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

Diff of /FigKernelPackages/Tracer.pm

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

revision 1.9, Wed May 4 03:05:12 2005 UTC revision 1.116, Thu Feb 5 06:40:13 2009 UTC
# Line 1  Line 1 
1    # -*- perl -*-
2    ########################################################################
3    # Copyright (c) 2003-2006 University of Chicago and Fellowship
4    # for Interpretations of Genomes. All Rights Reserved.
5    #
6    # This file is part of the SEED Toolkit.
7    #
8    # The SEED Toolkit is free software. You can redistribute
9    # it and/or modify it under the terms of the SEED Toolkit
10    # Public License.
11    #
12    # You should have received a copy of the SEED Toolkit Public License
13    # along with this program; if not write to the University of Chicago
14    # at info@ci.uchicago.edu or the Fellowship for Interpretation of
15    # Genomes at veronika@thefig.info or download a copy from
16    # http://www.theseed.org/LICENSE.TXT.
17    ########################################################################
18    
19  package Tracer;  package Tracer;
20    
         require Exporter;  
         @ISA = ('Exporter');  
         @EXPORT = qw(Trace T TSetup QTrace Confess Cluck Min Max Assert);  
         @EXPORT_OK = qw(GetFile GetOptions Merge MergeOptions ParseCommand ParseRecord UnEscape Escape);  
21          use strict;          use strict;
22          use Carp qw(longmess croak);      use base qw(Exporter);
23        use vars qw(@EXPORT @EXPORT_OK);
24        @EXPORT = qw(Trace T TSetup QTrace Confess Cluck Min Max Assert Open OpenDir TICK StandardSetup EmergencyKey ETracing Constrain Insure ChDir Emergency Warn TraceDump IDHASH);
25        @EXPORT_OK = qw(GetFile GetOptions Merge MergeOptions ParseCommand ParseRecord UnEscape Escape PrintLine PutLine);
26        use Carp qw(longmess croak carp);
27          use CGI;          use CGI;
28        use Cwd;
29          use FIG_Config;          use FIG_Config;
30      use PageBuilder;      use PageBuilder;
31        use Digest::MD5;
32        use File::Basename;
33        use File::Path;
34        use File::stat;
35        use LWP::UserAgent;
36        use Time::HiRes 'gettimeofday';
37        use URI::Escape;
38        use Time::Local;
39        use POSIX qw(strftime);
40        use Time::Zone;
41        use Fcntl qw(:DEFAULT :flock);
42        use Data::Dumper;
43    
44    
45  =head1 Tracing and Debugging Helpers  =head1 Tracing and Debugging Helpers
46    
47  =head2 Introduction  =head2 Tracing
48    
49  This package provides simple tracing for debugging and reporting purposes. To use it simply call the  This package provides simple tracing for debugging and reporting purposes. To use it simply call the
50  L</TSetup> method to set the options and call L</Trace> to write out trace messages. Each trace  L</TSetup> or L</ETracing> method to set the options and call L</Trace> to write out trace messages.
51  message has a I<trace level> and I<category> associated with it. In addition, the tracing package itself  L</TSetup> and L</ETracing> both establish a I<trace level> and a list of I<categories>. Similarly,
52  has a list of categories and a single trace level set by the B<TSetup> method. Only messages whose trace  each trace message has a I<trace level> and I<category> associated with it. Only messages whose trace
53  level is less than or equal to this package's trace level and whose category is activated will  level is less than or equal to the setup trace level and whose category is activated will
54  be written. Thus, a higher trace level on a message indicates that the message  be written. Thus, a higher trace level on a message indicates that the message
55  is less likely to be seen. A higher trace level passed to B<Setup> means more trace messages will  is less likely to be seen, while a higher trace level passed to B<TSetup> means more trace messages will
56  appear. To generate a trace message, use the following syntax.  appear.
57    
58    =head3 Putting Trace Messages in Your Code
59    
60    To generate a trace message, use the following syntax.
61    
62  C<< Trace($message) if T(errors => 4); >>      Trace($message) if T(errors => 4);
63    
64  This statement will produce a trace message if the trace level is 4 or more and the C<errors>  This statement will produce a trace message if the trace level is 4 or more and the C<errors>
65  category is active. Note that the special category C<main> is always active, so  category is active. There is a special category C<main> that is always active, so
66    
67  C<< Trace($message) if T(main => 4); >>      Trace($message) if T(main => 4);
68    
69  will trace if the trace level is 4 or more.  will trace if the trace level is 4 or more.
70    
# Line 36  Line 72 
72  following call is made in the B<Sprout> package, it will appear if the C<Sprout> category is  following call is made in the B<Sprout> package, it will appear if the C<Sprout> category is
73  active and the trace level is 2 or more.  active and the trace level is 2 or more.
74    
75  C<< Trace($message) if T(2); >>      Trace($message) if T(2);
76    
77  To set up tracing, you call the C</Setup> method. The method takes as input a trace level, a list  In scripts, where no package name is available, the category defaults to C<main>.
78  of category names, and a set of options. The trace level and list of category names are  
79    =head3 Custom Tracing
80    
81    Many programs have customized tracing configured using the L</TSetup> method. This is no longer
82    the preferred method, but a knowledge of how custom tracing works can make the more modern
83    L</Emergency Tracing> easier to understand.
84    
85    To set up custom tracing, you call the L</TSetup> method. The method takes as input a trace level,
86    a list of category names, and a destination. The trace level and list of category names are
87  specified as a space-delimited string. Thus  specified as a space-delimited string. Thus
88    
89  C<< TSetup('3 errors Sprout ERDB', 'HTML'); >>      TSetup('3 errors Sprout ERDB', 'TEXT');
90    
91  sets the trace level to 3, activates the C<errors>, C<Sprout>, and C<ERDB> categories, and  sets the trace level to 3, activates the C<errors>, C<Sprout>, and C<ERDB> categories, and
92  specifies that messages should be output as HTML paragraphs. The parameters are formatted  specifies that messages should be sent to the standard output.
93  to make it easier to input tracing configuration on a web form.  
94    To turn on tracing for ALL categories, use an asterisk. The call below sets every category to
95    level 3 and writes the output to the standard error output. This sort of thing might be
96    useful in a CGI environment.
97    
98  In addition to HTML and file output for trace messages, you can specify that the trace messages      TSetup('3 *', 'WARN');
99    
100    In addition standard error and file output for trace messages, you can specify that the trace messages
101  be queued. The messages can then be retrieved by calling the L</QTrace> method. This approach  be queued. The messages can then be retrieved by calling the L</QTrace> method. This approach
102  is useful if you are building a web page. Instead of having the trace messages interspersed with  is useful if you are building a web page. Instead of having the trace messages interspersed with
103  the page output, they can be gathered together and displayed at the end of the page. This makes  the page output, they can be gathered together and displayed at the end of the page. This makes
104  it easier to debug page formatting problems.  it easier to debug page formatting problems.
105    
106  Finally, you can specify that all trace messages be emitted as warnings.  Finally, you can specify that all trace messages be emitted to a file, or the standard output and
107    a file at the same time. To trace to a file, specify the filename with an output character in front
108    of it.
109    
110        TSetup('4 SQL', ">$fileName");
111    
112    To trace to the standard output and a file at the same time, put a C<+> in front of the angle
113    bracket.
114    
115        TSetup('3 *', "+>$fileName");
116    
117  The flexibility of tracing makes it superior to simple use of directives like C<die> and C<warn>.  The flexibility of tracing makes it superior to simple use of directives like C<die> and C<warn>.
118  Tracer calls can be left in the code with minimal overhead and then turned on only when needed.  Tracer calls can be left in the code with minimal overhead and then turned on only when needed.
119  Thus, debugging information is available and easily retrieved even when the application is  Thus, debugging information is available and easily retrieved even when the application is
120  being used out in the field.  being used out in the field.
121    
122    =head3 Trace Levels
123    
124    There is no hard and fast rule on how to use trace levels. The following is therefore only
125    a suggestion.
126    
127    =over 4
128    
129    =item Error 0
130    
131    Message indicates an error that may lead to incorrect results or that has stopped the
132    application entirely.
133    
134    =item Warning 1
135    
136    Message indicates something that is unexpected but that probably did not interfere
137    with program execution.
138    
139    =item Notice 2
140    
141    Message indicates the beginning or end of a major task.
142    
143    =item Information 3
144    
145    Message indicates a subtask. In the FIG system, a subtask generally relates to a single
146    genome. This would be a big loop that is not expected to execute more than 500 times or so.
147    
148    =item Detail 4
149    
150    Message indicates a low-level loop iteration.
151    
152    =back
153    
154    The format of trace messages is important because some utilities analyze trace files.
155    There are three fields-- the time stamp, the category name, and the text.
156    The time stamp is between square brackets and the category name between angle brackets.
157    After the category name there is a colon (C<:>) followed by the message text.
158    If the square brackets or angle brackets are missing, then the trace management
159    utilities assume that they are encountering a set of pre-formatted lines.
160    
161    Note, however, that this formatting is done automatically by the tracing functions. You
162    only need to know about it if you want to parse a trace file.
163    
164    =head3 Emergency Tracing
165    
166    Sometimes, you need a way for tracing to happen automatically without putting parameters
167    in a form or on the command line. Emergency tracing does this. You invoke emergency tracing
168    from the debug form, which is accessed from the [[DebugConsole]]. Emergency tracing requires
169    that you specify a tracing key. For command-line tools, the key is
170    taken from the C<TRACING> environment variable. For web services, the key is taken from
171    a cookie. Either way, the key tells the tracing facility who you are, so that you control
172    the tracing in your environment without stepping on other users.
173    
174    The key can be anything you want. If you don't have a key, the C<SetPassword> page will
175    generate one for you.
176    
177    You can activate and de-activate emergency tracing from the debugging control panel, as
178    well as display the trace file itself.
179    
180    To enable emergency tracing in your code, call
181    
182        ETracing($cgi)
183    
184    from a web script and
185    
186        ETracing()
187    
188    from a command-line script.
189    
190    The web script will look for the tracing key in the cookies, and the command-line
191    script will look for it in the C<TRACING> environment variable. If you are
192    using the L</StandardSetup> method or a [[WebApplication]], emergency tracing
193    will be configured automatically.
194    
195  =cut  =cut
196    
197  # Declare the configuration variables.  # Declare the configuration variables.
198    
199  my $Destination = "NONE";       # Description of where to send the trace output.  my $Destination = "WARN";   # Description of where to send the trace output.
200    my $TeeFlag = 0;            # TRUE if output is going to a file and to the
201                                # standard output
202  my %Categories = ( main => 1 );  my %Categories = ( main => 1 );
203                                                          # hash of active category names                                                          # hash of active category names
204    my @LevelNames = qw(error warn notice info detail);
205  my $TraceLevel = 0;                     # trace level; a higher trace level produces more  my $TraceLevel = 0;                     # trace level; a higher trace level produces more
206                                                          # messages                                                          # messages
207  my @Queue = ();                         # queued list of trace messages.  my @Queue = ();                         # queued list of trace messages.
208  my $LastCategory = "main";  # name of the last category interrogated  my $LastCategory = "main";  # name of the last category interrogated
209    my $LastLevel = 0;          # level of the last test call
210    my $SetupCount = 0;         # number of times TSetup called
211    my $AllTrace = 0;           # TRUE if we are tracing all categories.
212    my $SavedCGI;               # CGI object passed to ETracing
213    my $CommandLine;            # Command line passed to StandardSetup
214    umask 2;                    # Fix the damn umask so everything is group-writable.
215    
216  =head2 Public Methods  =head2 Tracing Methods
217    
218    =head3 Setups
219    
220        my $count = Tracer::Setups();
221    
222    Return the number of times L</TSetup> has been called.
223    
224    This method allows for the creation of conditional tracing setups where, for example, we
225    may want to set up tracing if nobody else has done it before us.
226    
227    =cut
228    
229    sub Setups {
230        return $SetupCount;
231    }
232    
233  =head3 TSetup  =head3 TSetup
234    
235  C<< TSetup($categoryList, $target); >>      TSetup($categoryList, $target);
236    
237  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
238  and interrogated by the L</Trace> and L</T> methods.  and interrogated by the L</Trace> and L</T> methods.
# Line 93  Line 248 
248    
249  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
250  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
251  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 ">"
252  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
253  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
254    cause tracing to the standard output with each line formatted as an HTML paragraph. C<TEXT>
255  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
256  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
257  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 113  Line 269 
269          my @categoryData = split /\s+/, $categoryList;          my @categoryData = split /\s+/, $categoryList;
270          # Extract the trace level.          # Extract the trace level.
271          $TraceLevel = shift @categoryData;          $TraceLevel = shift @categoryData;
272          # Build the category hash.      # Presume category-based tracing until we learn otherwise.
273        $AllTrace = 0;
274        # Build the category hash. Note that if we find a "*", we turn on non-category
275        # tracing. We must also clear away any pre-existing data.
276        %Categories = ( main => 1 );
277          for my $category (@categoryData) {          for my $category (@categoryData) {
278                  $Categories{$category} = 1;          if ($category eq '*') {
279                $AllTrace = 1;
280            } else {
281                $Categories{lc $category} = 1;
282            }
283          }          }
284          # Now we need to process the destination information. The most important special          # Now we need to process the destination information. The most important special
285          # case is the single ">", which requires we clear the file first. After doing      # case is when we're writing to a file. This is indicated by ">" (overwrite) and
286          # so, we tack on another ">" sign so that future trace messages are appended.      # ">>" (append). A leading "+" for either indicates that we are also writing to
287        # the standard output (tee mode).
288        if ($target =~ m/^\+?>>?/) {
289            if ($target =~ m/^\+/) {
290                $TeeFlag = 1;
291                $target = substr($target, 1);
292            }
293          if ($target =~ m/^>[^>]/) {          if ($target =~ m/^>[^>]/) {
294                # We need to initialize the file (which clears it).
295                  open TRACEFILE, $target;                  open TRACEFILE, $target;
296                  print TRACEFILE Now() . " Tracing initialized.\n";              print TRACEFILE "[" . Now() . "] [notice] [Tracer] Tracing initialized.\n";
297                  close TRACEFILE;                  close TRACEFILE;
298                # Set to append mode now that the file has been cleared.
299                  $Destination = ">$target";                  $Destination = ">$target";
300          } else {          } else {
301                $Destination = $target;
302            }
303        } else {
304                  $Destination = uc($target);                  $Destination = uc($target);
305          }          }
306        # Increment the setup counter.
307        $SetupCount++;
308  }  }
309    
310  =head3 SetLevel  =head3 SetLevel
311    
312  C<< Tracer::SetLevel($newLevel); >>      Tracer::SetLevel($newLevel);
313    
314  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.
315    
# Line 150  Line 327 
327      $TraceLevel = $_[0];      $TraceLevel = $_[0];
328  }  }
329    
330  =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  
331    
332  =cut      my $time = Tracer::ParseDate($dateString);
333    
334  sub LogErrors {  Convert a date into a PERL time number. This method expects a date-like string
335          # Get the file name.  and parses it into a number. The string must be vaguely date-like or it will
336          my ($fileName) = @_;  return an undefined value. Our requirement is that a month and day be
337          # Open the file as the standard error output.  present and that three pieces of the date string (time of day, month and day,
338          open STDERR, '>', $fileName;  year) be separated by likely delimiters, such as spaces, commas, and such-like.
 }  
339    
340  =head3 ReadOptions  If a time of day is present, it must be in military time with two digits for
341    everything but the hour.
342    
343  C<< my %options = Tracer::ReadOptions($fileName); >>  The year must be exactly four digits.
344    
345  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
346  format  equally innocuous. This means, however, that a sufficiently long sentence with date-like
347    parts in it may be interpreted as a date. Hopefully this will not be a problem.
348    
349  I<optionName>C<=>I<optionValue>C<; >I<comment>  It should be guaranteed that this method will parse the output of the L</Now> function.
350    
351  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.  
352    
353  =over 4  =over 4
354    
355  =item fileName  =item dateString
356    
357  Name of the file containing the option data.  The date string to convert.
358    
359  =item RETURN  =item RETURN
360    
361  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
362  value.  the date string is invalid. A valid date string must contain a month and day.
363    
364  =back  =back
365    
366  =cut  =cut
367    
368  sub ReadOptions {  # Universal month conversion table.
369          # Get the parameters.  use constant MONTHS => {    Jan =>  0, January   =>  0, '01' =>  0,  '1' =>  0,
370          my ($fileName) = @_;                              Feb =>  1, February  =>  1, '02' =>  1,  '2' =>  1,
371          # Open the file.                              Mar =>  2, March     =>  2, '03' =>  2,  '3' =>  2,
372          (open CONFIGFILE, "<$fileName") || Confess("Could not open option file $fileName.");                              Apr =>  3, April     =>  3, '04' =>  3,  '4' =>  3,
373          # Count the number of records read.                              May =>  4, May       =>  4, '05' =>  4,  '5' =>  4,
374          my ($records, $comments) = 0;                              Jun =>  5, June      =>  5, '06' =>  5,  '6' =>  5,
375          # Create the return hash.                              Jul =>  6, July      =>  6, '07' =>  6,  '7' =>  6,
376          my %retVal = ();                              Aug =>  7, August    =>  7, '08' =>  7,  '8' =>  7,
377          # Loop through the file, accumulating key-value pairs.                              Sep =>  8, September =>  8, '09' =>  8,  '9' =>  8,
378          while (my $line = <CONFIGFILE>) {                              Oct =>  9, October  =>   9, '10' =>  9,
379                  # Denote we've read a line.                              Nov => 10, November =>  10, '11' => 10,
380                  $records++;                              Dec => 11, December =>  11, '12' => 11
381                  # Determine the line type.                          };
                 if ($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  
382    
383  sub GetOptions {  sub ParseDate {
384          # Get the parameters.          # Get the parameters.
385          my ($defaults, $options) = @_;      my ($dateString) = @_;
386          # Check for overrides.      # Declare the return variable.
387          if ($options) {      my $retVal;
388                  # Loop through the overrides.      # Find the month and day of month. There are two ways that can happen. We check for the
389                  while (my ($option, $setting) = each %{$options}) {      # numeric style first. That way, if the user's done something like "Sun 12/22", then we
390                          # Insure this override exists.      # won't be fooled into thinking the month is Sunday.
391                          if (!exists $defaults->{$option}) {      if ($dateString =~ m#\b(\d{1,2})/(\d{1,2})\b# || $dateString =~ m#\b(\w+)\s(\d{1,2})\b#) {
392                                  croak "Unrecognized option $option encountered.";          my ($mon, $mday) = (MONTHS->{$1}, $2);
393            # Insist that the month and day are valid.
394            if (defined($mon) && $2 >= 1 && $2 <= 31) {
395                # Find the time.
396                my ($hour, $min, $sec) = (0, 0, 0);
397                if ($dateString =~ /\b(\d{1,2}):(\d{2}):(\d{2})\b/) {
398                    ($hour, $min, $sec) = ($1, $2, $3);
399                }
400                # Find the year.
401                my $year;
402                if ($dateString =~ /\b(\d{4})\b/) {
403                    $year = $1;
404                          } else {                          } else {
405                                  # Apply the override.                  # Get the default year, which is this one. Note we must convert it to
406                                  $defaults->{$option} = $setting;                  # the four-digit value expected by "timelocal".
407                    (undef, undef, undef, undef, undef, $year) = localtime();
408                    $year += 1900;
409                          }                          }
410                $retVal = timelocal($sec, $min, $hour, $mday, $mon, $year);
411                  }                  }
412          }          }
413          # Return the merged table.      # Return the result.
414          return $defaults;      return $retVal;
415  }  }
416    
417  =head3 MergeOptions  =head3 LogErrors
418    
419  C<< Tracer::MergeOptions(\%table, \%defaults); >>      Tracer::LogErrors($fileName);
420    
421  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.  
422    
423  =over 4  =over 4
424    
425  =item table  =item fileName
   
 Hash table to be updated with the default values.  
   
 =item defaults  
426    
427  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.
428    
429  =back  =back
430    
431  =cut  =cut
432    
433  sub MergeOptions {  sub LogErrors {
434          # Get the parameters.      # Get the file name.
435          my ($table, $defaults) = @_;      my ($fileName) = @_;
436          # Loop through the defaults.      # Open the file as the standard error output.
437          while (my ($key, $value) = each %{$defaults}) {      open STDERR, '>', $fileName;
                 if (!exists $table->{$key}) {  
                         $table->{$key} = $value;  
                 }  
         }  
438  }  }
439    
440  =head3 Trace  =head3 Trace
441    
442  C<< Trace($message); >>      Trace($message);
443    
444  Write a trace message to the target location specified in L</TSetup>. If there has not been  Write a trace message to the target location specified in L</TSetup>. If there has not been
445  any prior call to B<TSetup>.  any prior call to B<TSetup>.
# Line 371  Line 457 
457  sub Trace {  sub Trace {
458          # Get the parameters.          # Get the parameters.
459          my ($message) = @_;          my ($message) = @_;
460        # Strip off any line terminators at the end of the message. We will add
461        # new-line stuff ourselves.
462        my $stripped = Strip($message);
463        # Compute the caller information.
464        my ($callPackage, $callFile, $callLine) = caller();
465        my $callFileTitle = basename($callFile);
466        # Check the caller.
467        my $callerInfo = ($callFileTitle ne "Tracer.pm" ? " [$callFileTitle $callLine]" : "");
468          # Get the timestamp.          # Get the timestamp.
469          my $timeStamp = Now();          my $timeStamp = Now();
470          # Format the message. Note we strip off any line terminators at the end.      # Build the prefix.
471          my $formatted = "$timeStamp <$LastCategory>: " . Strip($message);      my $level = $LevelNames[$LastLevel] || "($LastLevel)";
472        my $prefix = "[$timeStamp] [$level] [$LastCategory]$callerInfo";
473        # Format the message.
474        my $formatted = "$prefix $stripped";
475          # Process according to the destination.          # Process according to the destination.
476          if ($Destination eq "TEXT") {          if ($Destination eq "TEXT") {
477                  # Write the message to the standard output.                  # Write the message to the standard output.
478                  print "$formatted\n";                  print "$formatted\n";
479          } elsif ($Destination eq "ERROR") {          } elsif ($Destination eq "ERROR") {
480                  # Write the message to the error output.          # Write the message to the error output. Here, we want our prefix fields.
481                  print STDERR "$formatted\n";                  print STDERR "$formatted\n";
482        } elsif ($Destination eq "WARN") {
483            # Emit the message to the standard error output. It is presumed that the
484            # error logger will add its own prefix fields, the notable exception being
485            # the caller info.
486            print STDERR "$callerInfo$stripped\n";
487          } elsif ($Destination eq "QUEUE") {          } elsif ($Destination eq "QUEUE") {
488                  # Push the message into the queue.                  # Push the message into the queue.
489                  push @Queue, "$formatted";                  push @Queue, "$formatted";
490          } elsif ($Destination eq "HTML") {          } elsif ($Destination eq "HTML") {
491                  # Convert the message to HTML and write it to the standard output.          # Convert the message to HTML.
492                  my $escapedMessage = CGI::escapeHTML($message);          my $escapedMessage = CGI::escapeHTML($stripped);
493                  print "<p>$formatted</p>\n";          # The stuff after the first line feed should be pre-formatted.
494      } elsif ($Destination eq "WARN") {          my @lines = split /\s*\n/, $escapedMessage;
495         # Emit the message as a warning.          # Get the normal portion.
496         warn $message;          my $line1 = shift @lines;
497            print "<p>$timeStamp $LastCategory $LastLevel: $line1</p>\n";
498            if (@lines) {
499                print "<pre>" . join("\n", @lines, "<pre>");
500            }
501          } elsif ($Destination =~ m/^>>/) {          } elsif ($Destination =~ m/^>>/) {
502                  # Write the trace message to an output file.                  # Write the trace message to an output file.
503                  open TRACING, $Destination;          open(TRACING, $Destination) || die "Tracing open for \"$Destination\" failed: $!";
504            # Lock the file.
505            flock TRACING, LOCK_EX;
506                  print TRACING "$formatted\n";                  print TRACING "$formatted\n";
507                  close TRACING;                  close TRACING;
508            # If the Tee flag is on, echo it to the standard output.
509            if ($TeeFlag) {
510                print "$formatted\n";
511            }
512          }          }
513  }  }
514    
515    =head3 TraceDump
516    
517        TraceDump($title, $object);
518    
519    Dump an object to the trace log. This method simply calls the C<Dumper>
520    function, but routes the output to the trace log instead of returning it
521    as a string. The output is arranged so that it comes out monospaced when
522    it appears in an HTML trace dump.
523    
524    =over 4
525    
526    =item title
527    
528    Title to give to the object being dumped.
529    
530    =item object
531    
532    Reference to a list, hash, or object to dump.
533    
534    =back
535    
536    =cut
537    
538    sub TraceDump {
539        # Get the parameters.
540        my ($title, $object) = @_;
541        # Trace the object.
542        Trace("Object dump for $title:\n" . Dumper($object));
543    }
544    
545  =head3 T  =head3 T
546    
547  C<< my $switch = T($category, $traceLevel); >>      my $switch = T($category, $traceLevel);
548    
549          or          or
550    
551  C<< my $switch = T($traceLevel); >>      my $switch = T($traceLevel);
552    
553  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
554  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 439  Line 581 
581                  my ($category, $traceLevel) = @_;                  my ($category, $traceLevel) = @_;
582                  if (!defined $traceLevel) {                  if (!defined $traceLevel) {
583                          # 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.
584                # The calling package is normally the first parameter. If it is
585                # omitted, the first parameter will be the tracelevel. So, the
586                # first thing we do is shift the so-called category into the
587                # $traceLevel variable where it belongs.
588                          $traceLevel = $category;                          $traceLevel = $category;
589                          my ($package, $fileName, $line) = caller;                          my ($package, $fileName, $line) = caller;
590              # If there is no calling package, we default to "main".              # If there is no calling package, we default to "main".
591                          if (!$package) {                          if (!$package) {
592                  $category = "main";                  $category = "main";
593                          } else {                          } else {
594                                  $category = $package;                  my @cats = split /::/, $package;
595                    $category = $cats[$#cats];
596                          }                          }
597                  }                  }
598          # Save the category name.          # Save the category name and level.
599          $LastCategory = $category;          $LastCategory = $category;
600                  # Use the category and tracelevel to compute the result.          $LastLevel = $traceLevel;
601                  $retVal = ($traceLevel <= $TraceLevel && exists $Categories{$category});          # Convert it to lower case before we hash it.
602            $category = lc $category;
603            # Validate the trace level.
604            if (ref $traceLevel) {
605                Confess("Bad trace level.");
606            } elsif (ref $TraceLevel) {
607                Confess("Bad trace config.");
608            }
609            # Make the check. Note that level 0 shows even if the category is turned off.
610            $retVal = ($traceLevel <= $TraceLevel && ($traceLevel == 0 || $AllTrace || exists $Categories{$category}));
611      }      }
612          # Return the computed result.          # Return the computed result.
613      return $retVal;      return $retVal;
614  }  }
615    
616  =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.  
617    
618  C<< my ($options, @arguments) = ParseCommand({ errors => 0, logFile => 'trace.log'}, @words); >>      my $data = QTrace($format);
619    
620  In this case, the list @words will be treated as a command line. There are two options available,  Return the queued trace data in the specified format.
 B<errors> and B<logFile>. If @words has the following format  
621    
622  C<< -logFile=error.log apple orange rutabaga >>  =over 4
623    
624  then at the end of the invocation, C<$options> will be  =item format
625    
626  C<< { errors => 0, logFile => 'error.log' } >>  C<html> to format the data as an HTML list, C<text> to format it as straight text.
627    
628  and C<@arguments> will contain  =back
629    
630  C<< apple orange rutabaga >>  =cut
631    
632    sub QTrace {
633        # Get the parameter.
634        my ($format) = @_;
635        # Create the return variable.
636        my $retVal = "";
637        # Only proceed if there is an actual queue.
638        if (@Queue) {
639            # Process according to the format.
640            if ($format =~ m/^HTML$/i) {
641                # Convert the queue into an HTML list.
642                $retVal = "<ul>\n";
643                for my $line (@Queue) {
644                    my $escapedLine = CGI::escapeHTML($line);
645                    $retVal .= "<li>$escapedLine</li>\n";
646                }
647                $retVal .= "</ul>\n";
648            } elsif ($format =~ m/^TEXT$/i) {
649                # Convert the queue into a list of text lines.
650                $retVal = join("\n", @Queue) . "\n";
651            }
652            # Clear the queue.
653            @Queue = ();
654        }
655        # Return the formatted list.
656        return $retVal;
657    }
658    
659    =head3 Confess
660    
661        Confess($message);
662    
663    Trace the call stack and abort the program with the specified message. When used with
664    the OR operator and the L</Assert> method, B<Confess> can function as a debugging assert.
665    So, for example
666    
667        Assert($recNum >= 0) || Confess("Invalid record number $recNum.");
668    
669    Will abort the program with a stack trace if the value of C<$recNum> is negative.
670    
671    =over 4
672    
673    =item message
674    
675    Message to include in the trace.
676    
677    =back
678    
679    =cut
680    
681    sub Confess {
682        # Get the parameters.
683        my ($message) = @_;
684        # Set up the category and level.
685        $LastCategory = "(confess)";
686        $LastLevel = 0;
687        # Trace the call stack.
688        Cluck($message);
689        # Abort the program.
690        croak(">>> $message");
691    }
692    
693    =head3 SaveCGI
694    
695        Tracer::SaveCGI($cgi);
696    
697    This method saves the CGI object but does not activate emergency tracing.
698    It is used to allow L</Warn> to work in situations where emergency
699    tracing is contra-indicated (e.g. the wiki).
700    
701    =over 4
702    
703    =item cgi
704    
705    Active CGI query object.
706    
707    =back
708    
709    =cut
710    
711    sub SaveCGI {
712        $SavedCGI = $_[0];
713    }
714    
715    =head3 Warn
716    
717        Warn($message, @options);
718    
719    This method traces an important message. If an RSS feed is configured
720    (via I<FIG_Config::error_feed>) and the tracing destination is C<WARN>,
721    then the message will be echoed to the feed. In general, a tracing
722    destination of C<WARN> indicates that the caller is running as a web
723    service in a production environment; however, this is not a requirement.
724    
725    To force warnings into the RSS feed even when the tracing destination
726    is not C<WARN>, simply specify the C<Feed> tracing module. This can be
727    configured automatically when L</StandardSetup> is used.
728    
729    The L</Cluck> method calls this one for its final message. Since
730    L</Confess> calls L</Cluck>, this means that any error which is caught
731    and confessed will put something in the feed. This insures that someone
732    will be alerted relatively quickly when a failure occurs.
733    
734    =over 4
735    
736    =item message
737    
738    Message to be traced.
739    
740    =item options
741    
742    A list containing zero or more options.
743    
744    =back
745    
746    The permissible options are as follows.
747    
748    =over 4
749    
750    =item noStack
751    
752    If specified, then the stack trace is not included in the output.
753    
754    =back
755    
756    =cut
757    
758    sub Warn {
759        # Get the parameters.
760        my $message = shift @_;
761        my %options = map { $_ => 1 } @_;
762        # Save $@;
763        my $savedError = $@;
764        # Trace the message.
765        Trace($message);
766        # This will contain the lock handle. If it's defined, it means we need to unlock.
767        my $lock;
768        # Check for feed forcing.
769        my $forceFeed = exists $Categories{feed};
770        # An error here would be disastrous. Note that if debug mode is specified,
771        # we do this stuff even in a test environment.
772        eval {
773            # Do we need to put this in the RSS feed?
774            if ($FIG_Config::error_feed && ($Destination eq 'WARN' || $forceFeed)) {
775                # Probably. We need to check first, however, to see if it's from an
776                # ignored IP. For non-CGI situations, we default the IP to the self-referent.
777                my $key = "127.0.0.1";
778                if (defined $SavedCGI) {
779                    # Get the IP address.
780                    $key = $ENV{HTTP_X_FORWARDED_FOR} || $ENV{REMOTE_ADDR};
781                }
782                # Is the IP address in the ignore list?
783                my $found = scalar(grep { $_ eq $key } @FIG_Config::error_ignore_ips);
784                if (! $found) {
785                    # No. We're good. We now need to compute the date, the link, and the title.
786                    # First, the date, in a very specific format.
787                    my $date = strftime("%a, %02e %b %H:%M:%S %Y ", localtime) .
788                        (tz_local_offset() / 30);
789                    # Environment data goes in here. We start with the date.
790                    my $environment = "$date.  ";
791                    # If we need to recap the message (because it's too long to be a title), we'll
792                    # put it in here.
793                    my $recap;
794                    # Copy the message and remove excess space.
795                    my $title = $message;
796                    $title =~ s/\s+/ /gs;
797                    # If it's too long, we have to split it up.
798                    if (length $title > 60) {
799                        # Put the full message in the environment string.
800                        $recap = $title;
801                        # Excerpt it as the title.
802                        $title = substr($title, 0, 50) . "...";
803                    }
804                    # If we have a CGI object, then this is a web error. Otherwise, it's
805                    # command-line.
806                    if (defined $SavedCGI) {
807                        # We're in a web service. The environment is the user's IP, and the link
808                        # is the URL that got us here.
809                        $environment .= "Event Reported at IP address $key process $$.";
810                        my $url = $SavedCGI->self_url();
811                        # We need the user agent string and (if available) the referrer.
812                        # The referrer will be the link.
813                        $environment .= " User Agent $ENV{HTTP_USER_AGENT}";
814                        if ($ENV{HTTP_REFERER}) {
815                            my $link = $ENV{HTTP_REFERER};
816                            $environment .= " referred from <a href=\"$link\">$link</a>.";
817                        } else {
818                            $environment .= " referrer unknown.";
819                        }
820                        # Close off the sentence with the original link.
821                        $environment .= " URL of event is <a href=\"$url\">$url</a>.";
822                    } else {
823                        # No CGI object, so we're a command-line tool. Use the tracing
824                        # key and the PID as the user identifier, and add the command.
825                        my $key = EmergencyKey();
826                        $environment .= "Event Reported by $key process $$.";
827                        if ($CommandLine) {
828                            # We're in a StandardSetup script, so we have the real command line.
829                            $environment .= "\n<pre>" . CGI::escapeHTML($CommandLine) . "</pre>\n";
830                        } elsif ($ENV{_}) {
831                            # We're in a BASH script, so the command has been stored in the _ variable.
832                            $environment .= "  Command = " . CGI::escapeHTML($ENV{_}) . "\n";
833                        }
834                    }
835                    # Build a GUID. We use the current time, the title, and the process ID,
836                    # then digest the result.
837                    my $guid = Digest::MD5::md5_base64(gettimeofday(), $title, $$);
838                    # Finally, the description. This is a stack trace plus various environmental stuff.
839                    # The trace is optional.
840                    my $stackTrace;
841                    if ($options{noStack}) {
842                        $stackTrace = "";
843                    } else {
844                        my @trace = LongMess();
845                        # Only proceed if we got something back.
846                        if (scalar(@trace) > 0) {
847                            $trace[0] =~ s/Tracer::Warn.+?called/Event occurred/;
848                            $stackTrace = "Stack trace:<pre>" . join("\n", @trace, "</pre>");
849                        }
850                    }
851                    # We got the stack trace. Now it's time to put it all together.
852                    # We have a goofy thing here in that we need to HTML-escape some sections of the description
853                    # twice. They will be escaped once here, and then once when written by XML::Simple. They are
854                    # unescaped once when processed by the RSS reader, and stuff in the description is treated as
855                    # HTML. So, anything escaped here is treated as a literal when viewed in the RSS reader, but
856                    # our <br>s and <pre>s are used to format the description.
857                    $recap = (defined $recap ? "<em>" . CGI::escapeHTML($recap) . "</em><br /><br />" : "");
858                    my $description = "$recap$environment  $stackTrace";
859                    # Okay, we have all the pieces. Create a hash of the new event.
860                    my $newItem = { title => $title,
861                                    description => $description,
862                                    category => $LastCategory,
863                                    pubDate => $date,
864                                    guid => $guid,
865                                  };
866                    # We need XML capability for this.
867                    require XML::Simple;
868                    # The RSS document goes in here.
869                    my $rss;
870                    # Get the name of the RSS file. It's in the FIG temporary directory.
871                    my $fileName = "$FIG_Config::temp/$FIG_Config::error_feed";
872                    # Open the config file and lock it.
873                    $lock = Open(undef, "<$FIG_Config::fig_disk/config/FIG_Config.pm");
874                    flock $lock, LOCK_EX;
875                    # Does it exist?
876                    if (-s $fileName) {
877                        # Slurp it in.
878                        $rss = XML::Simple::XMLin($fileName, ForceArray => ['item']);
879                    } else {
880                        my $size = -s $fileName;
881                        # Create an empty channel.
882                        $rss = {
883                            channel => {
884                                title => 'NMPDR Warning Feed',
885                                link => "$FIG_Config::temp_url/$FIG_Config::error_feed",
886                                description => "Important messages regarding the status of the NMPDR.",
887                                generator => "NMPDR Trace Facility",
888                                docs => "http://blogs.law.harvard.edu/tech/rss",
889                                item => []
890                            },
891                        };
892                    }
893                    # Get the channel object.
894                    my $channel = $rss->{channel};
895                    # Update the last-build date.
896                    $channel->{lastBuildDate} = $date;
897                    # Get the item array.
898                    my $items = $channel->{item};
899                    # Insure it has only 100 entries.
900                    while (scalar @{$items} > 100) {
901                        pop @{$items};
902                    }
903                    # Add our new item at the front.
904                    unshift @{$items}, $newItem;
905                    # Create the XML. Note we do not include the root or the declaration. XML Simple can't handle
906                    # the requirements for those.
907                    my $xml = XML::Simple::XMLout($channel, NoAttr => 1, RootName => 'channel', XmlDecl => '');
908                    # Here we put in the root and declaration. The problem is that the root has to have the version attribute
909                    # in it. So, we suppress the root and do it by hand, and that requires suppressing the declaration, too.
910                    $xml = "<?xml version=\"1.0\" encoding=\"utf-8\"?>\n<rss version=\"2.0\">$xml\n</rss>";
911                    # We don't use Open here because we can't afford an error.
912                    if (open XMLOUT, ">$fileName") {
913                        print XMLOUT $xml;
914                        close XMLOUT;
915                    }
916                }
917            }
918        };
919        if ($@) {
920            # If the feed failed, we need to know why. The error will be traced, but this method will not be involved
921            # (which is a good thing).
922            my $error = $@;
923            Trace("Feed Error: $error") if T(Feed => 0);
924        }
925        # Be sure to unlock.
926        if ($lock) {
927            flock $lock, LOCK_UN;
928            undef $lock;
929        }
930        # Restore the error message.
931        $@ = $savedError;
932    }
933    
934    
935    
936    
937    =head3 Assert
938    
939        Assert($condition1, $condition2, ... $conditionN);
940    
941    Return TRUE if all the conditions are true. This method can be used in conjunction with
942    the OR operator and the L</Confess> method as a debugging assert.
943    So, for example
944    
945        Assert($recNum >= 0) || Confess("Invalid record number $recNum.");
946    
947    Will abort the program with a stack trace if the value of C<$recNum> is negative.
948    
949    =cut
950    sub Assert {
951        my $retVal = 1;
952        LOOP: for my $condition (@_) {
953            if (! $condition) {
954                $retVal = 0;
955                last LOOP;
956            }
957        }
958        return $retVal;
959    }
960    
961    =head3 Cluck
962    
963        Cluck($message);
964    
965    Trace the call stack. Note that for best results, you should qualify the call with a
966    trace condition. For example,
967    
968        Cluck("Starting record parse.") if T(3);
969    
970    will only trace the stack if the trace level for the package is 3 or more.
971    
972    =over 4
973    
974    =item message
975    
976    Message to include in the trace.
977    
978    =back
979    
980    =cut
981    
982    sub Cluck {
983        # Get the parameters.
984        my ($message) = @_;
985        # Trace what's happening.
986        Trace("Stack trace for event: $message");
987        # Get the stack trace.
988        my @trace = LongMess();
989        # Convert the trace to a series of messages.
990        for my $line (@trace) {
991            # Replace the tab at the beginning with spaces.
992            $line =~ s/^\t/    /;
993            # Trace the line.
994            Trace($line);
995        }
996        # Issue a warning. This displays the event message and inserts it into the RSS error feed.
997        Warn($message);
998    }
999    
1000    =head3 LongMess
1001    
1002        my @lines = Tracer::LongMess();
1003    
1004    Return a stack trace with all tracing methods removed. The return will be in the form of a list
1005    of message strings.
1006    
1007    =cut
1008    
1009    sub LongMess {
1010        # Declare the return variable.
1011        my @retVal = ();
1012        my $confession = longmess("");
1013        for my $line (split /\s*\n/, $confession) {
1014            unless ($line =~ /Tracer\.pm/) {
1015                # Here we have a line worth keeping. Push it onto the result list.
1016                push @retVal, $line;
1017            }
1018        }
1019        # Return the result.
1020        return @retVal;
1021    }
1022    
1023    =head3 ETracing
1024    
1025        ETracing($parameter);
1026    
1027    Set up emergency tracing. Emergency tracing is tracing that is turned
1028    on automatically for any program that calls this method. The emergency
1029    tracing parameters are stored in a a file identified by a tracing key.
1030    If this method is called with a CGI object, then the tracing key is
1031    taken from a cookie. If it is called with no parameters, then the tracing
1032    key is taken from an environment variable. If it is called with a string,
1033    the tracing key is that string.
1034    
1035    =over 4
1036    
1037    =item parameter
1038    
1039    A parameter from which the tracing key is computed. If it is a scalar,
1040    that scalar is used as the tracing key. If it is a CGI object, the
1041    tracing key is taken from the C<IP> cookie. If it is omitted, the
1042    tracing key is taken from the C<TRACING> environment variable. If it
1043    is a CGI object and emergency tracing is not on, the C<Trace> and
1044    C<TF> parameters will be used to determine the type of tracing.
1045    
1046    =back
1047    
1048    =cut
1049    
1050    sub ETracing {
1051        # Get the parameter.
1052        my ($parameter) = @_;
1053        # Check for CGI mode.
1054        if (defined $parameter && ref $parameter eq 'CGI') {
1055            $SavedCGI = $parameter;
1056        } else {
1057            $SavedCGI = undef;
1058        }
1059        # Default to no tracing except errors.
1060        my ($tracing, $dest) = ("0", "WARN");
1061        # Check for emergency tracing.
1062        my $tkey = EmergencyKey($parameter);
1063        my $emergencyFile = EmergencyFileName($tkey);
1064        if (-e $emergencyFile) {
1065            # We have the file. Read in the data.
1066            my @tracing = GetFile($emergencyFile);
1067            # Pull off the time limit.
1068            my $expire = shift @tracing;
1069            # Convert it to seconds.
1070            $expire *= 3600;
1071            # Check the file data.
1072            my $stat = stat($emergencyFile);
1073            my ($now) = gettimeofday;
1074            if ($now - $stat->mtime > $expire) {
1075                # Delete the expired file.
1076                unlink $emergencyFile;
1077            } else {
1078                # Emergency tracing is on. Pull off the destination and
1079                # the trace level;
1080                $dest = shift @tracing;
1081                my $level = shift @tracing;
1082                # Convert the destination to a real tracing destination.
1083                # temp directory.
1084                $dest = EmergencyTracingDest($tkey, $dest);
1085                # Insure Tracer is specified.
1086                my %moduleHash = map { $_ => 1 } @tracing;
1087                $moduleHash{Tracer} = 1;
1088                # Set the trace parameter.
1089                $tracing = join(" ", $level, sort keys %moduleHash);
1090            }
1091        } elsif (defined $SavedCGI) {
1092            # There's no emergency tracing, but we have a CGI object, so check
1093            # for tracing from the form parameters.
1094            if ($SavedCGI->param('Trace')) {
1095                # Here the user has requested tracing via a form.
1096                $dest = ($SavedCGI->param('TF') ? ">$FIG_Config::temp/Trace$$.log" : "QUEUE");
1097                $tracing = $SavedCGI->param('Trace') . " Tracer";
1098            }
1099        }
1100        # Setup the tracing we've determined from all the stuff above.
1101        TSetup($tracing, $dest);
1102        # Check to see if we're a web script.
1103        if (defined $SavedCGI) {
1104            # Yes we are. Trace the form and environment data.
1105            TraceParms($SavedCGI);
1106            # Check for RAW mode. In raw mode, we print a fake header so that we see everything
1107            # emitted by the script in its raw form.
1108            if (T(Raw => 3)) {
1109                print CGI::header(-type => 'text/plain', -tracing => 'Raw');
1110            }
1111        }
1112    }
1113    
1114    =head3 EmergencyFileName
1115    
1116        my $fileName = Tracer::EmergencyFileName($tkey);
1117    
1118    Return the emergency tracing file name. This is the file that specifies
1119    the tracing information.
1120    
1121    =over 4
1122    
1123    =item tkey
1124    
1125    Tracing key for the current program.
1126    
1127    =item RETURN
1128    
1129    Returns the name of the file to contain the emergency tracing information.
1130    
1131    =back
1132    
1133    =cut
1134    
1135    sub EmergencyFileName {
1136        # Get the parameters.
1137        my ($tkey) = @_;
1138        # Compute the emergency tracing file name.
1139        return "$FIG_Config::temp/Emergency$tkey.txt";
1140    }
1141    
1142    =head3 EmergencyFileTarget
1143    
1144        my $fileName = Tracer::EmergencyFileTarget($tkey);
1145    
1146    Return the emergency tracing target file name. This is the file that receives
1147    the tracing output for file-based tracing.
1148    
1149    =over 4
1150    
1151    =item tkey
1152    
1153    Tracing key for the current program.
1154    
1155    =item RETURN
1156    
1157    Returns the name of the file to contain the trace output.
1158    
1159    =back
1160    
1161    =cut
1162    
1163    sub EmergencyFileTarget {
1164        # Get the parameters.
1165        my ($tkey) = @_;
1166        # Compute the emergency tracing file name.
1167        return "$FIG_Config::temp/trace$tkey.log";
1168    }
1169    
1170    =head3 EmergencyTracingDest
1171    
1172        my $dest = Tracer::EmergencyTracingDest($tkey, $myDest);
1173    
1174    This method converts an emergency tracing destination to a real
1175    tracing destination. The main difference is that if the
1176    destination is C<FILE> or C<APPEND>, we convert it to file
1177    output. If the destination is C<DUAL>, we convert it to file
1178    and standard output.
1179    
1180    =over 4
1181    
1182    =item tkey
1183    
1184    Tracing key for this environment.
1185    
1186    =item myDest
1187    
1188    Destination from the emergency tracing file.
1189    
1190    =item RETURN
1191    
1192    Returns a destination that can be passed into L</TSetup>.
1193    
1194    =back
1195    
1196    =cut
1197    
1198    sub EmergencyTracingDest {
1199        # Get the parameters.
1200        my ($tkey, $myDest) = @_;
1201        # Declare the return variable.
1202        my $retVal = $myDest;
1203        # Process according to the destination value.
1204        if ($myDest eq 'FILE') {
1205            $retVal = ">" . EmergencyFileTarget($tkey);
1206        } elsif ($myDest eq 'APPEND') {
1207            $retVal = ">>" . EmergencyFileTarget($tkey);
1208        } elsif ($myDest eq 'DUAL') {
1209            $retVal = "+>" . EmergencyFileTarget($tkey);
1210        } elsif ($myDest eq 'WARN') {
1211            $retVal = "WARN";
1212        }
1213        # Return the result.
1214        return $retVal;
1215    }
1216    
1217    =head3 Emergency
1218    
1219        Emergency($key, $hours, $dest, $level, @modules);
1220    
1221    Turn on emergency tracing. This method is normally invoked over the web from
1222    a debugging console, but it can also be called by the C<trace.pl> script.
1223    The caller specifies the duration of the emergency in hours, the desired tracing
1224    destination, the trace level, and a list of the trace modules to activate.
1225    For the length of the duration, when a program in an environment with the
1226    specified tracing key active invokes a Sprout CGI script, tracing will be
1227    turned on automatically. See L</TSetup> for more about tracing setup and
1228    L</ETracing> for more about emergency tracing.
1229    
1230    =over 4
1231    
1232    =item tkey
1233    
1234    The tracing key. This is used to identify the control file and the trace file.
1235    
1236    =item hours
1237    
1238    Number of hours to keep emergency tracing alive.
1239    
1240    =item dest
1241    
1242    Tracing destination. If no path information is specified for a file
1243    destination, it is put in the FIG temporary directory.
1244    
1245    =item level
1246    
1247    Tracing level. A higher level means more trace messages.
1248    
1249    =item modules
1250    
1251    A list of the tracing modules to activate.
1252    
1253    =back
1254    
1255    =cut
1256    
1257    sub Emergency {
1258        # Get the parameters.
1259        my ($tkey, $hours, $dest, $level, @modules) = @_;
1260        # Create the emergency file.
1261        my $specFile = EmergencyFileName($tkey);
1262        my $outHandle = Open(undef, ">$specFile");
1263        print $outHandle join("\n", $hours, $dest, $level, @modules, "");
1264    }
1265    
1266    =head3 EmergencyKey
1267    
1268        my $tkey = EmergencyKey($parameter);
1269    
1270    Return the Key to be used for emergency tracing. This could be an IP address,
1271     a session ID, or a user name, depending on the environment.
1272    
1273    =over 4
1274    
1275    =item parameter
1276    
1277    Parameter defining the method for finding the tracing key. If it is a scalar,
1278    then it is presumed to be the tracing key itself. If it is a CGI object, then
1279    the tracing key is taken from the C<IP> cookie. Otherwise, the tracing key is
1280    taken from the C<TRACING> environment variable.
1281    
1282    =item RETURN
1283    
1284    Returns the key to be used for labels in emergency tracing.
1285    
1286    =back
1287    
1288    =cut
1289    
1290    sub EmergencyKey {
1291        # Get the parameters.
1292        my ($parameter) = @_;
1293        # Declare the return variable.
1294        my $retVal;
1295        # Determine the parameter type.
1296        if (! defined $parameter || defined($ENV{TRACING})) {
1297            # Here we're supposed to check the environment. If that fails, we
1298            # get the effective login ID.
1299            $retVal = $ENV{TRACING} || scalar getpwuid($<);
1300        } else {
1301            my $ptype = ref $parameter;
1302            if ($ptype eq 'CGI') {
1303                # Here we were invoked from a web page. Look for a cookie.
1304                $retVal = $parameter->cookie('IP');
1305            } elsif (! $ptype) {
1306                # Here the key was passed in.
1307                $retVal = $parameter;
1308            }
1309        }
1310        # If no luck finding a key, use the PID.
1311        if (! defined $retVal) {
1312            $retVal = $$;
1313        }
1314        # Return the result.
1315        return $retVal;
1316    }
1317    
1318    
1319    =head3 TraceParms
1320    
1321        Tracer::TraceParms($cgi);
1322    
1323    Trace the CGI parameters at trace level CGI => 3 and the environment variables
1324    at level CGI => 4. A self-referencing URL is traced at level CGI => 2.
1325    
1326    =over 4
1327    
1328    =item cgi
1329    
1330    CGI query object containing the parameters to trace.
1331    
1332    =back
1333    
1334    =cut
1335    
1336    sub TraceParms {
1337        # Get the parameters.
1338        my ($cgi) = @_;
1339        if (T(CGI => 2)) {
1340            # Here we trace the GET-style URL for the script, but only if it's
1341            # relatively small.
1342            my $url = $cgi->url(-relative => 1, -query => 1);
1343            my $len = length($url);
1344            if ($len < 500) {
1345                Trace("[URL] $url");
1346            } elsif ($len > 2048) {
1347                Trace("[URL] URL is too long to use with GET ($len characters).");
1348            } else {
1349                Trace("[URL] URL length is $len characters.");
1350            }
1351        }
1352        if (T(CGI => 3)) {
1353            # Here we want to trace the parameter data.
1354            my @names = $cgi->param;
1355            for my $parmName (sort @names) {
1356                # Note we skip the Trace parameters, which are for our use only.
1357                if ($parmName ne 'Trace' && $parmName ne 'TF') {
1358                    my @values = $cgi->param($parmName);
1359                    Trace("[CGI] $parmName = " . join(", ", @values));
1360                }
1361            }
1362            # Display the request method.
1363            my $method = $cgi->request_method();
1364            Trace("Method: $method");
1365        }
1366        if (T(CGI => 4)) {
1367            # Here we want the environment data too.
1368            for my $envName (sort keys %ENV) {
1369                Trace("[ENV] $envName = $ENV{$envName}");
1370            }
1371        }
1372    }
1373    
1374    =head3 TraceImages
1375    
1376        Tracer::TraceImages($htmlString);
1377    
1378    Trace information about all of an html document's images. The tracing
1379    will be for type "IMG" at level 3. The image's source string
1380    will be displayed. This is generally either the URL of the image or
1381    raw data for the image itself. If the source is too long, only the first 300
1382    characters will be shown at trace level 3. The entire source will be shown,
1383    however, at trace level 4. This method is not very smart, and might catch
1384    Javascript code, but it is still useful when debugging the arcane
1385    behavior of images in multiple browser environments.
1386    
1387    =over 4
1388    
1389    =item htmlString
1390    
1391    HTML text for an outgoing web page.
1392    
1393    =back
1394    
1395    =cut
1396    
1397    sub TraceImages {
1398        # Only proceed if we're at the proper trace level.
1399        if (T(IMG => 3)) {
1400            # For performance reasons we're manipulating $_[0] instead of retrieving the string
1401            # into a variable called "$htmlString". This is because we expect html strings to be
1402            # long, and don't want to copy them any more than we have to.
1403            Trace(length($_[0]) . " characters in web page.");
1404            # Loop through the HTML, culling image tags.
1405            while ($_[0] =~ /<img\s+[^>]+?src="([^"]+)"/sgi) {
1406                # Extract the source string and determine whether or not it's too long.
1407                my $srcString = $1;
1408                my $pos = pos($_[0]) - length($srcString);
1409                my $excess = length($srcString) - 300;
1410                # We'll put the display string in here.
1411                my $srcDisplay = $srcString;
1412                # If it's a data string, split it at the comma.
1413                $srcDisplay =~ s/^(data[^,]+,)/$1\n/;
1414                # If there's no excess or we're at trace level 4, we're done. At level 3 with
1415                # a long string, however, we only show the first 300 characters.
1416                if ($excess > 0 && ! T(IMG => 4)) {
1417                    $srcDisplay = substr($srcDisplay,0,300) . "\nplus $excess characters.";
1418                }
1419                # Output the trace message.
1420                Trace("Image tag at position $pos:\n$srcDisplay");
1421            }
1422        }
1423    }
1424    
1425    =head2 Command-Line Utility Methods
1426    
1427    =head3 SendSMS
1428    
1429        my $msgID = Tracer::SendSMS($phoneNumber, $msg);
1430    
1431    Send a text message to a phone number using Clickatell. The FIG_Config file must contain the
1432    user name, password, and API ID for the relevant account in the hash reference variable
1433    I<$FIG_Config::phone>, using the keys C<user>, C<password>, and C<api_id>. For
1434    example, if the user name is C<BruceTheHumanPet>, the password is C<silly>, and the API ID
1435    is C<2561022>, then the FIG_Config file must contain
1436    
1437        $phone =  { user => 'BruceTheHumanPet',
1438                    password => 'silly',
1439                    api_id => '2561022' };
1440    
1441    The original purpose of this method was to insure Bruce would be notified immediately when the
1442    Sprout Load terminates. Care should be taken if you do not wish Bruce to be notified immediately
1443    when you call this method.
1444    
1445    The message ID will be returned if successful, and C<undef> if an error occurs.
1446    
1447    =over 4
1448    
1449    =item phoneNumber
1450    
1451    Phone number to receive the message, in international format. A United States phone number
1452    would be prefixed by "1". A British phone number would be prefixed by "44".
1453    
1454    =item msg
1455    
1456    Message to send to the specified phone.
1457    
1458    =item RETURN
1459    
1460    Returns the message ID if successful, and C<undef> if the message could not be sent.
1461    
1462    =back
1463    
1464    =cut
1465    
1466    sub SendSMS {
1467        # Get the parameters.
1468        my ($phoneNumber, $msg) = @_;
1469        # Declare the return variable. If we do not change it, C<undef> will be returned.
1470        my $retVal;
1471        # Only proceed if we have phone support.
1472        if (! defined $FIG_Config::phone) {
1473            Trace("Phone support not present in FIG_Config.") if T(1);
1474        } else {
1475            # Get the phone data.
1476            my $parms = $FIG_Config::phone;
1477            # Get the Clickatell URL.
1478            my $url = "http://api.clickatell.com/http/";
1479            # Create the user agent.
1480            my $ua = LWP::UserAgent->new;
1481            # Request a Clickatell session.
1482            my $resp = $ua->post("$url/sendmsg", { user => $parms->{user},
1483                                         password => $parms->{password},
1484                                         api_id => $parms->{api_id},
1485                                         to => $phoneNumber,
1486                                         text => $msg});
1487            # Check for an error.
1488            if (! $resp->is_success) {
1489                Trace("Alert failed.") if T(1);
1490            } else {
1491                # Get the message ID.
1492                my $rstring = $resp->content;
1493                if ($rstring =~ /^ID:\s+(.*)$/) {
1494                    $retVal = $1;
1495                } else {
1496                    Trace("Phone attempt failed with $rstring") if T(1);
1497                }
1498            }
1499        }
1500        # Return the result.
1501        return $retVal;
1502    }
1503    
1504    =head3 StandardSetup
1505    
1506        my ($options, @parameters) = StandardSetup(\@categories, \%options, $parmHelp, @ARGV);
1507    
1508    This method performs standard command-line parsing and tracing setup. The return
1509    values are a hash of the command-line options and a list of the positional
1510    parameters. Tracing is automatically set up and the command-line options are
1511    validated.
1512    
1513    This is a complex method that does a lot of grunt work. The parameters can
1514    be more easily understood, however, once they are examined individually.
1515    
1516    The I<categories> parameter is the most obtuse. It is a reference to a list of
1517    special-purpose tracing categories. Most tracing categories are PERL package
1518    names. So, for example, if you wanted to turn on tracing inside the B<Sprout>,
1519    B<ERDB>, and B<SproutLoad> packages, you would specify the categories
1520    
1521        ["Sprout", "SproutLoad", "ERDB"]
1522    
1523    This would cause trace messages in the specified three packages to appear in
1524    the output. There are two special tracing categories that are automatically
1525    handled by this method. In other words, if you used L</TSetup> you would need
1526    to include these categories manually, but if you use this method they are turned
1527    on automatically.
1528    
1529    =over 4
1530    
1531    =item SQL
1532    
1533    Traces SQL commands and activity.
1534    
1535    =item Tracer
1536    
1537    Traces error messages and call stacks.
1538    
1539    =back
1540    
1541    C<SQL> is only turned on if the C<-sql> option is specified in the command line.
1542    The trace level is specified using the C<-trace> command-line option. For example,
1543    the following command line for C<TransactFeatures> turns on SQL tracing and runs
1544    all tracing at level 3.
1545    
1546        TransactFeatures -trace=3 -sql register ../xacts IDs.tbl
1547    
1548    Standard tracing is output to the standard output and echoed to the file
1549    C<trace>I<$$>C<.log> in the FIG temporary directory, where I<$$> is the
1550    process ID. You can also specify the C<user> parameter to put a user ID
1551    instead of a process ID in the trace file name. So, for example
1552    
1553    The default trace level is 2. To get all messages, specify a trace level of 4.
1554    For a genome-by-genome update, use 3.
1555    
1556        TransactFeatures -trace=3 -sql -user=Bruce register ../xacts IDs.tbl
1557    
1558    would send the trace output to C<traceBruce.log> in the temporary directory.
1559    
1560    The I<options> parameter is a reference to a hash containing the command-line
1561    options, their default values, and an explanation of what they mean. Command-line
1562    options may be in the form of switches or keywords. In the case of a switch, the
1563    option value is 1 if it is specified and 0 if it is not specified. In the case
1564    of a keyword, the value is separated from the option name by an equal sign. You
1565    can see this last in the command-line example above.
1566    
1567    You can specify a different default trace level by setting C<$options->{trace}>
1568    prior to calling this method.
1569    
1570    An example at this point would help. Consider, for example, the command-line utility
1571    C<TransactFeatures>. It accepts a list of positional parameters plus the options
1572    C<safe>, C<noAlias>, C<start>, and C<tblFiles>. To start up this command, we execute
1573    the following code.
1574    
1575        my ($options, @parameters) = Tracer::StandardSetup(["DocUtils"],
1576                            { safe => [0, "use database transactions"],
1577                              noAlias => [0, "do not expect aliases in CHANGE transactions"],
1578                              start => [' ', "start with this genome"],
1579                              tblFiles => [0, "output TBL files containing the corrected IDs"] },
1580                            "<command> <transactionDirectory> <IDfile>",
1581                          @ARGV);
1582    
1583    
1584    The call to C<ParseCommand> specifies the default values for the options and
1585    stores the actual options in a hash that is returned as C<$options>. The
1586    positional parameters are returned in C<@parameters>.
1587    
1588    The following is a sample command line for C<TransactFeatures>.
1589    
1590        TransactFeatures -trace=2 -noAlias register ../xacts IDs.tbl
1591    
1592    Single and double hyphens are equivalent. So, you could also code the
1593    above command as
1594    
1595        TransactFeatures --trace=2 --noAlias register ../xacts IDs.tbl
1596    
1597    In this case, C<register>, C<../xacts>, and C<IDs.tbl> are the positional
1598    parameters, and would find themselves in I<@parameters> after executing the
1599    above code fragment. The tracing would be set to level 2, and the categories
1600    would be C<Tracer>, and <DocUtils>. C<Tracer> is standard,
1601    and C<DocUtils> was included because it came in within the first parameter
1602    to this method. The I<$options> hash would be
1603    
1604        { trace => 2, sql => 0, safe => 0,
1605          noAlias => 1, start => ' ', tblFiles => 0 }
1606    
1607    Use of C<StandardSetup> in this way provides a simple way of performing
1608    standard tracing setup and command-line parsing. Note that the caller is
1609    not even aware of the command-line switches C<-trace> and C<-sql>, which
1610    are used by this method to control the tracing. If additional tracing features
1611    need to be added in the future, they can be processed by this method without
1612    upsetting the command-line utilities.
1613    
1614    If the C<background> option is specified on the command line, then the
1615    standard and error outputs will be directed to files in the temporary
1616    directory, using the same suffix as the trace file. So, if the command
1617    line specified
1618    
1619        -user=Bruce -background
1620    
1621    then the trace output would go to C<traceBruce.log>, the standard output to
1622    C<outBruce.log>, and the error output to C<errBruce.log>. This is designed to
1623    simplify starting a command in the background.
1624    
1625    The user name is also used as the tracing key for L</Emergency Tracing>.
1626    Specifying a value of C<E> for the trace level causes emergency tracing to
1627    be used instead of custom tracing. If the user name is not specified,
1628    the tracing key is taken from the C<Tracing> environment variable. If there
1629    is no value for that variable, the tracing key will be computed from the active
1630    login ID.
1631    
1632    Since the default situation in StandardSetup is to trace to the standard
1633    output, errors that occur in command-line scripts will not generate
1634    RSS events. To force the events, use the C<warn> option.
1635    
1636        TransactFeatures -background -warn register ../xacts IDs.tbl
1637    
1638    Finally, if the special option C<-help> is specified, the option
1639    names will be traced at level 0 and the program will exit without processing.
1640    This provides a limited help capability. For example, if the user enters
1641    
1642        TransactFeatures -help
1643    
1644    he would see the following output.
1645    
1646        TransactFeatures [options] <command> <transactionDirectory> <IDfile>
1647            -trace    tracing level (default E)
1648            -sql      trace SQL commands
1649            -safe     use database transactions
1650            -noAlias  do not expect aliases in CHANGE transactions
1651            -start    start with this genome
1652            -tblFiles output TBL files containing the corrected IDs
1653            -forked   do not erase the trace file before tracing
1654    
1655    The caller has the option of modifying the tracing scheme by placing a value
1656    for C<trace> in the incoming options hash. The default value can be overridden,
1657    or the tracing to the standard output can be turned off by suffixing a minus
1658    sign to the trace level. So, for example,
1659    
1660        { trace => [0, "tracing level (default 0)"],
1661           ...
1662    
1663    would set the default trace level to 0 instead of E, while
1664    
1665        { trace => ["2-", "tracing level (default 2)"],
1666           ...
1667    
1668    would set the default to 2, but trace only to the log file, not to the
1669    standard output.
1670    
1671    The parameters to this method are as follows.
1672    
1673    =over 4
1674    
1675    =item categories
1676    
1677    Reference to a list of tracing category names. These should be names of
1678    packages whose internal workings will need to be debugged to get the
1679    command working.
1680    
1681    =item options
1682    
1683    Reference to a hash containing the legal options for the current command mapped
1684    to their default values and descriptions. The user can override the defaults
1685    by specifying the options as command-line switches prefixed by a hyphen.
1686    Tracing-related options may be added to this hash. If the C<-h> option is
1687    specified on the command line, the option descriptions will be used to
1688    explain the options. To turn off tracing to the standard output, add a
1689    minus sign to the value for C<trace> (see above).
1690    
1691    =item parmHelp
1692    
1693    A string that vaguely describes the positional parameters. This is used
1694    if the user specifies the C<-h> option.
1695    
1696    =item argv
1697    
1698    List of command line parameters, including the option switches, which must
1699    precede the positional parameters and be prefixed by a hyphen.
1700    
1701    =item RETURN
1702    
1703    Returns a list. The first element of the list is the reference to a hash that
1704    maps the command-line option switches to their values. These will either be the
1705    default values or overrides specified on the command line. The remaining
1706    elements of the list are the position parameters, in order.
1707    
1708    =back
1709    
1710    =cut
1711    
1712    sub StandardSetup {
1713        # Get the parameters.
1714        my ($categories, $options, $parmHelp, @argv) = @_;
1715        # Get the default tracing key.
1716        my $tkey = EmergencyKey();
1717        # Save the command line.
1718        $CommandLine = join(" ", $0, map { $_ =~ /\s/ ? "\"$_\"" : $_ } @argv);
1719        # Add the tracing options.
1720        if (! exists $options->{trace}) {
1721            $options->{trace} = ['2', "tracing level (E for emergency tracing)"];
1722        }
1723        if (! exists $options->{forked}) {
1724            $options->{forked} = [0, "keep old trace file"];
1725        }
1726        $options->{sql} = [0, "turn on SQL tracing"];
1727        $options->{help} = [0, "display command-line options"];
1728        $options->{user} = [$tkey, "tracing key"];
1729        $options->{background} = [0, "spool standard and error output"];
1730        $options->{warn} = [0, "send errors to RSS feed"];
1731        $options->{moreTracing} = ["", "comma-delimited list of additional trace modules for debugging"];
1732        # Create a parsing hash from the options hash. The parsing hash
1733        # contains the default values rather than the default value
1734        # and the description. While we're at it, we'll memorize the
1735        # length of the longest option name.
1736        my $longestName = 0;
1737        my %parseOptions = ();
1738        for my $key (keys %{$options}) {
1739            if (length $key > $longestName) {
1740                $longestName = length $key;
1741            }
1742            $parseOptions{$key} = $options->{$key}->[0];
1743        }
1744        # Parse the command line.
1745        my ($retOptions, @retParameters) = ParseCommand(\%parseOptions, @argv);
1746        # Get the logfile suffix.
1747        my $suffix = $retOptions->{user};
1748        # We'll put the trace file name in here. We need it later if background
1749        # mode is on.
1750        my $traceFileName;
1751        # Now we want to set up tracing. First, we need to know if the user
1752        # wants emergency tracing.
1753        if ($retOptions->{trace} eq 'E') {
1754            ETracing($retOptions->{user});
1755        } else {
1756            # Here the tracing is controlled from the command line.
1757            my @cats = @{$categories};
1758            if ($retOptions->{sql}) {
1759                push @cats, "SQL";
1760            }
1761            if ($retOptions->{warn}) {
1762                push @cats, "Feed";
1763            }
1764            # Add the default categories.
1765            push @cats, "Tracer";
1766            # Check for more tracing groups.
1767            if ($retOptions->{moreTracing}) {
1768                push @cats, split /,/, $retOptions->{moreTracing};
1769            }
1770            # Next, we create the category string by joining the categories.
1771            my $cats = join(" ", @cats);
1772            # Check to determine whether or not the caller wants to turn off tracing
1773            # to the standard output.
1774            my $traceLevel = $retOptions->{trace};
1775            my $textOKFlag = 1;
1776            if ($traceLevel =~ /^(.)-/) {
1777                $traceLevel = $1;
1778                $textOKFlag = 0;
1779            }
1780            # Now we set up the trace mode.
1781            my $traceMode;
1782            # Verify that we can open a file in the FIG temporary directory.
1783            my $traceFileName = "$FIG_Config::temp/trace$suffix.log";
1784            my $traceFileSpec = ($retOptions->{forked} ? ">>$traceFileName" : ">$traceFileName");
1785            if (open TESTTRACE, "$traceFileSpec") {
1786                # Here we can trace to a file.
1787                $traceMode = ">>$traceFileName";
1788                if ($textOKFlag) {
1789                    # Echo to standard output if the text-OK flag is set.
1790                    $traceMode = "+$traceMode";
1791                }
1792                # Close the test file.
1793                close TESTTRACE;
1794            } else {
1795                # Here we can't trace to a file. Complain about this.
1796                warn "Could not open trace file $traceFileName: $!\n";
1797                # We trace to the standard output if it's
1798                # okay, and the error log otherwise.
1799                if ($textOKFlag) {
1800                    $traceMode = "TEXT";
1801                } else {
1802                    $traceMode = "WARN";
1803                }
1804            }
1805            # Now set up the tracing.
1806            TSetup("$traceLevel $cats", $traceMode);
1807        }
1808        # Check for background mode.
1809        if ($retOptions->{background}) {
1810            my $outFileName = "$FIG_Config::temp/out$suffix$$.log";
1811            my $errFileName = "$FIG_Config::temp/err$suffix$$.log";
1812            # Spool the output.
1813            open STDOUT, ">$outFileName";
1814            # If we have a trace file, trace the errors to the log. Otherwise,
1815            # spool the errors.
1816            if (defined $traceFileName) {
1817                open STDERR, "| Tracer $traceFileName";
1818            } else {
1819                open STDERR, ">$errFileName";
1820            }
1821            # Check for phone support. If we have phone support and a phone number,
1822            # we want to turn it on.
1823            if ($ENV{PHONE} && defined($FIG_Config::phone)) {
1824                $retOptions->{phone} = $ENV{PHONE};
1825            }
1826        }
1827        # Check for the "help" option. If it is specified, dump the command-line
1828        # options and exit the program.
1829        if ($retOptions->{help}) {
1830            $0 =~ m#[/\\](\w+)(\.pl)?$#i;
1831            print "$1 [options] $parmHelp\n";
1832            for my $key (sort keys %{$options}) {
1833                my $name = Pad($key, $longestName, 0, ' ');
1834                my $desc = $options->{$key}->[1];
1835                if ($options->{$key}->[0]) {
1836                    $desc .= " (default " . $options->{$key}->[0] . ")";
1837                }
1838                print "  $name $desc\n";
1839            }
1840            exit(0);
1841        }
1842        # Trace the options, if applicable.
1843        if (T(3)) {
1844            my @parms = grep { $retOptions->{$_} } keys %{$retOptions};
1845            Trace("Selected options: " . join(", ", sort @parms) . ".");
1846        }
1847        # Return the parsed parameters.
1848        return ($retOptions, @retParameters);
1849    }
1850    
1851    =head3 ReadOptions
1852    
1853        my %options = Tracer::ReadOptions($fileName);
1854    
1855    Read a set of options from a file. Each option is encoded in a line of text that has the
1856    format
1857    
1858    I<optionName>C<=>I<optionValue>C<; >I<comment>
1859    
1860    The option name must consist entirely of letters, digits, and the punctuation characters
1861    C<.> and C<_>, and is case sensitive. Blank lines and lines in which the first nonblank
1862    character is a semi-colon will be ignored. The return hash will map each option name to
1863    the corresponding option value.
1864    
1865    =over 4
1866    
1867    =item fileName
1868    
1869    Name of the file containing the option data.
1870    
1871    =item RETURN
1872    
1873    Returns a hash mapping the option names specified in the file to their corresponding option
1874    value.
1875    
1876    =back
1877    
1878    =cut
1879    
1880    sub ReadOptions {
1881        # Get the parameters.
1882        my ($fileName) = @_;
1883        # Open the file.
1884        (open CONFIGFILE, "<$fileName") || Confess("Could not open option file $fileName.");
1885        # Count the number of records read.
1886        my ($records, $comments) = 0;
1887        # Create the return hash.
1888        my %retVal = ();
1889        # Loop through the file, accumulating key-value pairs.
1890        while (my $line = <CONFIGFILE>) {
1891            # Denote we've read a line.
1892            $records++;
1893            # Determine the line type.
1894            if ($line =~ /^\s*[\n\r]/) {
1895                # A blank line is a comment.
1896                $comments++;
1897            } elsif ($line =~ /^\s*([A-Za-z0-9_\.]+)=([^;]*);/) {
1898                # Here we have an option assignment.
1899                retVal{$1} = $2;
1900            } elsif ($line =~ /^\s*;/) {
1901                # Here we have a text comment.
1902                $comments++;
1903            } else {
1904                # Here we have an invalid line.
1905                Trace("Invalid option statement in record $records.") if T(0);
1906            }
1907        }
1908        # Return the hash created.
1909        return %retVal;
1910    }
1911    
1912    =head3 GetOptions
1913    
1914        Tracer::GetOptions(\%defaults, \%options);
1915    
1916    Merge a specified set of options into a table of defaults. This method takes two hash references
1917    as input and uses the data from the second to update the first. If the second does not exist,
1918    there will be no effect. An error will be thrown if one of the entries in the second hash does not
1919    exist in the first.
1920    
1921    Consider the following example.
1922    
1923        my $optionTable = GetOptions({ dbType => 'mySQL', trace => 0 }, $options);
1924    
1925    In this example, the variable B<$options> is expected to contain at most two options-- B<dbType> and
1926    B<trace>. The default database type is C<mySQL> and the default trace level is C<0>. If the value of
1927    B<$options> is C<< {dbType => 'Oracle'} >>, then the database type will be changed to C<Oracle> and
1928    the trace level will remain at 0. If B<$options> is undefined, then the database type and trace level
1929    will remain C<mySQL> and C<0>. If, on the other hand, B<$options> is defined as
1930    
1931        {databaseType => 'Oracle'}
1932    
1933    an error will occur because the B<databaseType> option does not exist.
1934    
1935    =over 4
1936    
1937    =item defaults
1938    
1939    Table of default option values.
1940    
1941    =item options
1942    
1943    Table of overrides, if any.
1944    
1945    =item RETURN
1946    
1947    Returns a reference to the default table passed in as the first parameter.
1948    
1949    =back
1950    
1951    =cut
1952    
1953    sub GetOptions {
1954        # Get the parameters.
1955        my ($defaults, $options) = @_;
1956        # Check for overrides.
1957        if ($options) {
1958            # Loop through the overrides.
1959            while (my ($option, $setting) = each %{$options}) {
1960                # Insure this override exists.
1961                if (!exists $defaults->{$option}) {
1962                    croak "Unrecognized option $option encountered.";
1963                } else {
1964                    # Apply the override.
1965                    $defaults->{$option} = $setting;
1966                }
1967            }
1968        }
1969        # Return the merged table.
1970        return $defaults;
1971    }
1972    
1973    =head3 MergeOptions
1974    
1975        Tracer::MergeOptions(\%table, \%defaults);
1976    
1977    Merge default values into a hash table. This method looks at the key-value pairs in the
1978    second (default) hash, and if a matching key is not found in the first hash, the default
1979    pair is copied in. The process is similar to L</GetOptions>, but there is no error-
1980    checking and no return value.
1981    
1982    =over 4
1983    
1984    =item table
1985    
1986    Hash table to be updated with the default values.
1987    
1988    =item defaults
1989    
1990    Default values to be merged into the first hash table if they are not already present.
1991    
1992    =back
1993    
1994    =cut
1995    
1996    sub MergeOptions {
1997        # Get the parameters.
1998        my ($table, $defaults) = @_;
1999        # Loop through the defaults.
2000        while (my ($key, $value) = each %{$defaults}) {
2001            if (!exists $table->{$key}) {
2002                $table->{$key} = $value;
2003            }
2004        }
2005    }
2006    
2007    =head3 UnparseOptions
2008    
2009        my $optionString = Tracer::UnparseOptions(\%options);
2010    
2011    Convert an option hash into a command-line string. This will not
2012    necessarily be the same text that came in, but it will nonetheless
2013    produce the same ultimate result when parsed by L</StandardSetup>.
2014    
2015    =over 4
2016    
2017    =item options
2018    
2019    Reference to a hash of options to convert into an option string.
2020    
2021    =item RETURN
2022    
2023    Returns a string that will parse to the same set of options when
2024    parsed by L</StandardSetup>.
2025    
2026    =back
2027    
2028    =cut
2029    
2030    sub UnparseOptions {
2031        # Get the parameters.
2032        my ($options) = @_;
2033        # The option segments will be put in here.
2034        my @retVal = ();
2035        # Loop through the options.
2036        for my $key (keys %$options) {
2037            # Get the option value.
2038            my $value = $options->{$key};
2039            # Only use it if it's nonempty.
2040            if (defined $value && $value ne "") {
2041                my $segment = "--$key=$value";
2042                # Quote it if necessary.
2043                if ($segment =~ /[ |<>*]/) {
2044                    $segment = '"' . $segment . '"';
2045                }
2046                # Add it to the return list.
2047                push @retVal, $segment;
2048            }
2049        }
2050        # Return the result.
2051        return join(" ", @retVal);
2052    }
2053    
2054    =head3 ParseCommand
2055    
2056        my ($options, @arguments) = Tracer::ParseCommand(\%optionTable, @inputList);
2057    
2058    Parse a command line consisting of a list of parameters. The initial parameters may be option
2059    specifiers of the form C<->I<option> or C<->I<option>C<=>I<value>. The options are stripped
2060    off and merged into a table of default options. The remainder of the command line is
2061    returned as a list of positional arguments. For example, consider the following invocation.
2062    
2063        my ($options, @arguments) = ParseCommand({ errors => 0, logFile => 'trace.log'}, @words);
2064    
2065    In this case, the list @words will be treated as a command line and there are two options available,
2066    B<errors> and B<logFile>. If @words has the following format
2067    
2068        -logFile=error.log apple orange rutabaga
2069    
2070    then at the end of the invocation, C<$options> will be
2071    
2072        { errors => 0, logFile => 'error.log' }
2073    
2074    and C<@arguments> will contain
2075    
2076        apple orange rutabaga
2077    
2078  The parser allows for some escape sequences. See L</UnEscape> for a description. There is no  The parser allows for some escape sequences. See L</UnEscape> for a description. There is no
2079  support for quote characters.  support for quote characters. Options can be specified with single or double hyphens.
2080    
2081    =over 4
2082    
2083    =item optionTable
2084    
2085    Table of default options.
2086    
2087    =item inputList
2088    
2089    List of words on the command line.
2090    
2091    =item RETURN
2092    
2093    Returns a reference to the option table and a list of the positional arguments.
2094    
2095    =back
2096    
2097    =cut
2098    
2099    sub ParseCommand {
2100        # Get the parameters.
2101        my ($optionTable, @inputList) = @_;
2102        # Process any options in the input list.
2103        my %overrides = ();
2104        while ((@inputList > 0) && ($inputList[0] =~ /^--?/)) {
2105            # Get the current option.
2106            my $arg = shift @inputList;
2107            # Pull out the option name.
2108            $arg =~ /^--?([^=]*)/g;
2109            my $name = $1;
2110            # Check for an option value.
2111            if ($arg =~ /\G=(.*)$/g) {
2112                # Here we have a value for the option.
2113                $overrides{$name} = UnEscape($1);
2114            } else {
2115                # Here there is no value, so we use 1.
2116                $overrides{$name} = 1;
2117            }
2118        }
2119        # Merge the options into the defaults.
2120        GetOptions($optionTable, \%overrides);
2121        # Translate the remaining parameters.
2122        my @retVal = ();
2123        for my $inputParm (@inputList) {
2124            push @retVal, UnEscape($inputParm);
2125        }
2126        # Return the results.
2127        return ($optionTable, @retVal);
2128    }
2129    
2130    
2131    =head2 File Utility Methods
2132    
2133    =head3 GetFile
2134    
2135        my @fileContents = Tracer::GetFile($fileName);
2136    
2137        or
2138    
2139        my $fileContents = Tracer::GetFile($fileName);
2140    
2141    Return the entire contents of a file. In list context, line-ends are removed and
2142    each line is a list element. In scalar context, line-ends are replaced by C<\n>.
2143    
2144    =over 4
2145    
2146    =item fileName
2147    
2148    Name of the file to read.
2149    
2150    =item RETURN
2151    
2152    In a list context, returns the entire file as a list with the line terminators removed.
2153    In a scalar context, returns the entire file as a string. If an error occurs opening
2154    the file, an empty list will be returned.
2155    
2156    =back
2157    
2158    =cut
2159    
2160    sub GetFile {
2161        # Get the parameters.
2162        my ($fileName) = @_;
2163        # Declare the return variable.
2164        my @retVal = ();
2165        # Open the file for input.
2166        my $handle = Open(undef, "<$fileName");
2167        # Read the whole file into the return variable, stripping off any terminator
2168        # characters.
2169        my $lineCount = 0;
2170        while (my $line = <$handle>) {
2171            $lineCount++;
2172            $line = Strip($line);
2173            push @retVal, $line;
2174        }
2175        # Close it.
2176        close $handle;
2177        my $actualLines = @retVal;
2178        Trace("$actualLines lines read from file $fileName.") if T(File => 2);
2179        # Return the file's contents in the desired format.
2180        if (wantarray) {
2181            return @retVal;
2182        } else {
2183            return join "\n", @retVal;
2184        }
2185    }
2186    
2187    =head3 PutFile
2188    
2189        Tracer::PutFile($fileName, \@lines);
2190    
2191    Write out a file from a list of lines of text.
2192    
2193    =over 4
2194    
2195    =item fileName
2196    
2197    Name of the output file.
2198    
2199    =item lines
2200    
2201    Reference to a list of text lines. The lines will be written to the file in order, with trailing
2202    new-line characters. Alternatively, may be a string, in which case the string will be written without
2203    modification.
2204    
2205    =back
2206    
2207    =cut
2208    
2209    sub PutFile {
2210        # Get the parameters.
2211        my ($fileName, $lines) = @_;
2212        # Open the output file.
2213        my $handle = Open(undef, ">$fileName");
2214        # Count the lines written.
2215        if (ref $lines ne 'ARRAY') {
2216            # Here we have a scalar, so we write it raw.
2217            print $handle $lines;
2218            Trace("Scalar put to file $fileName.") if T(File => 3);
2219        } else {
2220            # Write the lines one at a time.
2221            my $count = 0;
2222            for my $line (@{$lines}) {
2223                print $handle "$line\n";
2224                $count++;
2225            }
2226            Trace("$count lines put to file $fileName.") if T(File => 3);
2227        }
2228        # Close the output file.
2229        close $handle;
2230    }
2231    
2232    =head3 ParseRecord
2233    
2234        my @fields = Tracer::ParseRecord($line);
2235    
2236    Parse a tab-delimited data line. The data line is split into field values. Embedded tab
2237    and new-line characters in the data line must be represented as C<\t> and C<\n>, respectively.
2238    These will automatically be converted.
2239    
2240    =over 4
2241    
2242    =item line
2243    
2244    Line of data containing the tab-delimited fields.
2245    
2246    =item RETURN
2247    
2248    Returns a list of the fields found in the data line.
2249    
2250    =back
2251    
2252    =cut
2253    
2254    sub ParseRecord {
2255        # Get the parameter.
2256        my ($line) = @_;
2257        # Remove the trailing new-line, if any.
2258        chomp $line;
2259        # Split the line read into pieces using the tab character.
2260        my @retVal = split /\t/, $line;
2261        # Trim and fix the escapes in each piece.
2262        for my $value (@retVal) {
2263            # Trim leading whitespace.
2264            $value =~ s/^\s+//;
2265            # Trim trailing whitespace.
2266            $value =~ s/\s+$//;
2267            # Delete the carriage returns.
2268            $value =~ s/\r//g;
2269            # Convert the escapes into their real values.
2270            $value =~ s/\\t/"\t"/ge;
2271            $value =~ s/\\n/"\n"/ge;
2272        }
2273        # Return the result.
2274        return @retVal;
2275    }
2276    
2277    =head3 Merge
2278    
2279        my @mergedList = Tracer::Merge(@inputList);
2280    
2281    Sort a list of strings and remove duplicates.
2282    
2283    =over 4
2284    
2285    =item inputList
2286    
2287    List of scalars to sort and merge.
2288    
2289    =item RETURN
2290    
2291    Returns a list containing the same elements sorted in ascending order with duplicates
2292    removed.
2293    
2294    =back
2295    
2296    =cut
2297    
2298    sub Merge {
2299        # Get the input list in sort order.
2300        my @inputList = sort @_;
2301        # Only proceed if the list has at least two elements.
2302        if (@inputList > 1) {
2303            # Now we want to move through the list splicing out duplicates.
2304            my $i = 0;
2305            while ($i < @inputList) {
2306                # Get the current entry.
2307                my $thisEntry = $inputList[$i];
2308                # Find out how many elements duplicate the current entry.
2309                my $j = $i + 1;
2310                my $dup1 = $i + 1;
2311                while ($j < @inputList && $inputList[$j] eq $thisEntry) { $j++; };
2312                # If the number is nonzero, splice out the duplicates found.
2313                if ($j > $dup1) {
2314                    splice @inputList, $dup1, $j - $dup1;
2315                }
2316                # Now the element at position $dup1 is different from the element before it
2317                # at position $i. We push $i forward one position and start again.
2318                $i++;
2319            }
2320        }
2321        # Return the merged list.
2322        return @inputList;
2323    }
2324    
2325    =head3 Open
2326    
2327        my $handle = Open($fileHandle, $fileSpec, $message);
2328    
2329    Open a file.
2330    
2331    The I<$fileSpec> is essentially the second argument of the PERL C<open>
2332    function. The mode is specified using Unix-like shell information. So, for
2333    example,
2334    
2335        Open(\*LOGFILE, '>>/usr/spool/news/twitlog', "Could not open twit log.");
2336    
2337    would open for output appended to the specified file, and
2338    
2339        Open(\*DATASTREAM, "| sort -u >$outputFile", "Could not open $outputFile.");
2340    
2341    would open a pipe that sorts the records written and removes duplicates. Note
2342    the use of file handle syntax in the Open call. To use anonymous file handles,
2343    code as follows.
2344    
2345        my $logFile = Open(undef, '>>/usr/spool/news/twitlog', "Could not open twit log.");
2346    
2347    The I<$message> parameter is used if the open fails. If it is set to C<0>, then
2348    the open returns TRUE if successful and FALSE if an error occurred. Otherwise, a
2349    failed open will throw an exception and the third parameter will be used to construct
2350    an error message. If the parameter is omitted, a standard message is constructed
2351    using the file spec.
2352    
2353        Could not open "/usr/spool/news/twitlog"
2354    
2355    Note that the mode characters are automatically cleaned from the file name.
2356    The actual error message from the file system will be captured and appended to the
2357    message in any case.
2358    
2359        Could not open "/usr/spool/news/twitlog": file not found.
2360    
2361    In some versions of PERL the only error message we get is a number, which
2362    corresponds to the C++ C<errno> value.
2363    
2364        Could not open "/usr/spool/news/twitlog": 6.
2365    
2366    =over 4
2367    
2368    =item fileHandle
2369    
2370    File handle. If this parameter is C<undef>, a file handle will be generated
2371    and returned as the value of this method.
2372    
2373    =item fileSpec
2374    
2375    File name and mode, as per the PERL C<open> function.
2376    
2377    =item message (optional)
2378    
2379    Error message to use if the open fails. If omitted, a standard error message
2380    will be generated. In either case, the error information from the file system
2381    is appended to the message. To specify a conditional open that does not throw
2382    an error if it fails, use C<0>.
2383    
2384    =item RETURN
2385    
2386    Returns the name of the file handle assigned to the file, or C<undef> if the
2387    open failed.
2388    
2389    =back
2390    
2391    =cut
2392    
2393    sub Open {
2394        # Get the parameters.
2395        my ($fileHandle, $fileSpec, $message) = @_;
2396        # Attempt to open the file.
2397        my $rv = open $fileHandle, $fileSpec;
2398        # If the open failed, generate an error message.
2399        if (! $rv) {
2400            # Save the system error message.
2401            my $sysMessage = $!;
2402            # See if we need a default message.
2403            if (!$message) {
2404                # Clean any obvious mode characters and leading spaces from the
2405                # filename.
2406                my ($fileName) = FindNamePart($fileSpec);
2407                $message = "Could not open \"$fileName\"";
2408            }
2409            # Terminate with an error using the supplied message and the
2410            # error message from the file system.
2411            Confess("$message: $!");
2412        }
2413        # Return the file handle.
2414        return $fileHandle;
2415    }
2416    
2417    =head3 FindNamePart
2418    
2419        my ($fileName, $start, $len) = Tracer::FindNamePart($fileSpec);
2420    
2421    Extract the portion of a file specification that contains the file name.
2422    
2423    A file specification is the string passed to an C<open> call. It specifies the file
2424    mode and name. In a truly complex situation, it can specify a pipe sequence. This
2425    method assumes that the file name is whatever follows the first angle bracket
2426    sequence.  So, for example, in the following strings the file name is
2427    C</usr/fig/myfile.txt>.
2428    
2429        >>/usr/fig/myfile.txt
2430        </usr/fig/myfile.txt
2431        | sort -u > /usr/fig/myfile.txt
2432    
2433    If the method cannot find a file name using its normal methods, it will return the
2434    whole incoming string.
2435    
2436    =over 4
2437    
2438    =item fileSpec
2439    
2440    File specification string from which the file name is to be extracted.
2441    
2442    =item RETURN
2443    
2444    Returns a three-element list. The first element contains the file name portion of
2445    the specified string, or the whole string if a file name cannot be found via normal
2446    methods. The second element contains the start position of the file name portion and
2447    the third element contains the length.
2448    
2449    =back
2450    
2451    =cut
2452    #: Return Type $;
2453    sub FindNamePart {
2454        # Get the parameters.
2455        my ($fileSpec) = @_;
2456        # Default to the whole input string.
2457        my ($retVal, $pos, $len) = ($fileSpec, 0, length $fileSpec);
2458        # Parse out the file name if we can.
2459        if ($fileSpec =~ m/(<|>>?)(.+?)(\s*)$/) {
2460            $retVal = $2;
2461            $len = length $retVal;
2462            $pos = (length $fileSpec) - (length $3) - $len;
2463        }
2464        # Return the result.
2465        return ($retVal, $pos, $len);
2466    }
2467    
2468    =head3 OpenDir
2469    
2470        my @files = OpenDir($dirName, $filtered, $flag);
2471    
2472    Open a directory and return all the file names. This function essentially performs
2473    the functions of an C<opendir> and C<readdir>. If the I<$filtered> parameter is
2474    set to TRUE, all filenames beginning with a period (C<.>), dollar sign (C<$>),
2475    or pound sign (C<#>) and all filenames ending with a tilde C<~>) will be
2476    filtered out of the return list. If the directory does not open and I<$flag> is not
2477    set, an exception is thrown. So, for example,
2478    
2479        my @files = OpenDir("/Volumes/fig/contigs", 1);
2480    
2481    is effectively the same as
2482    
2483        opendir(TMP, "/Volumes/fig/contigs") || Confess("Could not open /Volumes/fig/contigs.");
2484        my @files = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir(TMP);
2485    
2486    Similarly, the following code
2487    
2488        my @files = grep { $_ =~ /^\d/ } OpenDir("/Volumes/fig/orgs", 0, 1);
2489    
2490    Returns the names of all files in C</Volumes/fig/orgs> that begin with digits and
2491    automatically returns an empty list if the directory fails to open.
2492    
2493    =over 4
2494    
2495    =item dirName
2496    
2497    Name of the directory to open.
2498    
2499    =item filtered
2500    
2501    TRUE if files whose names begin with a period (C<.>) should be automatically removed
2502    from the list, else FALSE.
2503    
2504    =item flag
2505    
2506    TRUE if a failure to open is okay, else FALSE
2507    
2508    =back
2509    
2510    =cut
2511    #: Return Type @;
2512    sub OpenDir {
2513        # Get the parameters.
2514        my ($dirName, $filtered, $flag) = @_;
2515        # Declare the return variable.
2516        my @retVal = ();
2517        # Open the directory.
2518        if (opendir(my $dirHandle, $dirName)) {
2519            # The directory opened successfully. Get the appropriate list according to the
2520            # strictures of the filter parameter.
2521            if ($filtered) {
2522                @retVal = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir $dirHandle;
2523            } else {
2524                @retVal = readdir $dirHandle;
2525            }
2526        } elsif (! $flag) {
2527            # Here the directory would not open and it's considered an error.
2528            Confess("Could not open directory $dirName.");
2529        }
2530        # Return the result.
2531        return @retVal;
2532    }
2533    
2534    
2535    =head3 Insure
2536    
2537        Insure($dirName, $chmod);
2538    
2539    Insure a directory is present.
2540    
2541    =over 4
2542    
2543    =item dirName
2544    
2545    Name of the directory to check. If it does not exist, it will be created.
2546    
2547    =item chmod (optional)
2548    
2549    Security privileges to be given to the directory if it is created.
2550    
2551    =back
2552    
2553    =cut
2554    
2555    sub Insure {
2556        my ($dirName, $chmod) = @_;
2557        if (! -d $dirName) {
2558            Trace("Creating $dirName directory.") if T(2);
2559            eval {
2560                mkpath $dirName;
2561                # If we have permissions specified, set them here.
2562                if (defined($chmod)) {
2563                    chmod $chmod, $dirName;
2564                }
2565            };
2566            if ($@) {
2567                Confess("Error creating $dirName: $@");
2568            }
2569        }
2570    }
2571    
2572    =head3 ChDir
2573    
2574        ChDir($dirName);
2575    
2576    Change to the specified directory.
2577    
2578    =over 4
2579    
2580    =item dirName
2581    
2582    Name of the directory to which we want to change.
2583    
2584    =back
2585    
2586    =cut
2587    
2588    sub ChDir {
2589        my ($dirName) = @_;
2590        if (! -d $dirName) {
2591            Confess("Cannot change to directory $dirName: no such directory.");
2592        } else {
2593            Trace("Changing to directory $dirName.") if T(File => 4);
2594            my $okFlag = chdir $dirName;
2595            if (! $okFlag) {
2596                Confess("Error switching to directory $dirName.");
2597            }
2598        }
2599    }
2600    
2601    =head3 SetPermissions
2602    
2603        Tracer::SetPermissions($dirName, $group, $mask, %otherMasks);
2604    
2605    Set the permissions for a directory and all the files and folders inside it.
2606    In addition, the group ownership will be changed to the specified value.
2607    
2608    This method is more vulnerable than most to permission and compatability
2609    problems, so it does internal error recovery.
2610    
2611    =over 4
2612    
2613    =item dirName
2614    
2615    Name of the directory to process.
2616    
2617    =item group
2618    
2619    Name of the group to be assigned.
2620    
2621    =item mask
2622    
2623    Permission mask. Bits that are C<1> in this mask will be ORed into the
2624    permission bits of any file or directory that does not already have them
2625    set to 1.
2626    
2627    =item otherMasks
2628    
2629    Map of search patterns to permission masks. If a directory name matches
2630    one of the patterns, that directory and all its members and subdirectories
2631    will be assigned the new pattern. For example, the following would
2632    assign 0664 to most files, but would use 0777 for directories named C<tmp>.
2633    
2634        Tracer::SetPermissions($dirName, 'fig', 01664, '^tmp$' => 01777);
2635    
2636    The list is ordered, so the following would use 0777 for C<tmp1> and
2637    0666 for C<tmp>, C<tmp2>, or C<tmp3>.
2638    
2639        Tracer::SetPermissions($dirName, 'fig', 01664, '^tmp1' => 0777,
2640                                                       '^tmp' => 0666);
2641    
2642    Note that the pattern matches are all case-insensitive, and only directory
2643    names are matched, not file names.
2644    
2645    =back
2646    
2647    =cut
2648    
2649    sub SetPermissions {
2650        # Get the parameters.
2651        my ($dirName, $group, $mask, @otherMasks) = @_;
2652        # Set up for error recovery.
2653        eval {
2654            # Switch to the specified directory.
2655            ChDir($dirName);
2656            # Get the group ID.
2657            my $gid = getgrnam($group);
2658            # Get the mask for tracing.
2659            my $traceMask = sprintf("%04o", $mask) . "($mask)";
2660            Trace("Fixing permissions for directory $dirName using group $group($gid) and mask $traceMask.") if T(File => 2);
2661            my $fixCount = 0;
2662            my $lookCount = 0;
2663            # @dirs will be a stack of directories to be processed.
2664            my @dirs = (getcwd());
2665            while (scalar(@dirs) > 0) {
2666                # Get the current directory.
2667                my $dir = pop @dirs;
2668                # Check for a match to one of the specified directory names. To do
2669                # that, we need to pull the individual part of the name off of the
2670                # whole path.
2671                my $simpleName = $dir;
2672                if ($dir =~ m!/([^/]+)$!) {
2673                    $simpleName = $1;
2674                }
2675                Trace("Simple directory name for $dir is $simpleName.") if T(File => 4);
2676                # Search for a match.
2677                my $match = 0;
2678                my $i;
2679                for ($i = 0; $i < $#otherMasks && ! $match; $i += 2) {
2680                    my $pattern = $otherMasks[$i];
2681                    if ($simpleName =~ /$pattern/i) {
2682                        $match = 1;
2683                    }
2684                }
2685                # Find out if we have a match. Note we use $i-1 because the loop added 2
2686                # before terminating due to the match.
2687                if ($match && $otherMasks[$i-1] != $mask) {
2688                    # This directory matches one of the incoming patterns, and it's
2689                    # a different mask, so we process it recursively with that mask.
2690                    SetPermissions($dir, $group, $otherMasks[$i-1], @otherMasks);
2691                } else {
2692                    # Here we can process normally. Get all of the non-hidden members.
2693                    my @submems = OpenDir($dir, 1);
2694                    for my $submem (@submems) {
2695                        # Get the full name.
2696                        my $thisMem = "$dir/$submem";
2697                        Trace("Checking member $thisMem.") if T(4);
2698                        $lookCount++;
2699                        if ($lookCount % 1000 == 0) {
2700                            Trace("$lookCount members examined. Current is $thisMem. Mask is $traceMask") if T(File => 3);
2701                        }
2702                        # Fix the group.
2703                        chown -1, $gid, $thisMem;
2704                        # Insure this member is not a symlink.
2705                        if (! -l $thisMem) {
2706                            # Get its info.
2707                            my $fileInfo = stat $thisMem;
2708                            # Only proceed if we got the info. Otherwise, it's a hard link
2709                            # and we want to skip it anyway.
2710                            if ($fileInfo) {
2711                                my $fileMode = $fileInfo->mode;
2712                                if (($fileMode & $mask) != $mask) {
2713                                    # Fix this member.
2714                                    $fileMode |= $mask;
2715                                    chmod $fileMode, $thisMem;
2716                                    $fixCount++;
2717                                }
2718                                # If it's a subdirectory, stack it.
2719                                if (-d $thisMem) {
2720                                    push @dirs, $thisMem;
2721                                }
2722                            }
2723                        }
2724                    }
2725                }
2726            }
2727            Trace("$lookCount files and directories processed, $fixCount fixed.") if T(File => 2);
2728        };
2729        # Check for an error.
2730        if ($@) {
2731            Confess("SetPermissions error: $@");
2732        }
2733    }
2734    
2735    =head3 GetLine
2736    
2737        my @data = Tracer::GetLine($handle);
2738    
2739    Read a line of data from a tab-delimited file.
2740    
2741    =over 4
2742    
2743    =item handle
2744    
2745    Open file handle from which to read.
2746    
2747    =item RETURN
2748    
2749    Returns a list of the fields in the record read. The fields are presumed to be
2750    tab-delimited. If we are at the end of the file, then an empty list will be
2751    returned. If an empty line is read, a single list item consisting of a null
2752    string will be returned.
2753    
2754    =back
2755    
2756    =cut
2757    
2758    sub GetLine {
2759        # Get the parameters.
2760        my ($handle) = @_;
2761        # Declare the return variable.
2762        my @retVal = ();
2763        Trace("File position is " . tell($handle) . ". EOF flag is " . eof($handle) . ".") if T(File => 4);
2764        # Read from the file.
2765        my $line = <$handle>;
2766        # Only proceed if we found something.
2767        if (defined $line) {
2768            # Remove the new-line. We are a bit over-cautious here because the file may be coming in via an
2769            # upload control and have a nonstandard EOL combination.
2770            $line =~ s/(\r|\n)+$//;
2771            # Here we do some fancy tracing to help in debugging complicated EOL marks.
2772            if (T(File => 4)) {
2773                my $escapedLine = $line;
2774                $escapedLine =~ s/\n/\\n/g;
2775                $escapedLine =~ s/\r/\\r/g;
2776                $escapedLine =~ s/\t/\\t/g;
2777                Trace("Line read: -->$escapedLine<--");
2778            }
2779            # If the line is empty, return a single empty string; otherwise, parse
2780            # it into fields.
2781            if ($line eq "") {
2782                push @retVal, "";
2783            } else {
2784                push @retVal, split /\t/,$line;
2785            }
2786        } else {
2787            # Trace the reason the read failed.
2788            Trace("End of file: $!") if T(File => 3);
2789        }
2790        # Return the result.
2791        return @retVal;
2792    }
2793    
2794    =head3 PutLine
2795    
2796        Tracer::PutLine($handle, \@fields, $eol);
2797    
2798    Write a line of data to a tab-delimited file. The specified field values will be
2799    output in tab-separated form, with a trailing new-line.
2800    
2801    =over 4
2802    
2803    =item handle
2804    
2805    Output file handle.
2806    
2807    =item fields
2808    
2809    List of field values.
2810    
2811    =item eol (optional)
2812    
2813    End-of-line character (default is "\n").
2814    
2815    =back
2816    
2817    =cut
2818    
2819    sub PutLine {
2820        # Get the parameters.
2821        my ($handle, $fields, $eol) = @_;
2822        # Write the data.
2823        print $handle join("\t", @{$fields}) . ($eol || "\n");
2824    }
2825    
2826    
2827    =head3 PrintLine
2828    
2829        Tracer::PrintLine($line);
2830    
2831    Print a line of text with a trailing new-line.
2832    
2833    =over 4
2834    
2835    =item line
2836    
2837    Line of text to print.
2838    
2839    =back
2840    
2841    =cut
2842    
2843    sub PrintLine {
2844        # Get the parameters.
2845        my ($line) = @_;
2846        # Print the line.
2847        print "$line\n";
2848    }
2849    
2850    
2851    =head2 Other Useful Methods
2852    
2853    =head3 IDHASH
2854    
2855        my $hash = SHTargetSearch::IDHASH(@keys);
2856    
2857    This is a dinky little method that converts a list of values to a reference
2858    to hash of values to labels. The values and labels are the same.
2859    
2860    =cut
2861    
2862    sub IDHASH {
2863        my %retVal = map { $_ => $_ } @_;
2864        return \%retVal;
2865    }
2866    
2867    =head3 Pluralize
2868    
2869        my $plural = Tracer::Pluralize($word);
2870    
2871    This is a very simple pluralization utility. It adds an C<s> at the end
2872    of the input word unless it already ends in an C<s>, in which case it
2873    adds C<es>.
2874    
2875  =over 4  =over 4
2876    
2877  =item optionTable  =item word
2878    
2879  Table of default options.  Singular word to pluralize.
2880    
2881    =item RETURN
2882    
2883    Returns the probable plural form of the word.
2884    
2885    =back
2886    
2887    =cut
2888    
2889    sub Pluralize {
2890        # Get the parameters.
2891        my ($word) = @_;
2892        # Declare the return variable.
2893        my $retVal;
2894        if ($word =~ /s$/) {
2895            $retVal = $word . 'es';
2896        } else {
2897            $retVal = $word . 's';
2898        }
2899        # Return the result.
2900        return $retVal;
2901    }
2902    
2903    =head3 Numeric
2904    
2905        my $okFlag = Tracer::Numeric($string);
2906    
2907    Return the value of the specified string if it is numeric, or an undefined value
2908    if it is not numeric.
2909    
2910    =over 4
2911    
2912    =item string
2913    
2914    String to check.
2915    
2916    =item RETURN
2917    
2918    Returns the numeric value of the string if successful, or C<undef> if the string
2919    is not numeric.
2920    
2921    =back
2922    
2923    =cut
2924    
2925    sub Numeric {
2926        # Get the parameters.
2927        my ($string) = @_;
2928        # We'll put the value in here if we succeed.
2929        my $retVal;
2930        # Get a working copy of the string.
2931        my $copy = $string;
2932        # Trim leading and trailing spaces.
2933        $copy =~ s/^\s+//;
2934        $copy =~ s/\s+$//;
2935        # Check the result.
2936        if ($copy =~ /^[+-]?\d+$/) {
2937            $retVal = $copy;
2938        } elsif ($copy =~ /^([+-]\d+|\d*)[eE][+-]?\d+$/) {
2939            $retVal = $copy;
2940        } elsif ($copy =~ /^([+-]\d+|\d*)\.\d*([eE][+-]?\d+)?$/) {
2941            $retVal = $copy;
2942        }
2943        # Return the result.
2944        return $retVal;
2945    }
2946    
2947    
2948    =head3 ParseParm
2949    
2950        my $listValue = Tracer::ParseParm($string);
2951    
2952    Convert a parameter into a list reference. If the parameter is undefined,
2953    an undefined value will be returned. Otherwise, it will be parsed as a
2954    comma-separated list of values.
2955    
2956    =over 4
2957    
2958    =item string
2959    
2960    Incoming string.
2961    
2962    =item RETURN
2963    
2964    Returns a reference to a list of values, or C<undef> if the incoming value
2965    was undefined.
2966    
2967    =back
2968    
2969    =cut
2970    
2971    sub ParseParm {
2972        # Get the parameters.
2973        my ($string) = @_;
2974        # Declare the return variable.
2975        my $retVal;
2976        # Check for data.
2977        if (defined $string) {
2978            # We have some, so split it into a list.
2979            $retVal = [ split /\s*,\s*/, $string];
2980        }
2981        # Return the result.
2982        return $retVal;
2983    }
2984    
2985    =head3 Now
2986    
2987        my $string = Tracer::Now();
2988    
2989    Return a displayable time stamp containing the local time. Whatever format this
2990    method produces must be parseable by L</ParseDate>.
2991    
2992    =cut
2993    
2994    sub Now {
2995        return DisplayTime(time);
2996    }
2997    
2998    =head3 DisplayTime
2999    
3000        my $string = Tracer::DisplayTime($time);
3001    
3002    Convert a time value to a displayable time stamp. Whatever format this
3003    method produces must be parseable by L</ParseDate>.
3004    
3005    =over 4
3006    
3007    =item time
3008    
3009    Time to display, in seconds since the epoch, or C<undef> if the time is unknown.
3010    
3011    =item RETURN
3012    
3013    Returns a displayable time, or C<(n/a)> if the incoming time is undefined.
3014    
3015    =back
3016    
3017    =cut
3018    
3019    sub DisplayTime {
3020        my ($time) = @_;
3021        my $retVal = "(n/a)";
3022        if (defined $time) {
3023            my ($sec,$min,$hour,$mday,$mon,$year,$wday,$yday,$isdst) = localtime($time);
3024            $retVal = _p2($mon+1) . "/" . _p2($mday) . "/" . ($year + 1900) . " " .
3025                      _p2($hour) . ":" . _p2($min) . ":" . _p2($sec);
3026        }
3027        return $retVal;
3028    }
3029    
3030    # Pad a number to 2 digits.
3031    sub _p2 {
3032        my ($value) = @_;
3033        $value = "0$value" if ($value < 10);
3034        return $value;
3035    }
3036    
3037    =head3 Escape
3038    
3039        my $codedString = Tracer::Escape($realString);
3040    
3041    Escape a string for use in a command. Tabs will be replaced by C<\t>, new-lines
3042    replaced by C<\n>, carriage returns will be deleted, and backslashes will be doubled. The
3043    result is to reverse the effect of L</UnEscape>.
3044    
3045    =over 4
3046    
3047    =item realString
3048    
3049    String to escape.
3050    
3051    =item RETURN
3052    
3053    Escaped equivalent of the real string.
3054    
3055    =back
3056    
3057    =cut
3058    
3059    sub Escape {
3060        # Get the parameter.
3061        my ($realString) = @_;
3062        # Initialize the return variable.
3063        my $retVal = "";
3064        # Loop through the parameter string, looking for sequences to escape.
3065        while (length $realString > 0) {
3066            # Look for the first sequence to escape.
3067            if ($realString =~ /^(.*?)([\n\t\r\\])/) {
3068                # Here we found it. The text preceding the sequence is in $1. The sequence
3069                # itself is in $2. First, move the clear text to the return variable.
3070                $retVal .= $1;
3071                # Strip the processed section off the real string.
3072                $realString = substr $realString, (length $2) + (length $1);
3073                # Get the matched character.
3074                my $char = $2;
3075                # If we have a CR, we are done.
3076                if ($char ne "\r") {
3077                    # It's not a CR, so encode the escape sequence.
3078                    $char =~ tr/\t\n/tn/;
3079                    $retVal .= "\\" . $char;
3080                }
3081            } else {
3082                # Here there are no more escape sequences. The rest of the string is
3083                # transferred unmodified.
3084                $retVal .= $realString;
3085                $realString = "";
3086            }
3087        }
3088        # Return the result.
3089        return $retVal;
3090    }
3091    
3092    =head3 UnEscape
3093    
3094        my $realString = Tracer::UnEscape($codedString);
3095    
3096    Replace escape sequences with their actual equivalents. C<\t> will be replaced by
3097    a tab, C<\n> by a new-line character, and C<\\> by a backslash. C<\r> codes will
3098    be deleted.
3099    
3100    =over 4
3101    
3102    =item codedString
3103    
3104    String to un-escape.
3105    
3106    =item RETURN
3107    
3108    Returns a copy of the original string with the escape sequences converted to their actual
3109    values.
3110    
3111    =back
3112    
3113    =cut
3114    
3115    sub UnEscape {
3116        # Get the parameter.
3117        my ($codedString) = @_;
3118        # Initialize the return variable.
3119        my $retVal = "";
3120        # Only proceed if the incoming string is nonempty.
3121        if (defined $codedString) {
3122            # Loop through the parameter string, looking for escape sequences. We can't do
3123            # translating because it causes problems with the escaped slash. ("\\t" becomes
3124            # "\<tab>" no matter what we do.)
3125            while (length $codedString > 0) {
3126                # Look for the first escape sequence.
3127                if ($codedString =~ /^(.*?)\\(\\|n|t|r)/) {
3128                    # Here we found it. The text preceding the sequence is in $1. The sequence
3129                    # itself is in $2. First, move the clear text to the return variable.
3130                    $retVal .= $1;
3131                    $codedString = substr $codedString, (2 + length $1);
3132                    # Get the escape value.
3133                    my $char = $2;
3134                    # If we have a "\r", we are done.
3135                    if ($char ne 'r') {
3136                        # Here it's not an 'r', so we convert it.
3137                        $char =~ tr/\\tn/\\\t\n/;
3138                        $retVal .= $char;
3139                    }
3140                } else {
3141                    # Here there are no more escape sequences. The rest of the string is
3142                    # transferred unmodified.
3143                    $retVal .= $codedString;
3144                    $codedString = "";
3145                }
3146            }
3147        }
3148        # Return the result.
3149        return $retVal;
3150    }
3151    
3152    =head3 Percent
3153    
3154        my $percent = Tracer::Percent($number, $base);
3155    
3156    Returns the percent of the base represented by the given number. If the base
3157    is zero, returns zero.
3158    
3159    =over 4
3160    
3161    =item number
3162    
3163    Percent numerator.
3164    
3165    =item base
3166    
3167    Percent base.
3168    
3169    =item RETURN
3170    
3171    Returns the percentage of the base represented by the numerator.
3172    
3173    =back
3174    
3175    =cut
3176    
3177    sub Percent {
3178        # Get the parameters.
3179        my ($number, $base) = @_;
3180        # Declare the return variable.
3181        my $retVal = 0;
3182        # Compute the percent.
3183        if ($base != 0) {
3184            $retVal = $number * 100 / $base;
3185        }
3186        # Return the result.
3187        return $retVal;
3188    }
3189    
3190    =head3 In
3191    
3192        my $flag = Tracer::In($value, $min, $max);
3193    
3194    Return TRUE if the value is between the minimum and the maximum, else FALSE.
3195    
3196    =cut
3197    
3198    sub In {
3199        return ($_[0] <= $_[2] && $_[0] >= $_[1]);
3200    }
3201    
3202    
3203    =head3 Constrain
3204    
3205        my $constrained = Constrain($value, $min, $max);
3206    
3207    Modify a numeric value to bring it to a point in between a maximum and a minimum.
3208    
3209    =over 4
3210    
3211    =item value
3212    
3213    Value to constrain.
3214    
3215    =item min (optional)
3216    
3217    Minimum permissible value. If this parameter is undefined, no minimum constraint will be applied.
3218    
3219    =item max (optional)
3220    
3221    Maximum permissible value. If this parameter is undefined, no maximum constraint will be applied.
3222    
3223    =item RETURN
3224    
3225    Returns the incoming value, constrained according to the other parameters.
3226    
3227    =back
3228    
3229    =cut
3230    
3231    sub Constrain {
3232        # Get the parameters.
3233        my ($value, $min, $max) = @_;
3234        # Declare the return variable.
3235        my $retVal = $value;
3236        # Apply the minimum constraint.
3237        if (defined $min && $retVal < $min) {
3238            $retVal = $min;
3239        }
3240        # Apply the maximum constraint.
3241        if (defined $max && $retVal > $max) {
3242            $retVal = $max;
3243        }
3244        # Return the result.
3245        return $retVal;
3246    }
3247    
3248    =head3 Min
3249    
3250        my $min = Min($value1, $value2, ... $valueN);
3251    
3252    Return the minimum argument. The arguments are treated as numbers.
3253    
3254    =over 4
3255    
3256  =item inputList  =item $value1, $value2, ... $valueN
3257    
3258  List of words on the command line.  List of numbers to compare.
3259    
3260  =item RETURN  =item RETURN
3261    
3262  Returns a reference to the option table and a list of the positional arguments.  Returns the lowest number in the list.
3263    
3264  =back  =back
3265    
3266  =cut  =cut
3267    
3268  sub ParseCommand {  sub Min {
3269          # Get the parameters.      # Get the parameters. Note that we prime the return value with the first parameter.
3270          my ($optionTable, @inputList) = @_;      my ($retVal, @values) = @_;
3271          # Process any options in the input list.      # Loop through the remaining parameters, looking for the lowest.
3272          my %overrides = ();      for my $value (@values) {
3273          while ((@inputList > 0) && ($inputList[0] =~ /^-/)) {          if ($value < $retVal) {
3274                  # Get the current option.              $retVal = $value;
                 my $arg = shift @inputList;  
                 # Pull out the option name.  
                 $arg =~ /^-([^=]*)/g;  
                 my $name = $1;  
                 # Check for an option value.  
                 if ($arg =~ /\G=(.*)$/g) {  
                         # Here we have a value for the option.  
                         $overrides{$name} = UnEscape($1);  
                 } else {  
                         # Here there is no value, so we use 1.  
                         $overrides{$name} = 1;  
                 }  
3275          }          }
         # Merge the options into the defaults.  
         GetOptions($optionTable, \%overrides);  
         # Translate the remaining parameters.  
         my @retVal = ();  
         for my $inputParm (@inputList) {  
                 push @retVal, UnEscape($inputParm);  
3276          }          }
3277          # Return the results.      # Return the minimum found.
3278          return ($optionTable, @retVal);      return $retVal;
3279  }  }
3280    
3281  =head3 Escape  =head3 Max
3282    
3283  C<< my $codedString = Tracer::Escape($realString); >>      my $max = Max($value1, $value2, ... $valueN);
3284    
3285  Escape a string for use in a command length. Spaces will be replaced by C<\b>,  Return the maximum argument. The arguments are treated as numbers.
 tabs replaced by C<\t>, new-lines replaced by C<\n>, and backslashes will be  
 doubled. The effect is to exactly reverse the effect of L</UnEscape>.  
3286    
3287  =over 4  =over 4
3288    
3289  =item realString  =item $value1, $value2, ... $valueN
3290    
3291  String to escape.  List of numbers to compare.
3292    
3293  =item RETURN  =item RETURN
3294    
3295  Escaped equivalent of the real string.  Returns the highest number in the list.
3296    
3297  =back  =back
3298    
3299  =cut  =cut
3300    
3301  sub Escape {  sub Max {
3302          # Get the parameter.      # Get the parameters. Note that we prime the return value with the first parameter.
3303          my ($realString) = @_;      my ($retVal, @values) = @_;
3304          # Initialize the return variable.      # Loop through the remaining parameters, looking for the highest.
3305          my $retVal = "";      for my $value (@values) {
3306          # Loop through the parameter string, looking for sequences to escape.          if ($value > $retVal) {
3307          while (length $realString > 0) {              $retVal = $value;
                 # Look for the first sequence to escape.  
                 if ($realString =~ /^(.*?)([ \n\t\\])/) {  
                         # Here we found it. The text preceding the sequence is in $1. The sequence  
                         # itself is in $2. First, move the clear text to the return variable.  
                         $retVal .= $1;  
                         $realString = substr $realString, (length $2 + length $1);  
                         # Encode the escape sequence.  
                         my $char = $2;  
                         $char =~ tr/ \t\n/btn/;  
                         $retVal .= "\\" . $char;  
                 } else {  
                         # Here there are no more escape sequences. The rest of the string is  
                         # transferred unmodified.  
                         $retVal .= $realString;  
                         $realString = "";  
3308                  }                  }
3309          }          }
3310          # Return the result.      # Return the maximum found.
3311          return $retVal;          return $retVal;
3312  }  }
3313    
3314  =head3 UnEscape  =head3 Strip
3315    
3316  C<< my $realString = Tracer::UnEscape($codedString); >>      my $string = Tracer::Strip($line);
3317    
3318  Replace escape sequences with their actual equivalents. C<\b> will be replaced by a space,  Strip all line terminators off a string. This is necessary when dealing with files
3319  C<\t> by a tab, C<\n> by a new-line character, and C<\\> by a back-slash.  that may have been transferred back and forth several times among different
3320    operating environments.
3321    
3322  =over 4  =over 4
3323    
3324  =item codedString  =item line
3325    
3326  String to un-escape.  Line of text to be stripped.
3327    
3328  =item RETURN  =item RETURN
3329    
3330  Returns a copy of the original string with the escape sequences converted to their actual  The same line of text with all the line-ending characters chopped from the end.
 values.  
3331    
3332  =back  =back
3333    
3334  =cut  =cut
3335    
3336  sub UnEscape {  sub Strip {
3337          # Get the parameter.      # Get a copy of the parameter string.
3338          my ($codedString) = @_;      my ($string) = @_;
3339          # Initialize the return variable.      my $retVal = (defined $string ? $string : "");
3340          my $retVal = "";      # Strip the line terminator characters.
3341          # Only proceed if the incoming string is nonempty.      $retVal =~ s/(\r|\n)+$//g;
         if (defined $codedString) {  
                 # Loop through the parameter string, looking for escape sequences. We can't do  
                 # translating because it causes problems with the escaped slash. ("\\b" becomes  
                 # "\ " no matter what we do.)  
                 while (length $codedString > 0) {  
                         # Look for the first escape sequence.  
                         if ($codedString =~ /^(.*?)\\(\\|b|n|t)/) {  
                                 # Here we found it. The text preceding the sequence is in $1. The sequence  
                                 # itself is in $2. First, move the clear text to the return variable.  
                                 $retVal .= $1;  
                                 $codedString = substr $codedString, (2 + length $1);  
                                 # Decode the escape sequence.  
                                 my $char = $2;  
                                 $char =~ tr/\\btn/\\ \t\n/;  
                                 $retVal .= $char;  
                         } else {  
                                 # Here there are no more escape sequences. The rest of the string is  
                                 # transferred unmodified.  
                                 $retVal .= $codedString;  
                                 $codedString = "";  
                         }  
                 }  
         }  
3342          # Return the result.          # Return the result.
3343          return $retVal;          return $retVal;
3344  }  }
3345    
3346  =head3 ParseRecord  =head3 Trim
3347    
3348  C<< my @fields = Tracer::ParseRecord($line); >>      my $string = Tracer::Trim($line);
3349    
3350  Parse a tab-delimited data line. The data line is split into field values. Embedded tab  Trim all spaces from the beginning and ending of a string.
 and new-line characters in the data line must be represented as C<\t> and C<\n>, respectively.  
 These will automatically be converted.  
3351    
3352  =over 4  =over 4
3353    
3354  =item line  =item line
3355    
3356  Line of data containing the tab-delimited fields.  Line of text to be trimmed.
3357    
3358  =item RETURN  =item RETURN
3359    
3360  Returns a list of the fields found in the data line.  The same line of text with all whitespace chopped off either end.
3361    
3362  =back  =back
3363    
3364  =cut  =cut
3365    
3366  sub ParseRecord {  sub Trim {
3367          # Get the parameter.      # Get a copy of the parameter string.
3368          my ($line) = @_;      my ($string) = @_;
3369          # Remove the trailing new-line, if any.      my $retVal = (defined $string ? $string : "");
3370          chomp $line;      # Strip the front spaces.
3371          # Split the line read into pieces using the tab character.      $retVal =~ s/^\s+//;
3372          my @retVal = split /\t/, $line;      # Strip the back spaces.
3373          # Trim and fix the escapes in each piece.      $retVal =~ s/\s+$//;
         for my $value (@retVal) {  
                 # Trim leading whitespace.  
                 $value =~ s/^\s+//;  
                 # Trim trailing whitespace.  
                 $value =~ s/\s+$//;  
                 # Delete the carriage returns.  
                 $value =~ s/\r//g;  
                 # Convert the escapes into their real values.  
                 $value =~ s/\\t/"\t"/ge;  
                 $value =~ s/\\n/"\n"/ge;  
         }  
3374          # Return the result.          # Return the result.
3375          return @retVal;      return $retVal;
3376  }  }
3377    
3378  =head3 Merge  =head3 Pad
3379    
3380  C<< my @mergedList = Tracer::Merge(@inputList); >>      my $paddedString = Tracer::Pad($string, $len, $left, $padChar);
3381    
3382  Sort a list of strings and remove duplicates.  Pad a string to a specified length. The pad character will be a
3383    space, and the padding will be on the right side unless specified
3384    in the third parameter.
3385    
3386  =over 4  =over 4
3387    
3388  =item inputList  =item string
3389    
3390  List of scalars to sort and merge.  String to be padded.
3391    
3392    =item len
3393    
3394    Desired length of the padded string.
3395    
3396    =item left (optional)
3397    
3398    TRUE if the string is to be left-padded; otherwise it will be padded on the right.
3399    
3400    =item padChar (optional)
3401    
3402    Character to use for padding. The default is a space.
3403    
3404  =item RETURN  =item RETURN
3405    
3406  Returns a list containing the same elements sorted in ascending order with duplicates  Returns a copy of the original string with the pad character added to the
3407  removed.  specified end so that it achieves the desired length.
3408    
3409  =back  =back
3410    
3411  =cut  =cut
3412    
3413  sub Merge {  sub Pad {
3414          # Get the input list in sort order.      # Get the parameters.
3415          my @inputList = sort @_;      my ($string, $len, $left, $padChar) = @_;
3416          # Only proceed if the list has at least two elements.      # Compute the padding character.
3417          if (@inputList > 1) {      if (! defined $padChar) {
3418                  # Now we want to move through the list splicing out duplicates.          $padChar = " ";
                 my $i = 0;  
                 while ($i < @inputList) {  
                         # Get the current entry.  
                         my $thisEntry = $inputList[$i];  
                         # Find out how many elements duplicate the current entry.  
                         my $j = $i + 1;  
                         my $dup1 = $i + 1;  
                         while ($j < @inputList && $inputList[$j] eq $thisEntry) { $j++; };  
                         # If the number is nonzero, splice out the duplicates found.  
                         if ($j > $dup1) {  
                                 splice @inputList, $dup1, $j - $dup1;  
3419                          }                          }
3420                          # Now the element at position $dup1 is different from the element before it      # Compute the number of spaces needed.
3421                          # at position $i. We push $i forward one position and start again.      my $needed = $len - length $string;
3422                          $i++;      # Copy the string into the return variable.
3423        my $retVal = $string;
3424        # Only proceed if padding is needed.
3425        if ($needed > 0) {
3426            # Create the pad string.
3427            my $pad = $padChar x $needed;
3428            # Affix it to the return value.
3429            if ($left) {
3430                $retVal = $pad . $retVal;
3431            } else {
3432                $retVal .= $pad;
3433                  }                  }
3434          }          }
3435          # Return the merged list.      # Return the result.
3436          return @inputList;      return $retVal;
3437    }
3438    
3439    =head3 EOF
3440    
3441    This is a constant that is lexically greater than any useful string.
3442    
3443    =cut
3444    
3445    sub EOF {
3446        return "\xFF\xFF\xFF\xFF\xFF";
3447    }
3448    
3449    =head3 TICK
3450    
3451        my @results = TICK($commandString);
3452    
3453    Perform a back-tick operation on a command. If this is a Windows environment, any leading
3454    dot-slash (C<./> will be removed. So, for example, if you were doing
3455    
3456        `./protein.cgi`
3457    
3458    from inside a CGI script, it would work fine in Unix, but would issue an error message
3459    in Windows complaining that C<'.'> is not a valid command. If instead you code
3460    
3461        TICK("./protein.cgi")
3462    
3463    it will work correctly in both environments.
3464    
3465    =over 4
3466    
3467    =item commandString
3468    
3469    The command string to pass to the system.
3470    
3471    =item RETURN
3472    
3473    Returns the standard output from the specified command, as a list.
3474    
3475    =back
3476    
3477    =cut
3478    #: Return Type @;
3479    sub TICK {
3480        # Get the parameters.
3481        my ($commandString) = @_;
3482        # Chop off the dot-slash if this is Windows.
3483        if ($FIG_Config::win_mode) {
3484            $commandString =~ s!^\./!!;
3485        }
3486        # Activate the command and return the result.
3487        return `$commandString`;
3488    }
3489    
3490    
3491    =head3 CommaFormat
3492    
3493        my $formatted = Tracer::CommaFormat($number);
3494    
3495    Insert commas into a number.
3496    
3497    =over 4
3498    
3499    =item number
3500    
3501    A sequence of digits.
3502    
3503    =item RETURN
3504    
3505    Returns the same digits with commas strategically inserted.
3506    
3507    =back
3508    
3509    =cut
3510    
3511    sub CommaFormat {
3512        # Get the parameters.
3513        my ($number) = @_;
3514        # Pad the length up to a multiple of three.
3515        my $padded = "$number";
3516        $padded = " " . $padded while length($padded) % 3 != 0;
3517        # This is a fancy PERL trick. The parentheses in the SPLIT pattern
3518        # cause the delimiters to be included in the output stream. The
3519        # GREP removes the empty strings in between the delimiters.
3520        my $retVal = join(",", grep { $_ ne '' } split(/(...)/, $padded));
3521        # Clean out the spaces.
3522        $retVal =~ s/ //g;
3523        # Return the result.
3524        return $retVal;
3525  }  }
3526    
 =head3 GetFile  
3527    
3528  C<< my @fileContents = Tracer::GetFile($fileName); >>  =head3 CompareLists
3529    
3530        my ($inserted, $deleted) = Tracer::CompareLists(\@newList, \@oldList, $keyIndex);
3531    
3532  Return the entire contents of a file.  Compare two lists of tuples, and return a hash analyzing the differences. The lists
3533    are presumed to be sorted alphabetically by the value in the $keyIndex column.
3534    The return value contains a list of items that are only in the new list
3535    (inserted) and only in the old list (deleted).
3536    
3537  =over 4  =over 4
3538    
3539  =item fileName  =item newList
3540    
3541  Name of the file to read.  Reference to a list of new tuples.
3542    
3543    =item oldList
3544    
3545    Reference to a list of old tuples.
3546    
3547    =item keyIndex (optional)
3548    
3549    Index into each tuple of its key field. The default is 0.
3550    
3551  =item RETURN  =item RETURN
3552    
3553  In a list context, returns the entire file as a list with the line terminators removed.  Returns a 2-tuple consisting of a reference to the list of items that are only in the new
3554  In a scalar context, returns the entire file as a string.  list (inserted) followed by a reference to the list of items that are only in the old
3555    list (deleted).
3556    
3557  =back  =back
3558    
3559  =cut  =cut
3560    
3561  sub GetFile {  sub CompareLists {
3562          # Get the parameters.          # Get the parameters.
3563          my ($fileName) = @_;      my ($newList, $oldList, $keyIndex) = @_;
3564          # Declare the return variable.      if (! defined $keyIndex) {
3565          my @retVal = ();          $keyIndex = 0;
3566          # Open the file for input.      }
3567          my $ok = open INPUTFILE, "<$fileName";      # Declare the return variables.
3568          if (!$ok) {      my ($inserted, $deleted) = ([], []);
3569                  # If we had an error, trace it. We will automatically return a null value.      # Loop through the two lists simultaneously.
3570                  Trace("Could not open \"$fileName\" for input.") if T(0);      my ($newI, $oldI) = (0, 0);
3571        my ($newN, $oldN) = (scalar @{$newList}, scalar @{$oldList});