stuff above.
1075        TSetup($tracing, $dest);
1076        # Check to see if we're a web script.
1077        if (defined $SavedCGI) {
1078            # Yes we are. Trace the form and environment data.
1079            TraceParms($SavedCGI);
1080            # Check for RAW mode. In raw mode, we print a fake header so that we see everything
1081            # emitted by the script in its raw form.
1082            if (T(Raw => 3)) {
1083                print CGI::header(-type => 'text/plain', -tracing => 'Raw');
1084            }
1085        }
1086    }
1087    
1088    =head3 EmergencyFileName
1089    
1090        my $fileName = Tracer::EmergencyFileName($tkey);
1091    
1092    Return the emergency tracing file name. This is the file that specifies
1093    the tracing information.
1094    
1095    =over 4
1096    
1097    =item tkey
1098    
1099    Tracing key for the current program.
1100    
1101    =item RETURN
1102    
1103    Returns the name of the file to contain the emergency tracing information.
1104    
1105    =back
1106    
1107    =cut
1108    
1109    sub EmergencyFileName {
1110        # Get the parameters.
1111        my ($tkey) = @_;
1112        # Compute the emergency tracing file name.
1113        return "$FIG_Config::temp/Emergency$tkey.txt";
1114    }
1115    
1116    =head3 EmergencyFileTarget
1117    
1118        my $fileName = Tracer::EmergencyFileTarget($tkey);
1119    
1120    Return the emergency tracing target file name. This is the file that receives
1121    the tracing output for file-based tracing.
1122    
1123    =over 4
1124    
1125    =item tkey
1126    
1127    Tracing key for the current program.
1128    
1129    =item RETURN
1130    
1131    Returns the name of the file to contain the trace output.
1132    
1133    =back
1134    
1135    =cut
1136    
1137    sub EmergencyFileTarget {
1138        # Get the parameters.
1139        my ($tkey) = @_;
1140        # Compute the emergency tracing file name.
1141        return "$FIG_Config::temp/trace$tkey.log";
1142    }
1143    
1144    =head3 EmergencyTracingDest
1145    
1146        my $dest = Tracer::EmergencyTracingDest($tkey, $myDest);
1147    
1148    This method converts an emergency tracing destination to a real
1149    tracing destination. The main difference is that if the
1150    destination is C<FILE> or C<APPEND>, we convert it to file
1151    output. If the destination is C<DUAL>, we convert it to file
1152    and standard output.
1153    
1154    =over 4
1155    
1156    =item tkey
1157    
1158    Tracing key for this environment.
1159    
1160    =item myDest
1161    
1162    Destination from the emergency tracing file.
1163    
1164    =item RETURN
1165    
1166    Returns a destination that can be passed into L</TSetup>.
1167    
1168    =back
1169    
1170    =cut
1171    
1172    sub EmergencyTracingDest {
1173        # Get the parameters.
1174        my ($tkey, $myDest) = @_;
1175        # Declare the return variable.
1176        my $retVal = $myDest;
1177        # Process according to the destination value.
1178        if ($myDest eq 'FILE') {
1179            $retVal = ">" . EmergencyFileTarget($tkey);
1180        } elsif ($myDest eq 'APPEND') {
1181            $retVal = ">>" . EmergencyFileTarget($tkey);
1182        } elsif ($myDest eq 'DUAL') {
1183            $retVal = "+>" . EmergencyFileTarget($tkey);
1184        } elsif ($myDest eq 'WARN') {
1185            $retVal = "WARN";
1186        }
1187        # Return the result.
1188        return $retVal;
1189    }
1190    
1191    =head3 Emergency
1192    
1193        Emergency($key, $hours, $dest, $level, @modules);
1194    
1195    Turn on emergency tracing. This method is normally invoked over the web from
1196    a debugging console, but it can also be called by the C<trace.pl> script.
1197    The caller specifies the duration of the emergency in hours, the desired tracing
1198    destination, the trace level, and a list of the trace modules to activate.
1199    For the length of the duration, when a program in an environment with the
1200    specified tracing key active invokes a Sprout CGI script, tracing will be
1201    turned on automatically. See L</TSetup> for more about tracing setup and
1202    L</ETracing> for more about emergency tracing.
1203    
1204    =over 4
1205    
1206    =item tkey
1207    
1208    The tracing key. This is used to identify the control file and the trace file.
1209    
1210    =item hours
1211    
1212    Number of hours to keep emergency tracing alive.
1213    
1214    =item dest
1215    
1216    Tracing destination. If no path information is specified for a file
1217    destination, it is put in the FIG temporary directory.
1218    
1219    =item level
1220    
1221    Tracing level. A higher level means more trace messages.
1222    
1223    =item modules
1224    
1225    A list of the tracing modules to activate.
1226    
1227    =back
1228    
1229    =cut
1230    
1231    sub Emergency {
1232        # Get the parameters.
1233        my ($tkey, $hours, $dest, $level, @modules) = @_;
1234        # Create the emergency file.
1235        my $specFile = EmergencyFileName($tkey);
1236        my $outHandle = Open(undef, ">$specFile");
1237        print $outHandle join("\n", $hours, $dest, $level, @modules, "");
1238    }
1239    
1240    =head3 EmergencyKey
1241    
1242        my $tkey = EmergencyKey($parameter);
1243    
1244    Return the Key to be used for emergency tracing. This could be an IP address,
1245     a session ID, or a user name, depending on the environment.
1246    
1247    =over 4
1248    
1249    =item parameter
1250    
1251    Parameter defining the method for finding the tracing key. If it is a scalar,
1252    then it is presumed to be the tracing key itself. If it is a CGI object, then
1253    the tracing key is taken from the C<IP> cookie. Otherwise, the tracing key is
1254    taken from the C<TRACING> environment variable.
1255    
1256    =item RETURN
1257    
1258    Returns the key to be used for labels in emergency tracing.
1259    
1260    =back
1261    
1262    =cut
1263    
1264    sub EmergencyKey {
1265        # Get the parameters.
1266        my ($parameter) = @_;
1267        # Declare the return variable.
1268        my $retVal;
1269        # Determine the parameter type.
1270        if (! defined $parameter || defined($ENV{TRACING})) {
1271            # Here we're supposed to check the environment. If that fails, we
1272            # get the effective login ID.
1273            $retVal = $ENV{TRACING} || scalar getpwuid($<);
1274        } else {
1275            my $ptype = ref $parameter;
1276            if ($ptype eq 'CGI') {
1277                # Here we were invoked from a web page. Look for a cookie.
1278                $retVal = $parameter->cookie('IP');
1279            } elsif (! $ptype) {
1280                # Here the key was passed in.
1281                $retVal = $parameter;
1282            }
1283        }
1284        # If no luck finding a key, use the PID.
1285        if (! defined $retVal) {
1286            $retVal = $$;
1287        }
1288        # Return the result.
1289        return $retVal;
1290    }
1291    
1292    
1293    =head3 TraceParms
1294    
1295        Tracer::TraceParms($cgi);
1296    
1297    Trace the CGI parameters at trace level CGI => 3 and the environment variables
1298    at level CGI => 4. A self-referencing URL is traced at level CGI => 2.
1299    
1300    =over 4
1301    
1302    =item cgi
1303    
1304    CGI query object containing the parameters to trace.
1305    
1306    =back
1307    
1308    =cut
1309    
1310    sub TraceParms {
1311        # Get the parameters.
1312        my ($cgi) = @_;
1313        if (T(CGI => 2)) {
1314            # Here we trace the GET-style URL for the script.
1315            Trace("[URL] " . $cgi->url(-relative => 1, -query => 1));
1316        }
1317        if (T(CGI => 3)) {
1318            # Here we want to trace the parameter data.
1319            my @names = $cgi->param;
1320            for my $parmName (sort @names) {
1321                # Note we skip the Trace parameters, which are for our use only.
1322                if ($parmName ne 'Trace' && $parmName ne 'TF') {
1323                    my @values = $cgi->param($parmName);
1324                    Trace("[CGI] $parmName = " . join(", ", @values));
1325                }
1326            }
1327            # Display the request method.
1328            my $method = $cgi->request_method();
1329            Trace("Method: $method");
1330        }
1331        if (T(CGI => 4)) {
1332            # Here we want the environment data too.
1333            for my $envName (sort keys %ENV) {
1334                Trace("[ENV] $envName = $ENV{$envName}");
1335            }
1336        }
1337    }
1338    
1339    =head3 TraceImages
1340    
1341        Tracer::TraceImages($htmlString);
1342    
1343    Trace information about all of an html document's images. The tracing
1344    will be for type "IMG" at level 3. The image's source string
1345    will be displayed. This is generally either the URL of the image or
1346    raw data for the image itself. If the source is too long, only the first 300
1347    characters will be shown at trace level 3. The entire source will be shown,
1348    however, at trace level 4. This method is not very smart, and might catch
1349    Javascript code, but it is still useful when debugging the arcane
1350    behavior of images in multiple browser environments.
1351    
1352    =over 4
1353    
1354    =item htmlString
1355    
1356    HTML text for an outgoing web page.
1357    
1358    =back
1359    
1360    =cut
1361    
1362    sub TraceImages {
1363        # Only proceed if we're at the proper trace level.
1364        if (T(IMG => 3)) {
1365            # For performance reasons we're manipulating $_[0] instead of retrieving the string
1366            # into a variable called "$htmlString". This is because we expect html strings to be
1367            # long, and don't want to copy them any more than we have to.
1368            Trace(length($_[0]) . " characters in web page.");
1369            # Loop through the HTML, culling image tags.
1370            while ($_[0] =~ /<img\s+[^>]+?src="([^"]+)"/sgi) {
1371                # Extract the source string and determine whether or not it's too long.
1372                my $srcString = $1;
1373                my $pos = pos($_[0]) - length($srcString);
1374                my $excess = length($srcString) - 300;
1375                # We'll put the display string in here.
1376                my $srcDisplay = $srcString;
1377                # If it's a data string, split it at the comma.
1378                $srcDisplay =~ s/^(data[^,]+,)/$1\n/;
1379                # If there's no excess or we're at trace level 4, we're done. At level 3 with
1380                # a long string, however, we only show the first 300 characters.
1381                if ($excess > 0 && ! T(IMG => 4)) {
1382                    $srcDisplay = substr($srcDisplay,0,300) . "\nplus $excess characters.";
1383                }
1384                # Output the trace message.
1385                Trace("Image tag at position $pos:\n$srcDisplay");
1386            }
1387        }
1388    }
1389    
1390    =head2 Command-Line Utility Methods
1391    
1392    =head3 SendSMS
1393    
1394        my $msgID = Tracer::SendSMS($phoneNumber, $msg);
1395    
1396    Send a text message to a phone number using Clickatell. The FIG_Config file must contain the
1397    user name, password, and API ID for the relevant account in the hash reference variable
1398    I<$FIG_Config::phone>, using the keys C<user>, C<password>, and C<api_id>. For
1399    example, if the user name is C<BruceTheHumanPet>, the password is C<silly>, and the API ID
1400    is C<2561022>, then the FIG_Config file must contain
1401    
1402        $phone =  { user => 'BruceTheHumanPet',
1403                    password => 'silly',
1404                    api_id => '2561022' };
1405    
1406    The original purpose of this method was to insure Bruce would be notified immediately when the
1407    Sprout Load terminates. Care should be taken if you do not wish Bruce to be notified immediately
1408    when you call this method.
1409    
1410    The message ID will be returned if successful, and C<undef> if an error occurs.
1411    
1412    =over 4
1413    
1414    =item phoneNumber
1415    
1416    Phone number to receive the message, in international format. A United States phone number
1417    would be prefixed by "1". A British phone number would be prefixed by "44".
1418    
1419    =item msg
1420    
1421    Message to send to the specified phone.
1422    
1423    =item RETURN
1424    
1425    Returns the message ID if successful, and C<undef> if the message could not be sent.
1426    
1427    =back
1428    
1429    =cut
1430    
1431    sub SendSMS {
1432        # Get the parameters.
1433        my ($phoneNumber, $msg) = @_;
1434        # Declare the return variable. If we do not change it, C<undef> will be returned.
1435        my $retVal;
1436        # Only proceed if we have phone support.
1437        if (! defined $FIG_Config::phone) {
1438            Trace("Phone support not present in FIG_Config.") if T(1);
1439        } else {
1440            # Get the phone data.
1441            my $parms = $FIG_Config::phone;
1442            # Get the Clickatell URL.
1443            my $url = "http://api.clickatell.com/http/";
1444            # Create the user agent.
1445            my $ua = LWP::UserAgent->new;
1446            # Request a Clickatell session.
1447            my $resp = $ua->post("$url/sendmsg", { user => $parms->{user},
1448                                         password => $parms->{password},
1449                                         api_id => $parms->{api_id},
1450                                         to => $phoneNumber,
1451                                         text => $msg});
1452            # Check for an error.
1453            if (! $resp->is_success) {
1454                Trace("Alert failed.") if T(1);
1455            } else {
1456                # Get the message ID.
1457                my $rstring = $resp->content;
1458                if ($rstring =~ /^ID:\s+(.*)$/) {
1459                    $retVal = $1;
1460                } else {
1461                    Trace("Phone attempt failed with $rstring") if T(1);
1462                }
1463            }
1464        }
1465        # Return the result.
1466        return $retVal;
1467    }
1468    
1469    =head3 StandardSetup
1470    
1471        my ($options, @parameters) = StandardSetup(\@categories, \%options, $parmHelp, @ARGV);
1472    
1473    This method performs standard command-line parsing and tracing setup. The return
1474    values are a hash of the command-line options and a list of the positional
1475    parameters. Tracing is automatically set up and the command-line options are
1476    validated.
1477    
1478    This is a complex method that does a lot of grunt work. The parameters can
1479    be more easily understood, however, once they are examined individually.
1480    
1481    The I<categories> parameter is the most obtuse. It is a reference to a list of
1482    special-purpose tracing categories. Most tracing categories are PERL package
1483    names. So, for example, if you wanted to turn on tracing inside the B<Sprout>,
1484    B<ERDB>, and B<SproutLoad> packages, you would specify the categories
1485    
1486        ["Sprout", "SproutLoad", "ERDB"]
1487    
1488    This would cause trace messages in the specified three packages to appear in
1489    the output. There are two special tracing categories that are automatically
1490    handled by this method. In other words, if you used L</TSetup> you would need
1491    to include these categories manually, but if you use this method they are turned
1492    on automatically.
1493    
1494    =over 4
1495    
1496    =item SQL
1497    
1498    Traces SQL commands and activity.
1499    
1500    =item Tracer
1501    
1502    Traces error messages and call stacks.
1503    
1504    =back
1505    
1506    C<SQL> is only turned on if the C<-sql> option is specified in the command line.
1507    The trace level is specified using the C<-trace> command-line option. For example,
1508    the following command line for C<TransactFeatures> turns on SQL tracing and runs
1509    all tracing at level 3.
1510    
1511        TransactFeatures -trace=3 -sql register ../xacts IDs.tbl
1512    
1513    Standard tracing is output to the standard output and echoed to the file
1514    C<trace>I<$$>C<.log> in the FIG temporary directory, where I<$$> is the
1515    process ID. You can also specify the C<user> parameter to put a user ID
1516    instead of a process ID in the trace file name. So, for example
1517    
1518    The default trace level is 2. To get all messages, specify a trace level of 4.
1519    For a genome-by-genome update, use 3.
1520    
1521        TransactFeatures -trace=3 -sql -user=Bruce register ../xacts IDs.tbl
1522    
1523    would send the trace output to C<traceBruce.log> in the temporary directory.
1524    
1525    The I<options> parameter is a reference to a hash containing the command-line
1526    options, their default values, and an explanation of what they mean. Command-line
1527    options may be in the form of switches or keywords. In the case of a switch, the
1528    option value is 1 if it is specified and 0 if it is not specified. In the case
1529    of a keyword, the value is separated from the option name by an equal sign. You
1530    can see this last in the command-line example above.
1531    
1532    You can specify a different default trace level by setting C<$options->{trace}>
1533    prior to calling this method.
1534    
1535    An example at this point would help. Consider, for example, the command-line utility
1536    C<TransactFeatures>. It accepts a list of positional parameters plus the options
1537    C<safe>, C<noAlias>, C<start>, and C<tblFiles>. To start up this command, we execute
1538    the following code.
1539    
1540        my ($options, @parameters) = Tracer::StandardSetup(["DocUtils"],
1541                            { safe => [0, "use database transactions"],
1542                              noAlias => [0, "do not expect aliases in CHANGE transactions"],
1543                              start => [' ', "start with this genome"],
1544                              tblFiles => [0, "output TBL files containing the corrected IDs"] },
1545                            "<command> <transactionDirectory> <IDfile>",
1546                          @ARGV);
1547    
1548    
1549    The call to C<ParseCommand> specifies the default values for the options and
1550    stores the actual options in a hash that is returned as C<$options>. The
1551    positional parameters are returned in C<@parameters>.
1552    
1553    The following is a sample command line for C<TransactFeatures>.
1554    
1555        TransactFeatures -trace=2 -noAlias register ../xacts IDs.tbl
1556    
1557    Single and double hyphens are equivalent. So, you could also code the
1558    above command as
1559    
1560        TransactFeatures --trace=2 --noAlias register ../xacts IDs.tbl
1561    
1562    In this case, C<register>, C<../xacts>, and C<IDs.tbl> are the positional
1563    parameters, and would find themselves in I<@parameters> after executing the
1564    above code fragment. The tracing would be set to level 2, and the categories
1565    would be C<Tracer>, and <DocUtils>. C<Tracer> is standard,
1566    and C<DocUtils> was included because it came in within the first parameter
1567    to this method. The I<$options> hash would be
1568    
1569        { trace => 2, sql => 0, safe => 0,
1570          noAlias => 1, start => ' ', tblFiles => 0 }
1571    
1572    Use of C<StandardSetup> in this way provides a simple way of performing
1573    standard tracing setup and command-line parsing. Note that the caller is
1574    not even aware of the command-line switches C<-trace> and C<-sql>, which
1575    are used by this method to control the tracing. If additional tracing features
1576    need to be added in the future, they can be processed by this method without
1577    upsetting the command-line utilities.
1578    
1579    If the C<background> option is specified on the command line, then the
1580    standard and error outputs will be directed to files in the temporary
1581    directory, using the same suffix as the trace file. So, if the command
1582    line specified
1583    
1584        -user=Bruce -background
1585    
1586    then the trace output would go to C<traceBruce.log>, the standard output to
1587    C<outBruce.log>, and the error output to C<errBruce.log>. This is designed to
1588    simplify starting a command in the background.
1589    
1590    The user name is also used as the tracing key for L</Emergency Tracing>.
1591    Specifying a value of C<E> for the trace level causes emergency tracing to
1592    be used instead of custom tracing. If the user name is not specified,
1593    the tracing key is taken from the C<Tracing> environment variable. If there
1594    is no value for that variable, the tracing key will be computed from the active
1595    login ID.
1596    
1597    Since the default situation in StandardSetup is to trace to the standard
1598    output, errors that occur in command-line scripts will not generate
1599    RSS events. To force the events, use the C<warn> option.
1600    
1601        TransactFeatures -background -warn register ../xacts IDs.tbl
1602    
1603    Finally, if the special option C<-help> is specified, the option
1604    names will be traced at level 0 and the program will exit without processing.
1605    This provides a limited help capability. For example, if the user enters
1606    
1607        TransactFeatures -help
1608    
1609    he would see the following output.
1610    
1611        TransactFeatures [options] <command> <transactionDirectory> <IDfile>
1612            -trace    tracing level (default E)
1613            -sql      trace SQL commands
1614            -safe     use database transactions
1615            -noAlias  do not expect aliases in CHANGE transactions
1616            -start    start with this genome
1617            -tblFiles output TBL files containing the corrected IDs
1618            -forked   do not erase the trace file before tracing
1619    
1620    The caller has the option of modifying the tracing scheme by placing a value
1621    for C<trace> in the incoming options hash. The default value can be overridden,
1622    or the tracing to the standard output can be turned off by suffixing a minus
1623    sign to the trace level. So, for example,
1624    
1625        { trace => [0, "tracing level (default 0)"],
1626           ...
1627    
1628    would set the default trace level to 0 instead of E, while
1629    
1630        { trace => ["2-", "tracing level (default 2)"],
1631           ...
1632    
1633    would set the default to 2, but trace only to the log file, not to the
1634    standard output.
1635    
1636    The parameters to this method are as follows.
1637    
1638    =over 4
1639    
1640    =item categories
1641    
1642    Reference to a list of tracing category names. These should be names of
1643    packages whose internal workings will need to be debugged to get the
1644    command working.
1645    
1646    =item options
1647    
1648    Reference to a hash containing the legal options for the current command mapped
1649    to their default values and descriptions. The user can override the defaults
1650    by specifying the options as command-line switches prefixed by a hyphen.
1651    Tracing-related options may be added to this hash. If the C<-h> option is
1652    specified on the command line, the option descriptions will be used to
1653    explain the options. To turn off tracing to the standard output, add a
1654    minus sign to the value for C<trace> (see above).
1655    
1656    =item parmHelp
1657    
1658    A string that vaguely describes the positional parameters. This is used
1659    if the user specifies the C<-h> option.
1660    
1661    =item argv
1662    
1663    List of command line parameters, including the option switches, which must
1664    precede the positional parameters and be prefixed by a hyphen.
1665    
1666    =item RETURN
1667    
1668    Returns a list. The first element of the list is the reference to a hash that
1669    maps the command-line option switches to their values. These will either be the
1670    default values or overrides specified on the command line. The remaining
1671    elements of the list are the position parameters, in order.
1672    
1673    =back
1674    
1675    =cut
1676    
1677    sub StandardSetup {
1678        # Get the parameters.
1679        my ($categories, $options, $parmHelp, @argv) = @_;
1680        # Get the default tracing key.
1681        my $tkey = EmergencyKey();
1682        # Save the command line.
1683        $CommandLine = join(" ", $0, map { $_ =~ /\s/ ? "\"$_\"" : $_ } @argv);
1684        # Add the tracing options.
1685        if (! exists $options->{trace}) {
1686            $options->{trace} = ['2', "tracing level (E for emergency tracing)"];
1687        }
1688        if (! exists $options->{forked}) {
1689            $options->{forked} = [0, "keep old trace file"];
1690        }
1691        $options->{sql} = [0, "turn on SQL tracing"];
1692        $options->{help} = [0, "display command-line options"];
1693        $options->{user} = [$tkey, "tracing key"];
1694        $options->{background} = [0, "spool standard and error output"];
1695        $options->{warn} = [0, "send errors to RSS feed"];
1696        $options->{moreTracing} = ["", "comma-delimited list of additional trace modules for debugging"];
1697        # Create a parsing hash from the options hash. The parsing hash
1698        # contains the default values rather than the default value
1699        # and the description. While we're at it, we'll memorize the
1700        # length of the longest option name.
1701        my $longestName = 0;
1702        my %parseOptions = ();
1703        for my $key (keys %{$options}) {
1704            if (length $key > $longestName) {
1705                $longestName = length $key;
1706            }
1707            $parseOptions{$key} = $options->{$key}->[0];
1708        }
1709        # Parse the command line.
1710        my ($retOptions, @retParameters) = ParseCommand(\%parseOptions, @argv);
1711        # Get the logfile suffix.
1712        my $suffix = $retOptions->{user};
1713        # We'll put the trace file name in here. We need it later if background
1714        # mode is on.
1715        my $traceFileName;
1716        # Now we want to set up tracing. First, we need to know if the user
1717        # wants emergency tracing.
1718        if ($retOptions->{trace} eq 'E') {
1719            ETracing($retOptions->{user});
1720        } else {
1721            # Here the tracing is controlled from the command line.
1722            my @cats = @{$categories};
1723            if ($retOptions->{sql}) {
1724                push @cats, "SQL";
1725            }
1726            if ($retOptions->{warn}) {
1727                push @cats, "Feed";
1728            }
1729            # Add the default categories.
1730            push @cats, "Tracer";
1731            # Check for more tracing groups.
1732            if ($retOptions->{moreTracing}) {
1733                push @cats, split /,/, $retOptions->{moreTracing};
1734            }
1735            # Next, we create the category string by joining the categories.
1736            my $cats = join(" ", @cats);
1737            # Check to determine whether or not the caller wants to turn off tracing
1738            # to the standard output.
1739            my $traceLevel = $retOptions->{trace};
1740            my $textOKFlag = 1;
1741            if ($traceLevel =~ /^(.)-/) {
1742                $traceLevel = $1;
1743                $textOKFlag = 0;
1744            }
1745            # Now we set up the trace mode.
1746            my $traceMode;
1747            # Verify that we can open a file in the FIG temporary directory.
1748            my $traceFileName = "$FIG_Config::temp/trace$suffix.log";
1749            my $traceFileSpec = ($retOptions->{forked} ? ">>$traceFileName" : ">$traceFileName");
1750            if (open TESTTRACE, "$traceFileSpec") {
1751                # Here we can trace to a file.
1752                $traceMode = ">>$traceFileName";
1753                if ($textOKFlag) {
1754                    # Echo to standard output if the text-OK flag is set.
1755                    $traceMode = "+$traceMode";
1756                }
1757                # Close the test file.
1758                close TESTTRACE;
1759            } else {
1760                # Here we can't trace to a file. Complain about this.
1761                warn "Could not open trace file $traceFileName: $!\n";
1762                # We trace to the standard output if it's
1763                # okay, and the error log otherwise.
1764                if ($textOKFlag) {
1765                    $traceMode = "TEXT";
1766                } else {
1767                    $traceMode = "WARN";
1768                }
1769            }
1770            # Now set up the tracing.
1771            TSetup("$traceLevel $cats", $traceMode);
1772        }
1773        # Check for background mode.
1774        if ($retOptions->{background}) {
1775            my $outFileName = "$FIG_Config::temp/out$suffix$$.log";
1776            my $errFileName = "$FIG_Config::temp/err$suffix$$.log";
1777            # Spool the output.
1778            open STDOUT, ">$outFileName";
1779            # If we have a trace file, trace the errors to the log. Otherwise,
1780            # spool the errors.
1781            if (defined $traceFileName) {
1782                open STDERR, "| Tracer $traceFileName";
1783            } else {
1784                open STDERR, ">$errFileName";
1785            }
1786            # Check for phone support. If we have phone support and a phone number,
1787            # we want to turn it on.
1788            if ($ENV{PHONE} && defined($FIG_Config::phone)) {
1789                $retOptions->{phone} = $ENV{PHONE};
1790            }
1791        }
1792        # Check for the "help" option. If it is specified, dump the command-line
1793        # options and exit the program.
1794        if ($retOptions->{help}) {
1795            $0 =~ m#[/\\](\w+)(\.pl)?$#i;
1796            print "$1 [options] $parmHelp\n";
1797            for my $key (sort keys %{$options}) {
1798                my $name = Pad($key, $longestName, 0, ' ');
1799                my $desc = $options->{$key}->[1];
1800                if ($options->{$key}->[0]) {
1801                    $desc .= " (default " . $options->{$key}->[0] . ")";
1802                }
1803                print "  $name $desc\n";
1804            }
1805            exit(0);
1806        }
1807        # Trace the options, if applicable.
1808        if (T(3)) {
1809            my @parms = grep { $retOptions->{$_} } keys %{$retOptions};
1810            Trace("Selected options: " . join(", ", sort @parms) . ".");
1811        }
1812        # Return the parsed parameters.
1813        return ($retOptions, @retParameters);
1814    }
1815    
1816    =head3 ReadOptions
1817    
1818        my %options = Tracer::ReadOptions($fileName);
1819    
1820    Read a set of options from a file. Each option is encoded in a line of text that has the
1821    format
1822    
1823    I<optionName>C<=>I<optionValue>C<; >I<comment>
1824    
1825    The option name must consist entirely of letters, digits, and the punctuation characters
1826    C<.> and C<_>, and is case sensitive. Blank lines and lines in which the first nonblank
1827    character is a semi-colon will be ignored. The return hash will map each option name to
1828    the corresponding option value.
1829    
1830    =over 4
1831    
1832    =item fileName
1833    
1834    Name of the file containing the option data.
1835    
1836    =item RETURN
1837    
1838    Returns a hash mapping the option names specified in the file to their corresponding option
1839    value.
1840    
1841    =back
1842    
1843    =cut
1844    
1845    sub ReadOptions {
1846        # Get the parameters.
1847        my ($fileName) = @_;
1848        # Open the file.
1849        (open CONFIGFILE, "<$fileName") || Confess("Could not open option file $fileName.");
1850        # Count the number of records read.
1851        my ($records, $comments) = 0;
1852        # Create the return hash.
1853        my %retVal = ();
1854        # Loop through the file, accumulating key-value pairs.
1855        while (my $line = <CONFIGFILE>) {
1856            # Denote we've read a line.
1857            $records++;
1858            # Determine the line type.
1859            if ($line =~ /^\s*[\n\r]/) {
1860                # A blank line is a comment.
1861                $comments++;
1862            } elsif ($line =~ /^\s*([A-Za-z0-9_\.]+)=([^;]*);/) {
1863                # Here we have an option assignment.
1864                retVal{$1} = $2;
1865            } elsif ($line =~ /^\s*;/) {
1866                # Here we have a text comment.
1867                $comments++;
1868            } else {
1869                # Here we have an invalid line.
1870                Trace("Invalid option statement in record $records.") if T(0);
1871            }
1872        }
1873        # Return the hash created.
1874        return %retVal;
1875    }
1876    
1877    =head3 GetOptions
1878    
1879        Tracer::GetOptions(\%defaults, \%options);
1880    
1881    Merge a specified set of options into a table of defaults. This method takes two hash references
1882    as input and uses the data from the second to update the first. If the second does not exist,
1883    there will be no effect. An error will be thrown if one of the entries in the second hash does not
1884    exist in the first.
1885    
1886    Consider the following example.
1887    
1888        my $optionTable = GetOptions({ dbType => 'mySQL', trace => 0 }, $options);
1889    
1890    In this example, the variable B<$options> is expected to contain at most two options-- B<dbType> and
1891    B<trace>. The default database type is C<mySQL> and the default trace level is C<0>. If the value of
1892    B<$options> is C<< {dbType => 'Oracle'} >>, then the database type will be changed to C<Oracle> and
1893    the trace level will remain at 0. If B<$options> is undefined, then the database type and trace level
1894    will remain C<mySQL> and C<0>. If, on the other hand, B<$options> is defined as
1895    
1896        {databaseType => 'Oracle'}
1897    
1898    an error will occur because the B<databaseType> option does not exist.
1899    
1900    =over 4
1901    
1902    =item defaults
1903    
1904    Table of default option values.
1905    
1906    =item options
1907    
1908    Table of overrides, if any.
1909    
1910    =item RETURN
1911    
1912    Returns a reference to the default table passed in as the first parameter.
1913    
1914    =back
1915    
1916    =cut
1917    
1918    sub GetOptions {
1919        # Get the parameters.
1920        my ($defaults, $options) = @_;
1921        # Check for overrides.
1922        if ($options) {
1923            # Loop through the overrides.
1924            while (my ($option, $setting) = each %{$options}) {
1925                # Insure this override exists.
1926                if (!exists $defaults->{$option}) {
1927                    croak "Unrecognized option $option encountered.";
1928                } else {
1929                    # Apply the override.
1930                    $defaults->{$option} = $setting;
1931                }
1932            }
1933        }
1934        # Return the merged table.
1935        return $defaults;
1936    }
1937    
1938    =head3 MergeOptions
1939    
1940        Tracer::MergeOptions(\%table, \%defaults);
1941    
1942    Merge default values into a hash table. This method looks at the key-value pairs in the
1943    second (default) hash, and if a matching key is not found in the first hash, the default
1944    pair is copied in. The process is similar to L</GetOptions>, but there is no error-
1945    checking and no return value.
1946    
1947    =over 4
1948    
1949    =item table
1950    
1951    Hash table to be updated with the default values.
1952    
1953    =item defaults
1954    
1955    Default values to be merged into the first hash table if they are not already present.
1956    
1957    =back
1958    
1959    =cut
1960    
1961    sub MergeOptions {
1962        # Get the parameters.
1963        my ($table, $defaults) = @_;
1964        # Loop through the defaults.
1965        while (my ($key, $value) = each %{$defaults}) {
1966            if (!exists $table->{$key}) {
1967                $table->{$key} = $value;
1968            }
1969        }
1970    }
1971    
1972    =head3 UnparseOptions
1973    
1974        my $optionString = Tracer::UnparseOptions(\%options);
1975    
1976    Convert an option hash into a command-line string. This will not
1977    necessarily be the same text that came in, but it will nonetheless
1978    produce the same ultimate result when parsed by L</StandardSetup>.
1979    
1980    =over 4
1981    
1982    =item options
1983    
1984    Reference to a hash of options to convert into an option string.
1985    
1986    =item RETURN
1987    
1988    Returns a string that will parse to the same set of options when
1989    parsed by L</StandardSetup>.
1990    
1991    =back
1992    
1993    =cut
1994    
1995    sub UnparseOptions {
1996        # Get the parameters.
1997        my ($options) = @_;
1998        # The option segments will be put in here.
1999        my @retVal = ();
2000        # Loop through the options.
2001        for my $key (keys %$options) {
2002            # Get the option value.
2003            my $value = $options->{$key};
2004            # Only use it if it's nonempty.
2005            if (defined $value && $value ne "") {
2006                my $segment = "--$key=$value";
2007                # Quote it if necessary.
2008                if ($segment =~ /[ |<>*]/) {
2009                    $segment = '"' . $segment . '"';
2010                }
2011                # Add it to the return list.
2012                push @retVal, $segment;
2013            }
2014        }
2015        # Return the result.
2016        return join(" ", @retVal);
2017    }
2018    
2019    =head3 ParseCommand
2020    
2021        my ($options, @arguments) = Tracer::ParseCommand(\%optionTable, @inputList);
2022    
2023    Parse a command line consisting of a list of parameters. The initial parameters may be option
2024    specifiers of the form C<->I<option> or C<->I<option>C<=>I<value>. The options are stripped
2025    off and merged into a table of default options. The remainder of the command line is
2026    returned as a list of positional arguments. For example, consider the following invocation.
2027    
2028        my ($options, @arguments) = ParseCommand({ errors => 0, logFile => 'trace.log'}, @words);
2029    
2030    In this case, the list @words will be treated as a command line and there are two options available,
2031    B<errors> and B<logFile>. If @words has the following format
2032    
2033        -logFile=error.log apple orange rutabaga
2034    
2035    then at the end of the invocation, C<$options> will be
2036    
2037        { errors => 0, logFile => 'error.log' }
2038    
2039    and C<@arguments> will contain
2040    
2041        apple orange rutabaga
2042    
2043    The parser allows for some escape sequences. See L</UnEscape> for a description. There is no
2044    support for quote characters. Options can be specified with single or double hyphens.
2045    
2046    =over 4
2047    
2048    =item optionTable
2049    
2050    Table of default options.
2051    
2052    =item inputList
2053    
2054    List of words on the command line.
2055    
2056    =item RETURN
2057    
2058    Returns a reference to the option table and a list of the positional arguments.
2059    
2060    =back
2061    
2062    =cut
2063    
2064    sub ParseCommand {
2065        # Get the parameters.
2066        my ($optionTable, @inputList) = @_;
2067        # Process any options in the input list.
2068          my %overrides = ();          my %overrides = ();
2069          while ((@inputList > 0) && ($inputList[0] =~ /^-/)) {      while ((@inputList > 0) && ($inputList[0] =~ /^--?/)) {
2070                  # Get the current option.                  # Get the current option.
2071                  my $arg = shift @inputList;                  my $arg = shift @inputList;
2072                  # Pull out the option name.                  # Pull out the option name.
2073                  $arg =~ /^-([^=]*)/g;          $arg =~ /^--?([^=]*)/g;
2074                  my $name = $1;                  my $name = $1;
2075                  # Check for an option value.                  # Check for an option value.
2076                  if ($arg =~ /\G=(.*)$/g) {                  if ($arg =~ /\G=(.*)$/g) {
2077                          # Here we have a value for the option.                          # Here we have a value for the option.
2078                          $overrides{$name} = UnEscape($1);                          $overrides{$name} = UnEscape($1);
2079                  } else {                  } else {
2080                          # Here there is no value, so we use 1.              # Here there is no value, so we use 1.
2081                          $overrides{$name} = 1;              $overrides{$name} = 1;
2082            }
2083        }
2084        # Merge the options into the defaults.
2085        GetOptions($optionTable, \%overrides);
2086        # Translate the remaining parameters.
2087        my @retVal = ();
2088        for my $inputParm (@inputList) {
2089            push @retVal, UnEscape($inputParm);
2090        }
2091        # Return the results.
2092        return ($optionTable, @retVal);
2093    }
2094    
2095    
2096    =head2 File Utility Methods
2097    
2098    =head3 GetFile
2099    
2100        my @fileContents = Tracer::GetFile($fileName);
2101    
2102        or
2103    
2104        my $fileContents = Tracer::GetFile($fileName);
2105    
2106    Return the entire contents of a file. In list context, line-ends are removed and
2107    each line is a list element. In scalar context, line-ends are replaced by C<\n>.
2108    
2109    =over 4
2110    
2111    =item fileName
2112    
2113    Name of the file to read.
2114    
2115    =item RETURN
2116    
2117    In a list context, returns the entire file as a list with the line terminators removed.
2118    In a scalar context, returns the entire file as a string. If an error occurs opening
2119    the file, an empty list will be returned.
2120    
2121    =back
2122    
2123    =cut
2124    
2125    sub GetFile {
2126        # Get the parameters.
2127        my ($fileName) = @_;
2128        # Declare the return variable.
2129        my @retVal = ();
2130        # Open the file for input.
2131        my $handle = Open(undef, "<$fileName");
2132        # Read the whole file into the return variable, stripping off any terminator
2133        # characters.
2134        my $lineCount = 0;
2135        while (my $line = <$handle>) {
2136            $lineCount++;
2137            $line = Strip($line);
2138            push @retVal, $line;
2139        }
2140        # Close it.
2141        close $handle;
2142        my $actualLines = @retVal;
2143        Trace("$actualLines lines read from file $fileName.") if T(File => 2);
2144        # Return the file's contents in the desired format.
2145        if (wantarray) {
2146            return @retVal;
2147        } else {
2148            return join "\n", @retVal;
2149        }
2150    }
2151    
2152    =head3 PutFile
2153    
2154        Tracer::PutFile($fileName, \@lines);
2155    
2156    Write out a file from a list of lines of text.
2157    
2158    =over 4
2159    
2160    =item fileName
2161    
2162    Name of the output file.
2163    
2164    =item lines
2165    
2166    Reference to a list of text lines. The lines will be written to the file in order, with trailing
2167    new-line characters. Alternatively, may be a string, in which case the string will be written without
2168    modification.
2169    
2170    =back
2171    
2172    =cut
2173    
2174    sub PutFile {
2175        # Get the parameters.
2176        my ($fileName, $lines) = @_;
2177        # Open the output file.
2178        my $handle = Open(undef, ">$fileName");
2179        # Count the lines written.
2180        if (ref $lines ne 'ARRAY') {
2181            # Here we have a scalar, so we write it raw.
2182            print $handle $lines;
2183            Trace("Scalar put to file $fileName.") if T(File => 3);
2184        } else {
2185            # Write the lines one at a time.
2186            my $count = 0;
2187            for my $line (@{$lines}) {
2188                print $handle "$line\n";
2189                $count++;
2190            }
2191            Trace("$count lines put to file $fileName.") if T(File => 3);
2192        }
2193        # Close the output file.
2194        close $handle;
2195    }
2196    
2197    =head3 ParseRecord
2198    
2199        my @fields = Tracer::ParseRecord($line);
2200    
2201    Parse a tab-delimited data line. The data line is split into field values. Embedded tab
2202    and new-line characters in the data line must be represented as C<\t> and C<\n>, respectively.
2203    These will automatically be converted.
2204    
2205    =over 4
2206    
2207    =item line
2208    
2209    Line of data containing the tab-delimited fields.
2210    
2211    =item RETURN
2212    
2213    Returns a list of the fields found in the data line.
2214    
2215    =back
2216    
2217    =cut
2218    
2219    sub ParseRecord {
2220        # Get the parameter.
2221        my ($line) = @_;
2222        # Remove the trailing new-line, if any.
2223        chomp $line;
2224        # Split the line read into pieces using the tab character.
2225        my @retVal = split /\t/, $line;
2226        # Trim and fix the escapes in each piece.
2227        for my $value (@retVal) {
2228            # Trim leading whitespace.
2229            $value =~ s/^\s+//;
2230            # Trim trailing whitespace.
2231            $value =~ s/\s+$//;
2232            # Delete the carriage returns.
2233            $value =~ s/\r//g;
2234            # Convert the escapes into their real values.
2235            $value =~ s/\\t/"\t"/ge;
2236            $value =~ s/\\n/"\n"/ge;
2237        }
2238        # Return the result.
2239        return @retVal;
2240    }
2241    
2242    =head3 Merge
2243    
2244        my @mergedList = Tracer::Merge(@inputList);
2245    
2246    Sort a list of strings and remove duplicates.
2247    
2248    =over 4
2249    
2250    =item inputList
2251    
2252    List of scalars to sort and merge.
2253    
2254    =item RETURN
2255    
2256    Returns a list containing the same elements sorted in ascending order with duplicates
2257    removed.
2258    
2259    =back
2260    
2261    =cut
2262    
2263    sub Merge {
2264        # Get the input list in sort order.
2265        my @inputList = sort @_;
2266        # Only proceed if the list has at least two elements.
2267        if (@inputList > 1) {
2268            # Now we want to move through the list splicing out duplicates.
2269            my $i = 0;
2270            while ($i < @inputList) {
2271                # Get the current entry.
2272                my $thisEntry = $inputList[$i];
2273                # Find out how many elements duplicate the current entry.
2274                my $j = $i + 1;
2275                my $dup1 = $i + 1;
2276                while ($j < @inputList && $inputList[$j] eq $thisEntry) { $j++; };
2277                # If the number is nonzero, splice out the duplicates found.
2278                if ($j > $dup1) {
2279                    splice @inputList, $dup1, $j - $dup1;
2280                }
2281                # Now the element at position $dup1 is different from the element before it
2282                # at position $i. We push $i forward one position and start again.
2283                $i++;
2284            }
2285        }
2286        # Return the merged list.
2287        return @inputList;
2288    }
2289    
2290    =head3 Open
2291    
2292        my $handle = Open($fileHandle, $fileSpec, $message);
2293    
2294    Open a file.
2295    
2296    The I<$fileSpec> is essentially the second argument of the PERL C<open>
2297    function. The mode is specified using Unix-like shell information. So, for
2298    example,
2299    
2300        Open(\*LOGFILE, '>>/usr/spool/news/twitlog', "Could not open twit log.");
2301    
2302    would open for output appended to the specified file, and
2303    
2304        Open(\*DATASTREAM, "| sort -u >$outputFile", "Could not open $outputFile.");
2305    
2306    would open a pipe that sorts the records written and removes duplicates. Note
2307    the use of file handle syntax in the Open call. To use anonymous file handles,
2308    code as follows.
2309    
2310        my $logFile = Open(undef, '>>/usr/spool/news/twitlog', "Could not open twit log.");
2311    
2312    The I<$message> parameter is used if the open fails. If it is set to C<0>, then
2313    the open returns TRUE if successful and FALSE if an error occurred. Otherwise, a
2314    failed open will throw an exception and the third parameter will be used to construct
2315    an error message. If the parameter is omitted, a standard message is constructed
2316    using the file spec.
2317    
2318        Could not open "/usr/spool/news/twitlog"
2319    
2320    Note that the mode characters are automatically cleaned from the file name.
2321    The actual error message from the file system will be captured and appended to the
2322    message in any case.
2323    
2324        Could not open "/usr/spool/news/twitlog": file not found.
2325    
2326    In some versions of PERL the only error message we get is a number, which
2327    corresponds to the C++ C<errno> value.
2328    
2329        Could not open "/usr/spool/news/twitlog": 6.
2330    
2331    =over 4
2332    
2333    =item fileHandle
2334    
2335    File handle. If this parameter is C<undef>, a file handle will be generated
2336    and returned as the value of this method.
2337    
2338    =item fileSpec
2339    
2340    File name and mode, as per the PERL C<open> function.
2341    
2342    =item message (optional)
2343    
2344    Error message to use if the open fails. If omitted, a standard error message
2345    will be generated. In either case, the error information from the file system
2346    is appended to the message. To specify a conditional open that does not throw
2347    an error if it fails, use C<0>.
2348    
2349    =item RETURN
2350    
2351    Returns the name of the file handle assigned to the file, or C<undef> if the
2352    open failed.
2353    
2354    =back
2355    
2356    =cut
2357    
2358    sub Open {
2359        # Get the parameters.
2360        my ($fileHandle, $fileSpec, $message) = @_;
2361        # Attempt to open the file.
2362        my $rv = open $fileHandle, $fileSpec;
2363        # If the open failed, generate an error message.
2364        if (! $rv) {
2365            # Save the system error message.
2366            my $sysMessage = $!;
2367            # See if we need a default message.
2368            if (!$message) {
2369                # Clean any obvious mode characters and leading spaces from the
2370                # filename.
2371                my ($fileName) = FindNamePart($fileSpec);
2372                $message = "Could not open \"$fileName\"";
2373            }
2374            # Terminate with an error using the supplied message and the
2375            # error message from the file system.
2376            Confess("$message: $!");
2377        }
2378        # Return the file handle.
2379        return $fileHandle;
2380    }
2381    
2382    =head3 FindNamePart
2383    
2384        my ($fileName, $start, $len) = Tracer::FindNamePart($fileSpec);
2385    
2386    Extract the portion of a file specification that contains the file name.
2387    
2388    A file specification is the string passed to an C<open> call. It specifies the file
2389    mode and name. In a truly complex situation, it can specify a pipe sequence. This
2390    method assumes that the file name is whatever follows the first angle bracket
2391    sequence.  So, for example, in the following strings the file name is
2392    C</usr/fig/myfile.txt>.
2393    
2394        >>/usr/fig/myfile.txt
2395        </usr/fig/myfile.txt
2396        | sort -u > /usr/fig/myfile.txt
2397    
2398    If the method cannot find a file name using its normal methods, it will return the
2399    whole incoming string.
2400    
2401    =over 4
2402    
2403    =item fileSpec
2404    
2405    File specification string from which the file name is to be extracted.
2406    
2407    =item RETURN
2408    
2409    Returns a three-element list. The first element contains the file name portion of
2410    the specified string, or the whole string if a file name cannot be found via normal
2411    methods. The second element contains the start position of the file name portion and
2412    the third element contains the length.
2413    
2414    =back
2415    
2416    =cut
2417    #: Return Type $;
2418    sub FindNamePart {
2419        # Get the parameters.
2420        my ($fileSpec) = @_;
2421        # Default to the whole input string.
2422        my ($retVal, $pos, $len) = ($fileSpec, 0, length $fileSpec);
2423        # Parse out the file name if we can.
2424        if ($fileSpec =~ m/(<|>>?)(.+?)(\s*)$/) {
2425            $retVal = $2;
2426            $len = length $retVal;
2427            $pos = (length $fileSpec) - (length $3) - $len;
2428        }
2429        # Return the result.
2430        return ($retVal, $pos, $len);
2431    }
2432    
2433    =head3 OpenDir
2434    
2435        my @files = OpenDir($dirName, $filtered, $flag);
2436    
2437    Open a directory and return all the file names. This function essentially performs
2438    the functions of an C<opendir> and C<readdir>. If the I<$filtered> parameter is
2439    set to TRUE, all filenames beginning with a period (C<.>), dollar sign (C<$>),
2440    or pound sign (C<#>) and all filenames ending with a tilde C<~>) will be
2441    filtered out of the return list. If the directory does not open and I<$flag> is not
2442    set, an exception is thrown. So, for example,
2443    
2444        my @files = OpenDir("/Volumes/fig/contigs", 1);
2445    
2446    is effectively the same as
2447    
2448        opendir(TMP, "/Volumes/fig/contigs") || Confess("Could not open /Volumes/fig/contigs.");
2449        my @files = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir(TMP);
2450    
2451    Similarly, the following code
2452    
2453        my @files = grep { $_ =~ /^\d/ } OpenDir("/Volumes/fig/orgs", 0, 1);
2454    
2455    Returns the names of all files in C</Volumes/fig/orgs> that begin with digits and
2456    automatically returns an empty list if the directory fails to open.
2457    
2458    =over 4
2459    
2460    =item dirName
2461    
2462    Name of the directory to open.
2463    
2464    =item filtered
2465    
2466    TRUE if files whose names begin with a period (C<.>) should be automatically removed
2467    from the list, else FALSE.
2468    
2469    =item flag
2470    
2471    TRUE if a failure to open is okay, else FALSE
2472    
2473    =back
2474    
2475    =cut
2476    #: Return Type @;
2477    sub OpenDir {
2478        # Get the parameters.
2479        my ($dirName, $filtered, $flag) = @_;
2480        # Declare the return variable.
2481        my @retVal = ();
2482        # Open the directory.
2483        if (opendir(my $dirHandle, $dirName)) {
2484            # The directory opened successfully. Get the appropriate list according to the
2485            # strictures of the filter parameter.
2486            if ($filtered) {
2487                @retVal = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir $dirHandle;
2488            } else {
2489                @retVal = readdir $dirHandle;
2490            }
2491        } elsif (! $flag) {
2492            # Here the directory would not open and it's considered an error.
2493            Confess("Could not open directory $dirName.");
2494        }
2495        # Return the result.
2496        return @retVal;
2497    }
2498    
2499    
2500    =head3 Insure
2501    
2502        Insure($dirName, $chmod);
2503    
2504    Insure a directory is present.
2505    
2506    =over 4
2507    
2508    =item dirName
2509    
2510    Name of the directory to check. If it does not exist, it will be created.
2511    
2512    =item chmod (optional)
2513    
2514    Security privileges to be given to the directory if it is created.
2515    
2516    =back
2517    
2518    =cut
2519    
2520    sub Insure {
2521        my ($dirName, $chmod) = @_;
2522        if (! -d $dirName) {
2523            Trace("Creating $dirName directory.") if T(2);
2524            eval {
2525                mkpath $dirName;
2526                # If we have permissions specified, set them here.
2527                if (defined($chmod)) {
2528                    chmod $chmod, $dirName;
2529                }
2530            };
2531            if ($@) {
2532                Confess("Error creating $dirName: $@");
2533            }
2534        }
2535    }
2536    
2537    =head3 ChDir
2538    
2539        ChDir($dirName);
2540    
2541    Change to the specified directory.
2542    
2543    =over 4
2544    
2545    =item dirName
2546    
2547    Name of the directory to which we want to change.
2548    
2549    =back
2550    
2551    =cut
2552    
2553    sub ChDir {
2554        my ($dirName) = @_;
2555        if (! -d $dirName) {
2556            Confess("Cannot change to directory $dirName: no such directory.");
2557        } else {
2558            Trace("Changing to directory $dirName.") if T(File => 4);
2559            my $okFlag = chdir $dirName;
2560            if (! $okFlag) {
2561                Confess("Error switching to directory $dirName.");
2562            }
2563        }
2564    }
2565    
2566    =head3 SetPermissions
2567    
2568        Tracer::SetPermissions($dirName, $group, $mask, %otherMasks);
2569    
2570    Set the permissions for a directory and all the files and folders inside it.
2571    In addition, the group ownership will be changed to the specified value.
2572    
2573    This method is more vulnerable than most to permission and compatability
2574    problems, so it does internal error recovery.
2575    
2576    =over 4
2577    
2578    =item dirName
2579    
2580    Name of the directory to process.
2581    
2582    =item group
2583    
2584    Name of the group to be assigned.
2585    
2586    =item mask
2587    
2588    Permission mask. Bits that are C<1> in this mask will be ORed into the
2589    permission bits of any file or directory that does not already have them
2590    set to 1.
2591    
2592    =item otherMasks
2593    
2594    Map of search patterns to permission masks. If a directory name matches
2595    one of the patterns, that directory and all its members and subdirectories
2596    will be assigned the new pattern. For example, the following would
2597    assign 0664 to most files, but would use 0777 for directories named C<tmp>.
2598    
2599        Tracer::SetPermissions($dirName, 'fig', 01664, '^tmp$' => 01777);
2600    
2601    The list is ordered, so the following would use 0777 for C<tmp1> and
2602    0666 for C<tmp>, C<tmp2>, or C<tmp3>.
2603    
2604        Tracer::SetPermissions($dirName, 'fig', 01664, '^tmp1' => 0777,
2605                                                       '^tmp' => 0666);
2606    
2607    Note that the pattern matches are all case-insensitive, and only directory
2608    names are matched, not file names.
2609    
2610    =back
2611    
2612    =cut
2613    
2614    sub SetPermissions {
2615        # Get the parameters.
2616        my ($dirName, $group, $mask, @otherMasks) = @_;
2617        # Set up for error recovery.
2618        eval {
2619            # Switch to the specified directory.
2620            ChDir($dirName);
2621            # Get the group ID.
2622            my $gid = getgrnam($group);
2623            # Get the mask for tracing.
2624            my $traceMask = sprintf("%04o", $mask) . "($mask)";
2625            Trace("Fixing permissions for directory $dirName using group $group($gid) and mask $traceMask.") if T(File => 2);
2626            my $fixCount = 0;
2627            my $lookCount = 0;
2628            # @dirs will be a stack of directories to be processed.
2629            my @dirs = (getcwd());
2630            while (scalar(@dirs) > 0) {
2631                # Get the current directory.
2632                my $dir = pop @dirs;
2633                # Check for a match to one of the specified directory names. To do
2634                # that, we need to pull the individual part of the name off of the
2635                # whole path.
2636                my $simpleName = $dir;
2637                if ($dir =~ m!/([^/]+)$!) {
2638                    $simpleName = $1;
2639                }
2640                Trace("Simple directory name for $dir is $simpleName.") if T(File => 4);
2641                # Search for a match.
2642                my $match = 0;
2643                my $i;
2644                for ($i = 0; $i < $#otherMasks && ! $match; $i += 2) {
2645                    my $pattern = $otherMasks[$i];
2646                    if ($simpleName =~ /$pattern/i) {
2647                        $match = 1;
2648                    }
2649                }
2650                # Find out if we have a match. Note we use $i-1 because the loop added 2
2651                # before terminating due to the match.
2652                if ($match && $otherMasks[$i-1] != $mask) {
2653                    # This directory matches one of the incoming patterns, and it's
2654                    # a different mask, so we process it recursively with that mask.
2655                    SetPermissions($dir, $group, $otherMasks[$i-1], @otherMasks);
2656                } else {
2657                    # Here we can process normally. Get all of the non-hidden members.
2658                    my @submems = OpenDir($dir, 1);
2659                    for my $submem (@submems) {
2660                        # Get the full name.
2661                        my $thisMem = "$dir/$submem";
2662                        Trace("Checking member $thisMem.") if T(4);
2663                        $lookCount++;
2664                        if ($lookCount % 1000 == 0) {
2665                            Trace("$lookCount members examined. Current is $thisMem. Mask is $traceMask") if T(File => 3);
2666                        }
2667                        # Fix the group.
2668                        chown -1, $gid, $thisMem;
2669                        # Insure this member is not a symlink.
2670                        if (! -l $thisMem) {
2671                            # Get its info.
2672                            my $fileInfo = stat $thisMem;
2673                            # Only proceed if we got the info. Otherwise, it's a hard link
2674                            # and we want to skip it anyway.
2675                            if ($fileInfo) {
2676                                my $fileMode = $fileInfo->mode;
2677                                if (($fileMode & $mask) != $mask) {
2678                                    # Fix this member.
2679                                    $fileMode |= $mask;
2680                                    chmod $fileMode, $thisMem;
2681                                    $fixCount++;
2682                                }
2683                                # If it's a subdirectory, stack it.
2684                                if (-d $thisMem) {
2685                                    push @dirs, $thisMem;
2686                                }
2687                            }
2688                        }
2689                    }
2690                }
2691            }
2692            Trace("$lookCount files and directories processed, $fixCount fixed.") if T(File => 2);
2693        };
2694        # Check for an error.
2695        if ($@) {
2696            Confess("SetPermissions error: $@");
2697        }
2698    }
2699    
2700    =head3 GetLine
2701    
2702        my @data = Tracer::GetLine($handle);
2703    
2704    Read a line of data from a tab-delimited file.
2705    
2706    =over 4
2707    
2708    =item handle
2709    
2710    Open file handle from which to read.
2711    
2712    =item RETURN
2713    
2714    Returns a list of the fields in the record read. The fields are presumed to be
2715    tab-delimited. If we are at the end of the file, then an empty list will be
2716    returned. If an empty line is read, a single list item consisting of a null
2717    string will be returned.
2718    
2719    =back
2720    
2721    =cut
2722    
2723    sub GetLine {
2724        # Get the parameters.
2725        my ($handle) = @_;
2726        # Declare the return variable.
2727        my @retVal = ();
2728        Trace("File position is " . tell($handle) . ". EOF flag is " . eof($handle) . ".") if T(File => 4);
2729        # Read from the file.
2730        my $line = <$handle>;
2731        # Only proceed if we found something.
2732        if (defined $line) {
2733            # Remove the new-line. We are a bit over-cautious here because the file may be coming in via an
2734            # upload control and have a nonstandard EOL combination.
2735            $line =~ s/(\r|\n)+$//;
2736            # Here we do some fancy tracing to help in debugging complicated EOL marks.
2737            if (T(File => 4)) {
2738                my $escapedLine = $line;
2739                $escapedLine =~ s/\n/\\n/g;
2740                $escapedLine =~ s/\r/\\r/g;
2741                $escapedLine =~ s/\t/\\t/g;
2742                Trace("Line read: -->$escapedLine<--");
2743            }
2744            # If the line is empty, return a single empty string; otherwise, parse
2745            # it into fields.
2746            if ($line eq "") {
2747                push @retVal, "";
2748            } else {
2749                push @retVal, split /\t/,$line;
2750            }
2751        } else {
2752            # Trace the reason the read failed.
2753            Trace("End of file: $!") if T(File => 3);
2754        }
2755        # Return the result.
2756        return @retVal;
2757    }
2758    
2759    =head3 PutLine
2760    
2761        Tracer::PutLine($handle, \@fields, $eol);
2762    
2763    Write a line of data to a tab-delimited file. The specified field values will be
2764    output in tab-separated form, with a trailing new-line.
2765    
2766    =over 4
2767    
2768    =item handle
2769    
2770    Output file handle.
2771    
2772    =item fields
2773    
2774    List of field values.
2775    
2776    =item eol (optional)
2777    
2778    End-of-line character (default is "\n").
2779    
2780    =back
2781    
2782    =cut
2783    
2784    sub PutLine {
2785        # Get the parameters.
2786        my ($handle, $fields, $eol) = @_;
2787        # Write the data.
2788        print $handle join("\t", @{$fields}) . ($eol || "\n");
2789    }
2790    
2791    
2792    =head3 PrintLine
2793    
2794        Tracer::PrintLine($line);
2795    
2796    Print a line of text with a trailing new-line.
2797    
2798    =over 4
2799    
2800    =item line
2801    
2802    Line of text to print.
2803    
2804    =back
2805    
2806    =cut
2807    
2808    sub PrintLine {
2809        # Get the parameters.
2810        my ($line) = @_;
2811        # Print the line.
2812        print "$line\n";
2813    }
2814    
2815    
2816    =head2 Other Useful Methods
2817    
2818    =head3 ParseParm
2819    
2820        my $listValue = Tracer::ParseParm($string);
2821    
2822    Convert a parameter into a list reference. If the parameter is undefined,
2823    an undefined value will be returned. Otherwise, it will be parsed as a
2824    comma-separated list of values.
2825    
2826    =over 4
2827    
2828    =item string
2829    
2830    Incoming string.
2831    
2832    =item RETURN
2833    
2834    Returns a reference to a list of values, or C<undef> if the incoming value
2835    was undefined.
2836    
2837    =back
2838    
2839    =cut
2840    
2841    sub ParseParm {
2842        # Get the parameters.
2843        my ($string) = @_;
2844        # Declare the return variable.
2845        my $retVal;
2846        # Check for data.
2847        if (defined $string) {
2848            # We have some, so split it into a list.
2849            $retVal = [ split /\s*,\s*/, $string];
2850                  }                  }
2851        # Return the result.
2852        return $retVal;
2853          }          }
2854          # Merge the options into the defaults.  
2855          GetOptions($optionTable, \%overrides);  =head3 Now
2856          # Translate the remaining parameters.  
2857          my @retVal = ();      my $string = Tracer::Now();
2858          for my $inputParm (@inputList) {  
2859                  push @retVal, UnEscape($inputParm);  Return a displayable time stamp containing the local time. Whatever format this
2860    method produces must be parseable by L</ParseDate>.
2861    
2862    =cut
2863    
2864    sub Now {
2865        return DisplayTime(time);
2866          }          }
2867          # Return the results.  
2868          return ($optionTable, @retVal);  =head3 DisplayTime
2869    
2870        my $string = Tracer::DisplayTime($time);
2871    
2872    Convert a time value to a displayable time stamp. Whatever format this
2873    method produces must be parseable by L</ParseDate>.
2874    
2875    =over 4
2876    
2877    =item time
2878    
2879    Time to display, in seconds since the epoch, or C<undef> if the time is unknown.
2880    
2881    =item RETURN
2882    
2883    Returns a displayable time, or C<(n/a)> if the incoming time is undefined.
2884    
2885    =back
2886    
2887    =cut
2888    
2889    sub DisplayTime {
2890        my ($time) = @_;
2891        my $retVal = "(n/a)";
2892        if (defined $time) {
2893            my ($sec,$min,$hour,$mday,$mon,$year,$wday,$yday,$isdst) = localtime($time);
2894            $retVal = _p2($mon+1) . "/" . _p2($mday) . "/" . ($year + 1900) . " " .
2895                      _p2($hour) . ":" . _p2($min) . ":" . _p2($sec);
2896        }
2897        return $retVal;
2898    }
2899    
2900    # Pad a number to 2 digits.
2901    sub _p2 {
2902        my ($value) = @_;
2903        $value = "0$value" if ($value < 10);
2904        return $value;
2905    }
2906    
2907    =head3 Escape
2908    
2909        my $codedString = Tracer::Escape($realString);
2910    
2911    Escape a string for use in a command. Tabs will be replaced by C<\t>, new-lines
2912    replaced by C<\n>, carriage returns will be deleted, and backslashes will be doubled. The
2913    result is to reverse the effect of L</UnEscape>.
2914    
2915    =over 4
2916    
2917    =item realString
2918    
2919    String to escape.
2920    
2921    =item RETURN
2922    
2923    Escaped equivalent of the real string.
2924    
2925    =back
2926    
2927    =cut
2928    
2929    sub Escape {
2930        # Get the parameter.
2931        my ($realString) = @_;
2932        # Initialize the return variable.
2933        my $retVal = "";
2934        # Loop through the parameter string, looking for sequences to escape.
2935        while (length $realString > 0) {
2936            # Look for the first sequence to escape.
2937            if ($realString =~ /^(.*?)([\n\t\r\\])/) {
2938                # Here we found it. The text preceding the sequence is in $1. The sequence
2939                # itself is in $2. First, move the clear text to the return variable.
2940                $retVal .= $1;
2941                # Strip the processed section off the real string.
2942                $realString = substr $realString, (length $2) + (length $1);
2943                # Get the matched character.
2944                my $char = $2;
2945                # If we have a CR, we are done.
2946                if ($char ne "\r") {
2947                    # It's not a CR, so encode the escape sequence.
2948                    $char =~ tr/\t\n/tn/;
2949                    $retVal .= "\\" . $char;
2950                }
2951            } else {
2952                # Here there are no more escape sequences. The rest of the string is
2953                # transferred unmodified.
2954                $retVal .= $realString;
2955                $realString = "";
2956            }
2957        }
2958        # Return the result.
2959        return $retVal;
2960  }  }
2961    
2962  =head3 UnEscape  =head3 UnEscape
2963    
2964  C<< my $realString = Tracer::UnEscape($codedString); >>      my $realString = Tracer::UnEscape($codedString);
2965    
2966  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
2967  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
2968    be deleted.
2969    
2970  =over 4  =over 4
2971    
# Line 555  Line 2987 
2987          my ($codedString) = @_;          my ($codedString) = @_;
2988          # Initialize the return variable.          # Initialize the return variable.
2989          my $retVal = "";          my $retVal = "";
2990        # Only proceed if the incoming string is nonempty.
2991        if (defined $codedString) {
2992          # 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
2993          # translating because it causes problems with the escaped slash. ("\\b" becomes          # translating because it causes problems with the escaped slash. ("\\t" becomes
2994          # "\ " no matter what we do.)          # "\<tab>" no matter what we do.)
2995          while (length $codedString > 0) {          while (length $codedString > 0) {
2996                  # Look for the first escape sequence.                  # Look for the first escape sequence.
2997                  if ($codedString =~ /^(.*?)\\(\\|b|n|t)/) {              if ($codedString =~ /^(.*?)\\(\\|n|t|r)/) {
2998                          # 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
2999                          # 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.
3000                          $retVal .= $1;                          $retVal .= $1;
3001                          $codedString = substr $codedString, (2 + length $1);                          $codedString = substr $codedString, (2 + length $1);
3002                          # Decode the escape sequence.                  # Get the escape value.
3003                          my $char = $2;                          my $char = $2;
3004                          $char =~ tr/\\btn/\\ \t\n/;                  # If we have a "\r", we are done.
3005                    if ($char ne 'r') {
3006                        # Here it's not an 'r', so we convert it.
3007                        $char =~ tr/\\tn/\\\t\n/;
3008                          $retVal .= $char;                          $retVal .= $char;
3009                    }
3010                  } else {                  } else {
3011                          # 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
3012                          # transferred unmodified.                          # transferred unmodified.
# Line 576  Line 3014 
3014                          $codedString = "";                          $codedString = "";
3015                  }                  }
3016          }          }
3017          # Return the result.      }
3018          return $retVal;      # Return the result.
3019        return $retVal;
3020    }
3021    
3022    =head3 Percent
3023    
3024        my $percent = Tracer::Percent($number, $base);
3025    
3026    Returns the percent of the base represented by the given number. If the base
3027    is zero, returns zero.
3028    
3029    =over 4
3030    
3031    =item number
3032    
3033    Percent numerator.
3034    
3035    =item base
3036    
3037    Percent base.
3038    
3039    =item RETURN
3040    
3041    Returns the percentage of the base represented by the numerator.
3042    
3043    =back
3044    
3045    =cut
3046    
3047    sub Percent {
3048        # Get the parameters.
3049        my ($number, $base) = @_;
3050        # Declare the return variable.
3051        my $retVal = 0;
3052        # Compute the percent.
3053        if ($base != 0) {
3054            $retVal = $number * 100 / $base;
3055        }
3056        # Return the result.
3057        return $retVal;
3058    }
3059    
3060    =head3 Constrain
3061    
3062        my $constrained = Constrain($value, $min, $max);
3063    
3064    Modify a numeric value to bring it to a point in between a maximum and a minimum.
3065    
3066    =over 4
3067    
3068    =item value
3069    
3070    Value to constrain.
3071    
3072    =item min (optional)
3073    
3074    Minimum permissible value. If this parameter is undefined, no minimum constraint will be applied.
3075    
3076    =item max (optional)
3077    
3078    Maximum permissible value. If this parameter is undefined, no maximum constraint will be applied.
3079    
3080    =item RETURN
3081    
3082    Returns the incoming value, constrained according to the other parameters.
3083    
3084    =back
3085    
3086    =cut
3087    
3088    sub Constrain {
3089        # Get the parameters.
3090        my ($value, $min, $max) = @_;
3091        # Declare the return variable.
3092        my $retVal = $value;
3093        # Apply the minimum constraint.
3094        if (defined $min && $retVal < $min) {
3095            $retVal = $min;
3096        }
3097        # Apply the maximum constraint.
3098        if (defined $max && $retVal > $max) {
3099            $retVal = $max;
3100        }
3101        # Return the result.
3102        return $retVal;
3103    }
3104    
3105    =head3 Min
3106    
3107        my $min = Min($value1, $value2, ... $valueN);
3108    
3109    Return the minimum argument. The arguments are treated as numbers.
3110    
3111    =over 4
3112    
3113    =item $value1, $value2, ... $valueN
3114    
3115    List of numbers to compare.
3116    
3117    =item RETURN
3118    
3119    Returns the lowest number in the list.
3120    
3121    =back
3122    
3123    =cut
3124    
3125    sub Min {
3126        # Get the parameters. Note that we prime the return value with the first parameter.
3127        my ($retVal, @values) = @_;
3128        # Loop through the remaining parameters, looking for the lowest.
3129        for my $value (@values) {
3130            if ($value < $retVal) {
3131                $retVal = $value;
3132            }
3133        }
3134        # Return the minimum found.
3135        return $retVal;
3136    }
3137    
3138    =head3 Max
3139    
3140        my $max = Max($value1, $value2, ... $valueN);
3141    
3142    Return the maximum argument. The arguments are treated as numbers.
3143    
3144    =over 4
3145    
3146    =item $value1, $value2, ... $valueN
3147    
3148    List of numbers to compare.
3149    
3150    =item RETURN
3151    
3152    Returns the highest number in the list.
3153    
3154    =back
3155    
3156    =cut
3157    
3158    sub Max {
3159        # Get the parameters. Note that we prime the return value with the first parameter.
3160        my ($retVal, @values) = @_;
3161        # Loop through the remaining parameters, looking for the highest.
3162        for my $value (@values) {
3163            if ($value > $retVal) {
3164                $retVal = $value;
3165            }
3166        }
3167        # Return the maximum found.
3168        return $retVal;
3169    }
3170    
3171    =head3 Strip
3172    
3173        my $string = Tracer::Strip($line);
3174    
3175    Strip all line terminators off a string. This is necessary when dealing with files
3176    that may have been transferred back and forth several times among different
3177    operating environments.
3178    
3179    =over 4
3180    
3181    =item line
3182    
3183    Line of text to be stripped.
3184    
3185    =item RETURN
3186    
3187    The same line of text with all the line-ending characters chopped from the end.
3188    
3189    =back
3190    
3191    =cut
3192    
3193    sub Strip {
3194        # Get a copy of the parameter string.
3195        my ($string) = @_;
3196        my $retVal = (defined $string ? $string : "");
3197        # Strip the line terminator characters.
3198        $retVal =~ s/(\r|\n)+$//g;
3199        # Return the result.
3200        return $retVal;
3201    }
3202    
3203    =head3 Pad
3204    
3205        my $paddedString = Tracer::Pad($string, $len, $left, $padChar);
3206    
3207    Pad a string to a specified length. The pad character will be a
3208    space, and the padding will be on the right side unless specified
3209    in the third parameter.
3210    
3211    =over 4
3212    
3213    =item string
3214    
3215    String to be padded.
3216    
3217    =item len
3218    
3219    Desired length of the padded string.
3220    
3221    =item left (optional)
3222    
3223    TRUE if the string is to be left-padded; otherwise it will be padded on the right.
3224    
3225    =item padChar (optional)
3226    
3227    Character to use for padding. The default is a space.
3228    
3229    =item RETURN
3230    
3231    Returns a copy of the original string with the pad character added to the
3232    specified end so that it achieves the desired length.
3233    
3234    =back
3235    
3236    =cut
3237    
3238    sub Pad {
3239        # Get the parameters.
3240        my ($string, $len, $left, $padChar) = @_;
3241        # Compute the padding character.
3242        if (! defined $padChar) {
3243            $padChar = " ";
3244        }
3245        # Compute the number of spaces needed.
3246        my $needed = $len - length $string;
3247        # Copy the string into the return variable.
3248        my $retVal = $string;
3249        # Only proceed if padding is needed.
3250        if ($needed > 0) {
3251            # Create the pad string.
3252            my $pad = $padChar x $needed;
3253            # Affix it to the return value.
3254            if ($left) {
3255                $retVal = $pad . $retVal;
3256            } else {
3257                $retVal .= $pad;
3258            }
3259        }
3260        # Return the result.
3261        return $retVal;
3262    }
3263    
3264    =head3 EOF
3265    
3266    This is a constant that is lexically greater than any useful string.
3267    
3268    =cut
3269    
3270    sub EOF {
3271        return "\xFF\xFF\xFF\xFF\xFF";
3272    }
3273    
3274    =head3 TICK
3275    
3276        my @results = TICK($commandString);
3277    
3278    Perform a back-tick operation on a command. If this is a Windows environment, any leading
3279    dot-slash (C<./> will be removed. So, for example, if you were doing
3280    
3281        `./protein.cgi`
3282    
3283    from inside a CGI script, it would work fine in Unix, but would issue an error message
3284    in Windows complaining that C<'.'> is not a valid command. If instead you code
3285    
3286        TICK("./protein.cgi")
3287    
3288    it will work correctly in both environments.
3289    
3290    =over 4
3291    
3292    =item commandString
3293    
3294    The command string to pass to the system.
3295    
3296    =item RETURN
3297    
3298    Returns the standard output from the specified command, as a list.
3299    
3300    =back
3301    
3302    =cut
3303    #: Return Type @;
3304    sub TICK {
3305        # Get the parameters.
3306        my ($commandString) = @_;
3307        # Chop off the dot-slash if this is Windows.
3308        if ($FIG_Config::win_mode) {
3309            $commandString =~ s!^\./!!;
3310        }
3311        # Activate the command and return the result.
3312        return `$commandString`;
3313  }  }
3314    
 =head3 ParseRecord  
3315    
3316  C<< my @fields = Tracer::ParseRecord($line); >>  =head3 CommaFormat
3317    
3318  Parse a tab-delimited data line. The data line is split into field values. Embedded tab      my $formatted = Tracer::CommaFormat($number);
3319  and new-line characters in the data line must be represented as C<\t> and C<\n>, respectively.  
3320  These will automatically be converted.  Insert commas into a number.
3321    
3322  =over 4  =over 4
3323    
3324  =item line  =item number
3325    
3326  Line of data containing the tab-delimited fields.  A sequence of digits.
3327    
3328  =item RETURN  =item RETURN
3329    
3330  Returns a list of the fields found in the data line.  Returns the same digits with commas strategically inserted.
3331    
3332  =back  =back
3333    
3334  =cut  =cut
3335    
3336  sub ParseRecord {  sub CommaFormat {
3337          # Get the parameter.      # Get the parameters.
3338          my ($line) = @_;      my ($number) = @_;
3339          # Remove the trailing new-line, if any.      # Pad the length up to a multiple of three.
3340          chomp $line;      my $padded = "$number";
3341          # Split the line read into pieces using the tab character.      $padded = " " . $padded while length($padded) % 3 != 0;
3342          my @retVal = split /\t/, $line;      # This is a fancy PERL trick. The parentheses in the SPLIT pattern
3343          # Trim and fix the escapes in each piece.      # cause the delimiters to be included in the output stream. The
3344          for my $value (@retVal) {      # GREP removes the empty strings in between the delimiters.
3345                  # Trim leading whitespace.      my $retVal = join(",", grep { $_ ne '' } split(/(...)/, $padded));
3346                  $value =~ s/^\s+//;      # Clean out the spaces.
3347                  # Trim trailing whitespace.      $retVal =~ s/ //g;
                 $value =~ s/\s+$//;  
                 # 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;  
         }  
3348          # Return the result.          # Return the result.
3349          return @retVal;      return $retVal;
3350  }  }
3351    
 =head3 Merge  
3352    
3353  C<< my @mergedList = Tracer::Merge(@inputList); >>  =head3 CompareLists
3354    
3355  Sort a list of strings and remove duplicates.      my ($inserted, $deleted) = Tracer::CompareLists(\@newList, \@oldList, $keyIndex);
3356    
3357    Compare two lists of tuples, and return a hash analyzing the differences. The lists
3358    are presumed to be sorted alphabetically by the value in the $keyIndex column.
3359    The return value contains a list of items that are only in the new list
3360    (inserted) and only in the old list (deleted).
3361    
3362  =over 4  =over 4
3363    
3364  =item inputList  =item newList
3365    
3366  List of scalars to sort and merge.  Reference to a list of new tuples.
3367    
3368    =item oldList
3369    
3370    Reference to a list of old tuples.
3371    
3372    =item keyIndex (optional)
3373    
3374    Index into each tuple of its key field. The default is 0.
3375    
3376  =item RETURN  =item RETURN
3377    
3378  Returns a list containing the same elements sorted in ascending order with duplicates  Returns a 2-tuple consisting of a reference to the list of items that are only in the new
3379  removed.  list (inserted) followed by a reference to the list of items that are only in the old
3380    list (deleted).
3381    
3382  =back  =back
3383    
3384  =cut  =cut
3385    
3386  sub Merge {  sub CompareLists {
3387          # Get the input list in sort order.      # Get the parameters.
3388          my @inputList = sort @_;      my ($newList, $oldList, $keyIndex) = @_;
3389          # Only proceed if the list has at least two elements.      if (! defined $keyIndex) {
3390          if (@inputList > 1) {          $keyIndex = 0;
3391                  # Now we want to move through the list splicing out duplicates.      }
3392                  my $i = 0;      # Declare the return variables.
3393                  while ($i < @inputList) {      my ($inserted, $deleted) = ([], []);
3394                          # Get the current entry.      # Loop through the two lists simultaneously.
3395                          my $thisEntry = $inputList[$i];      my ($newI, $oldI) = (0, 0);
3396                          # Find out how many elements duplicate the current entry.      my ($newN, $oldN) = (scalar @{$newList}, scalar @{$oldList});
3397                          my $j = $i + 1;      while ($newI < $newN || $oldI < $oldN) {
3398                          my $dup1 = $i + 1;          # Get the current object in each list. Note that if one
3399                          while ($j < @inputList && $inputList[$j] eq $thisEntry) { $j++; };          # of the lists is past the end, we'll get undef.
3400                          # If the number is nonzero, splice out the duplicates found.          my $newItem = $newList->[$newI];
3401                          if ($j > $dup1) {          my $oldItem = $oldList->[$oldI];
3402                                  splice @inputList, $dup1, $j - $dup1;          if (! defined($newItem) || defined($oldItem) && $newItem->[$keyIndex] gt $oldItem->[$keyIndex]) {
3403                          }              # The old item is not in the new list, so mark it deleted.
3404                          # Now the element at position $dup1 is different from the element before it              push @{$deleted}, $oldItem;
3405                          # at position $i. We push $i forward one position and start again.              $oldI++;
3406                          $i++;          } elsif (! defined($oldItem) || $oldItem->[$keyIndex] gt $newItem->[$keyIndex]) {
3407                # The new item is not in the old list, so mark it inserted.
3408                push @{$inserted}, $newItem;
3409                $newI++;
3410            } else {
3411                # The item is in both lists, so push forward.
3412                $oldI++;
3413                $newI++;
3414                  }                  }
3415          }          }
3416          # Return the merged list.      # Return the result.
3417          return @inputList;      return ($inserted, $deleted);
3418  }  }
3419    
3420  =head3 GetFile  =head3 Cmp
3421    
3422  C<< my @fileContents = Tracer::GetFile($fileName); >>      my $cmp = Tracer::Cmp($a, $b);
3423    
3424  Return the entire contents of a file.  This method performs a universal sort comparison. Each value coming in is
3425    separated into a leading text part and a trailing number part. The text
3426    part is string compared, and if both parts are equal, then the number
3427    parts are compared numerically. A stream of just numbers or a stream of
3428    just strings will sort correctly, and a mixed stream will sort with the
3429    numbers first. Strings with a label and a number will sort in the
3430    expected manner instead of lexically.
3431    
3432  =over 4  =over 4
3433    
3434  =item fileName  =item a
3435    
3436  Name of the file to read.  First item to compare.
3437    
3438    =item b
3439    
3440    Second item to compare.
3441    
3442  =item RETURN  =item RETURN
3443    
3444  In a list context, returns the entire file as a list with the line terminators removed.  Returns a negative number if the first item should sort first (is less), a positive
3445  In a scalar context, returns the entire file as a string.  number if the first item should sort second (is greater), and a zero if the items are
3446    equal.
3447    
3448  =back  =back
3449    
3450  =cut  =cut
3451    
3452  sub GetFile {  sub Cmp {
3453          # Get the parameters.          # Get the parameters.
3454          my ($fileName) = @_;      my ($a, $b) = @_;
3455          # Declare the return variable.      # Declare the return value.
3456          my @retVal = ();      my $retVal;
3457          # Open the file for input.      # Check for nulls.
3458          my $ok = open INPUTFILE, "<$fileName";      if (! defined($a)) {
3459          if (!$ok) {          $retVal = (! defined($b) ? 0 : -1);
3460                  # If we had an error, trace it. We will automatically return a null value.      } elsif (! defined($b)) {
3461                  Trace("Could not open \"$fileName\" for input.") if T(0);          $retVal = 1;
3462          } else {          } else {
3463                  # Read the whole file into the return variable, stripping off an terminator          # Here we have two real values. Parse the two strings.
3464          # characters.          $a =~ /^(\D*)(\d*)$/;
3465          my $lineCount = 0;          my $aParsed = [$1, $2];
3466                  while (my $line = <INPUTFILE>) {          $b =~ /^(\D*)(\d*)$/;
3467              $lineCount++;          my $bParsed = [$1, $2];
3468              $line =~ s/(\r|\n)+$//g;          # Compare the string parts.
3469                          push @retVal, $line;          $retVal = $aParsed->[0] cmp $bParsed->[0];
3470                  }          if (! $retVal) {
3471                  # Close it.              $retVal = $aParsed->[1] <=> $bParsed->[1];
                 close INPUTFILE;  
         my $actualLines = @retVal;  
         Trace("$lineCount lines read from $fileName. $actualLines processed.") if T(0);  
3472          }          }
         # Return the file's contents in the desired format.  
     if (wantarray) {  
             return @retVal;  
     } else {  
         return join "\n", @retVal;  
3473      }      }
3474        # Return the result.
3475        return $retVal;
3476  }  }
3477    
3478  =head3 QTrace  =head3 ListEQ
3479    
3480  C<< my $data = QTrace($format); >>      my $flag = Tracer::ListEQ(\@a, \@b);
3481    
3482  Return the queued trace data in the specified format.  Return TRUE if the specified lists contain the same strings in the same
3483    order, else FALSE.
3484    
3485  =over 4  =over 4
3486    
3487  =item format  =item a
3488    
3489  C<html> to format the data as an HTML list, C<text> to format it as straight text.  Reference to the first list.
3490    
3491    =item b
3492    
3493    Reference to the second list.
3494    
3495    =item RETURN
3496    
3497    Returns TRUE if the two parameters are identical string lists, else FALSE.
3498    
3499  =back  =back
3500    
3501  =cut  =cut
3502    
3503  sub QTrace {  sub ListEQ {
3504          # Get the parameter.      # Get the parameters.
3505          my ($format) = @_;      my ($a, $b) = @_;
3506          # Create the return variable.      # Declare the return variable. Start by checking the lengths.
3507          my $retVal = "";      my $n = scalar(@$a);
3508          # Process according to the format.      my $retVal = ($n == scalar(@$b));
3509          if ($format =~ m/^HTML$/i) {      # Now compare the list elements.
3510                  # Convert the queue into an HTML list.      for (my $i = 0; $retVal && $i < $n; $i++) {
3511                  $retVal = "<ul>\n";          $retVal = ($a->[$i] eq $b->[$i]);
                 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";  
3512          }          }
3513          # Clear the queue.      # Return the result.
         @Queue = ();  
         # Return the formatted list.  
3514          return $retVal;          return $retVal;
3515  }  }
3516    
3517  =head3 Confess  =head2 CGI Script Utilities
3518    
3519  C<< Confess($message); >>  =head3 ScriptSetup (deprecated)
3520    
3521  Trace the call stack and abort the program with the specified message. The stack      my ($cgi, $varHash) = ScriptSetup($noTrace);
 trace will only appear if the trace level for this package is 1 or more. When used with  
 the OR operator and the L</Assert> method, B<Confess> can function as a debugging assert.  
 So, for example  
3522    
3523  C<< Assert($recNum >= 0) || Confess("Invalid record number $recNum."); >>  Perform standard tracing and debugging setup for scripts. The value returned is
3524    the CGI object followed by a pre-built variable hash. At the end of the script,
3525    the client should call L</ScriptFinish> to output the web page.
3526    
3527  Will abort the program with a stack trace if the value of C<$recNum> is negative.  This method calls L</ETracing> to configure tracing, which allows the tracing
3528    to be configured via the emergency tracing form on the debugging control panel.
3529    Tracing will then be turned on automatically for all programs that use the L</ETracing>
3530    method, which includes every program that uses this method or L</StandardSetup>.
3531    
3532  =over 4  =over 4
3533    
3534  =item message  =item noTrace (optional)
3535    
3536  Message to include in the trace.  If specified, tracing will be suppressed. This is useful if the script wants to set up
3537    tracing manually.
3538    
3539    =item RETURN
3540