[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 1.106, Fri May 16 08:32:02 2008 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    
21          require Exporter;          require Exporter;
22          @ISA = ('Exporter');          @ISA = ('Exporter');
23          @EXPORT = qw(Trace T TSetup QTrace Confess Cluck Min Max Assert);      @EXPORT = qw(Trace T TSetup QTrace Confess Cluck Min Max Assert Open OpenDir TICK StandardSetup EmergencyKey ETracing Constrain Insure ChDir Emergency Warn);
24          @EXPORT_OK = qw(GetFile GetOptions Merge MergeOptions ParseCommand ParseRecord UnEscape Escape);      @EXPORT_OK = qw(GetFile GetOptions Merge MergeOptions ParseCommand ParseRecord UnEscape Escape PrintLine PutLine);
25          use strict;          use strict;
26          use Carp qw(longmess croak);      use Carp qw(longmess croak carp);
27          use CGI;          use CGI;
28        use Cwd;
29          use FIG_Config;          use FIG_Config;
30      use PageBuilder;      use PageBuilder;
31        use Digest::MD5;
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 ':flock';
42    
43    
44  =head1 Tracing and Debugging Helpers  =head1 Tracing and Debugging Helpers
45    
46  =head2 Introduction  =head2 Tracing
47    
48  This package provides simple tracing for debugging and reporting purposes. To use it simply call the  This package provides simple tracing for debugging and reporting purposes. To use it simply call the
49  L</TSetup> method to set the options and call L</Trace> to write out trace messages. Each trace  L</TSetup> or L</ETracing> method to set the options and call L</Trace> to write out trace messages.
50  message has a I<trace level> and I<category> associated with it. In addition, the tracing package itself  L</TSetup> and L</ETracing> both establish a I<trace level> and a list of I<categories>. Similarly,
51  has a list of categories and a single trace level set by the B<TSetup> method. Only messages whose trace  each trace message has a I<trace level> and I<category> associated with it. Only messages whose trace
52  level is less than or equal to this package's trace level and whose category is activated will  level is less than or equal to the setup trace level and whose category is activated will
53  be written. Thus, a higher trace level on a message indicates that the message  be written. Thus, a higher trace level on a message indicates that the message
54  is less likely to be seen. A higher trace level passed to B<Setup> means more trace messages will  is less likely to be seen, while a higher trace level passed to B<TSetup> means more trace messages will
55  appear. To generate a trace message, use the following syntax.  appear.
56    
57    =head3 Putting Trace Messages in Your Code
58    
59    To generate a trace message, use the following syntax.
60    
61  C<< Trace($message) if T(errors => 4); >>      Trace($message) if T(errors => 4);
62    
63  This statement will produce a trace message if the trace level is 4 or more and the C<errors>  This statement will produce a trace message if the trace level is 4 or more and the C<errors>
64  category is active. Note that the special category C<main> is always active, so  category is active. There is a special category C<main> that is always active, so
65    
66  C<< Trace($message) if T(main => 4); >>      Trace($message) if T(main => 4);
67    
68  will trace if the trace level is 4 or more.  will trace if the trace level is 4 or more.
69    
# Line 36  Line 71 
71  following call is made in the B<Sprout> package, it will appear if the C<Sprout> category is  following call is made in the B<Sprout> package, it will appear if the C<Sprout> category is
72  active and the trace level is 2 or more.  active and the trace level is 2 or more.
73    
74  C<< Trace($message) if T(2); >>      Trace($message) if T(2);
75    
76  To set up tracing, you call the C</Setup> method. The method takes as input a trace level, a list  In scripts, where no package name is available, the category defaults to C<main>.
77  of category names, and a set of options. The trace level and list of category names are  
78    =head3 Custom Tracing
79    
80    Many programs have customized tracing configured using the L</TSetup> method. This is no longer
81    the preferred method, but a knowledge of how custom tracing works can make the more modern
82    L</Emergency Tracing> easier to understand.
83    
84    To set up custom tracing, you call the L</TSetup> method. The method takes as input a trace level,
85    a list of category names, and a destination. The trace level and list of category names are
86  specified as a space-delimited string. Thus  specified as a space-delimited string. Thus
87    
88  C<< TSetup('3 errors Sprout ERDB', 'HTML'); >>      TSetup('3 errors Sprout ERDB', 'TEXT');
89    
90  sets the trace level to 3, activates the C<errors>, C<Sprout>, and C<ERDB> categories, and  sets the trace level to 3, activates the C<errors>, C<Sprout>, and C<ERDB> categories, and
91  specifies that messages should be output as HTML paragraphs. The parameters are formatted  specifies that messages should be sent to the standard output.
92  to make it easier to input tracing configuration on a web form.  
93    To turn on tracing for ALL categories, use an asterisk. The call below sets every category to
94    level 3 and writes the output to the standard error output. This sort of thing might be
95    useful in a CGI environment.
96    
97  In addition to HTML and file output for trace messages, you can specify that the trace messages      TSetup('3 *', 'WARN');
98    
99    In addition standard error and file output for trace messages, you can specify that the trace messages
100  be queued. The messages can then be retrieved by calling the L</QTrace> method. This approach  be queued. The messages can then be retrieved by calling the L</QTrace> method. This approach
101  is useful if you are building a web page. Instead of having the trace messages interspersed with  is useful if you are building a web page. Instead of having the trace messages interspersed with
102  the page output, they can be gathered together and displayed at the end of the page. This makes  the page output, they can be gathered together and displayed at the end of the page. This makes
103  it easier to debug page formatting problems.  it easier to debug page formatting problems.
104    
105  Finally, you can specify that all trace messages be emitted as warnings.  Finally, you can specify that all trace messages be emitted to a file, or the standard output and
106    a file at the same time. To trace to a file, specify the filename with an output character in front
107    of it.
108    
109        TSetup('4 SQL', ">$fileName");
110    
111    To trace to the standard output and a file at the same time, put a C<+> in front of the angle
112    bracket.
113    
114        TSetup('3 *', "+>$fileName");
115    
116  The flexibility of tracing makes it superior to simple use of directives like C<die> and C<warn>.  The flexibility of tracing makes it superior to simple use of directives like C<die> and C<warn>.
117  Tracer calls can be left in the code with minimal overhead and then turned on only when needed.  Tracer calls can be left in the code with minimal overhead and then turned on only when needed.
118  Thus, debugging information is available and easily retrieved even when the application is  Thus, debugging information is available and easily retrieved even when the application is
119  being used out in the field.  being used out in the field.
120    
121    =head3 Trace Levels
122    
123    There is no hard and fast rule on how to use trace levels. The following is therefore only
124    a suggestion.
125    
126    =over 4
127    
128    =item Error 0
129    
130    Message indicates an error that may lead to incorrect results or that has stopped the
131    application entirely.
132    
133    =item Warning 1
134    
135    Message indicates something that is unexpected but that probably did not interfere
136    with program execution.
137    
138    =item Notice 2
139    
140    Message indicates the beginning or end of a major task.
141    
142    =item Information 3
143    
144    Message indicates a subtask. In the FIG system, a subtask generally relates to a single
145    genome. This would be a big loop that is not expected to execute more than 500 times or so.
146    
147    =item Detail 4
148    
149    Message indicates a low-level loop iteration.
150    
151    =back
152    
153    The format of trace messages is important because some utilities analyze trace files.
154    There are three fields-- the time stamp, the category name, and the text.
155    The time stamp is between square brackets and the category name between angle brackets.
156    After the category name there is a colon (C<:>) followed by the message text.
157    If the square brackets or angle brackets are missing, then the trace management
158    utilities assume that they are encountering a set of pre-formatted lines.
159    
160    Note, however, that this formatting is done automatically by the tracing functions. You
161    only need to know about it if you want to parse a trace file.
162    
163    =head3 Emergency Tracing
164    
165    Sometimes, you need a way for tracing to happen automatically without putting parameters
166    in a form or on the command line. Emergency tracing does this. You invoke emergency tracing
167    from the debug form, which is accessed from the [[DebugConsole]]. Emergency tracing requires
168    that you specify a tracing key. For command-line tools, the key is
169    taken from the C<TRACING> environment variable. For web services, the key is taken from
170    a cookie. Either way, the key tells the tracing facility who you are, so that you control
171    the tracing in your environment without stepping on other users.
172    
173    The key can be anything you want. If you don't have a key, the C<SetPassword> page will
174    generate one for you.
175    
176    You can activate and de-activate emergency tracing from the debugging control panel, as
177    well as display the trace file itself.
178    
179    To enable emergency tracing in your code, call
180    
181        ETracing($cgi)
182    
183    from a web script and
184    
185        ETracing()
186    
187    from a command-line script.
188    
189    The web script will look for the tracing key in the cookies, and the command-line
190    script will look for it in the C<TRACING> environment variable. If you are
191    using the L</StandardSetup> method or a [[WebApplication]], emergency tracing
192    will be configured automatically.
193    
194  =cut  =cut
195    
196  # Declare the configuration variables.  # Declare the configuration variables.
197    
198  my $Destination = "NONE";       # Description of where to send the trace output.  my $Destination = "WARN";   # Description of where to send the trace output.
199    my $TeeFlag = 0;            # TRUE if output is going to a file and to the
200                                # standard output
201  my %Categories = ( main => 1 );  my %Categories = ( main => 1 );
202                                                          # hash of active category names                                                          # hash of active category names
203    my @LevelNames = qw(error warn notice info detail);
204  my $TraceLevel = 0;                     # trace level; a higher trace level produces more  my $TraceLevel = 0;                     # trace level; a higher trace level produces more
205                                                          # messages                                                          # messages
206  my @Queue = ();                         # queued list of trace messages.  my @Queue = ();                         # queued list of trace messages.
207  my $LastCategory = "main";  # name of the last category interrogated  my $LastCategory = "main";  # name of the last category interrogated
208    my $LastLevel = 0;          # level of the last test call
209    my $SetupCount = 0;         # number of times TSetup called
210    my $AllTrace = 0;           # TRUE if we are tracing all categories.
211    my $SavedCGI;               # CGI object passed to ETracing
212    my $CommandLine;            # Command line passed to StandardSetup
213    umask 2;                    # Fix the damn umask so everything is group-writable.
214    
215  =head2 Public Methods  =head2 Tracing Methods
216    
217    =head3 Setups
218    
219        my $count = Tracer::Setups();
220    
221    Return the number of times L</TSetup> has been called.
222    
223    This method allows for the creation of conditional tracing setups where, for example, we
224    may want to set up tracing if nobody else has done it before us.
225    
226    =cut
227    
228    sub Setups {
229        return $SetupCount;
230    }
231    
232  =head3 TSetup  =head3 TSetup
233    
234  C<< TSetup($categoryList, $target); >>      TSetup($categoryList, $target);
235    
236  This method is used to specify the trace options. The options are stored as package data  This method is used to specify the trace options. The options are stored as package data
237  and interrogated by the L</Trace> and L</T> methods.  and interrogated by the L</Trace> and L</T> methods.
# Line 93  Line 247 
247    
248  The destination for the trace output. To send the trace output to a file, specify the file  The destination for the trace output. To send the trace output to a file, specify the file
249  name preceded by a ">" symbol. If a double symbol is used (">>"), then the data is appended  name preceded by a ">" symbol. If a double symbol is used (">>"), then the data is appended
250  to the file. Otherwise the file is cleared before tracing begins. In addition to sending  to the file. Otherwise the file is cleared before tracing begins. Precede the first ">"
251  the trace messages to a file, you can specify a special destination. C<HTML> will cause  symbol with a C<+> to echo output to a file AND to the standard output. In addition to
252  tracing to the standard output with each line formatted as an HTML paragraph. C<TEXT>  sending the trace messages to a file, you can specify a special destination. C<HTML> will
253    cause tracing to the standard output with each line formatted as an HTML paragraph. C<TEXT>
254  will cause tracing to the standard output as ordinary text. C<ERROR> will cause trace  will cause tracing to the standard output as ordinary text. C<ERROR> will cause trace
255  messages to be sent to the standard error output as ordinary text. C<QUEUE> will cause trace  messages to be sent to the standard error output as ordinary text. C<QUEUE> will cause trace
256  messages to be stored in a queue for later retrieval by the L</QTrace> method. C<WARN> will  messages to be stored in a queue for later retrieval by the L</QTrace> method. C<WARN> will
# Line 113  Line 268 
268          my @categoryData = split /\s+/, $categoryList;          my @categoryData = split /\s+/, $categoryList;
269          # Extract the trace level.          # Extract the trace level.
270          $TraceLevel = shift @categoryData;          $TraceLevel = shift @categoryData;
271          # Build the category hash.      # Presume category-based tracing until we learn otherwise.
272        $AllTrace = 0;
273        # Build the category hash. Note that if we find a "*", we turn on non-category
274        # tracing. We must also clear away any pre-existing data.
275        %Categories = ( main => 1 );
276          for my $category (@categoryData) {          for my $category (@categoryData) {
277                  $Categories{$category} = 1;          if ($category eq '*') {
278                $AllTrace = 1;
279            } else {
280                $Categories{lc $category} = 1;
281            }
282          }          }
283          # Now we need to process the destination information. The most important special          # Now we need to process the destination information. The most important special
284          # case is the single ">", which requires we clear the file first. After doing      # case is when we're writing to a file. This is indicated by ">" (overwrite) and
285          # so, we tack on another ">" sign so that future trace messages are appended.      # ">>" (append). A leading "+" for either indicates that we are also writing to
286        # the standard output (tee mode).
287        if ($target =~ m/^\+?>>?/) {
288            if ($target =~ m/^\+/) {
289                $TeeFlag = 1;
290                $target = substr($target, 1);
291            }
292          if ($target =~ m/^>[^>]/) {          if ($target =~ m/^>[^>]/) {
293                # We need to initialize the file (which clears it).
294                  open TRACEFILE, $target;                  open TRACEFILE, $target;
295                  print TRACEFILE Now() . " Tracing initialized.\n";              print TRACEFILE "[" . Now() . "] [notice] [Tracer] Tracing initialized.\n";
296                  close TRACEFILE;                  close TRACEFILE;
297                # Set to append mode now that the file has been cleared.
298                  $Destination = ">$target";                  $Destination = ">$target";
299          } else {          } else {
300                $Destination = $target;
301            }
302        } else {
303                  $Destination = uc($target);                  $Destination = uc($target);
304          }          }
305        # Increment the setup counter.
306        $SetupCount++;
307  }  }
308    
309  =head3 SetLevel  =head3 SetLevel
310    
311  C<< Tracer::SetLevel($newLevel); >>      Tracer::SetLevel($newLevel);
312    
313  Modify the trace level. A higher trace level will cause more messages to appear.  Modify the trace level. A higher trace level will cause more messages to appear.
314    
# Line 150  Line 326 
326      $TraceLevel = $_[0];      $TraceLevel = $_[0];
327  }  }
328    
329  =head3 Now  =head3 ParseDate
   
 C<< my $string = Tracer::Now(); >>  
   
 Return a displayable time stamp containing the local time.  
   
 =cut  
   
 sub Now {  
         my ($sec,$min,$hour,$mday,$mon,$year,$wday,$yday,$isdst) = localtime(time);  
         my $retVal = _p2($mon+1) . "/" . _p2($mday) . "/" . ($year + 1900) . " " .  
                                  _p2($hour) . ":" . _p2($min) . ":" . _p2($sec);  
         return $retVal;  
 }  
   
 # Pad a number to 2 digits.  
 sub _p2 {  
         my ($value) = @_;  
         $value = "0$value" if ($value < 10);  
         return $value;  
 }  
   
 =head3 LogErrors  
   
 C<< Tracer::LogErrors($fileName); >>  
   
 Route the standard error output to a log file.  
   
 =over 4  
   
 =item fileName  
   
 Name of the file to receive the error output.  
   
 =back  
330    
331  =cut      my $time = Tracer::ParseDate($dateString);
332    
333  sub LogErrors {  Convert a date into a PERL time number. This method expects a date-like string
334          # Get the file name.  and parses it into a number. The string must be vaguely date-like or it will
335          my ($fileName) = @_;  return an undefined value. Our requirement is that a month and day be
336          # Open the file as the standard error output.  present and that three pieces of the date string (time of day, month and day,
337          open STDERR, '>', $fileName;  year) be separated by likely delimiters, such as spaces, commas, and such-like.
 }  
338    
339  =head3 ReadOptions  If a time of day is present, it must be in military time with two digits for
340    everything but the hour.
341    
342  C<< my %options = Tracer::ReadOptions($fileName); >>  The year must be exactly four digits.
343    
344  Read a set of options from a file. Each option is encoded in a line of text that has the  Additional stuff can be in the string. We presume it's time zones or weekdays or something
345  format  equally innocuous. This means, however, that a sufficiently long sentence with date-like
346    parts in it may be interpreted as a date. Hopefully this will not be a problem.
347    
348  I<optionName>C<=>I<optionValue>C<; >I<comment>  It should be guaranteed that this method will parse the output of the L</Now> function.
349    
350  The option name must consist entirely of letters, digits, and the punctuation characters  The parameters are as follows.
 C<.> and C<_>, and is case sensitive. Blank lines and lines in which the first nonblank  
 character is a semi-colon will be ignored. The return hash will map each option name to  
 the corresponding option value.  
351    
352  =over 4  =over 4
353    
354  =item fileName  =item dateString
355    
356  Name of the file containing the option data.  The date string to convert.
357    
358  =item RETURN  =item RETURN
359    
360  Returns a hash mapping the option names specified in the file to their corresponding option  Returns a PERL time, that is, a number of seconds since the epoch, or C<undef> if
361  value.  the date string is invalid. A valid date string must contain a month and day.
362    
363  =back  =back
364    
365  =cut  =cut
366    
367  sub ReadOptions {  # Universal month conversion table.
368          # Get the parameters.  use constant MONTHS => {    Jan =>  0, January   =>  0, '01' =>  0,  '1' =>  0,
369          my ($fileName) = @_;                              Feb =>  1, February  =>  1, '02' =>  1,  '2' =>  1,
370          # Open the file.                              Mar =>  2, March     =>  2, '03' =>  2,  '3' =>  2,
371          (open CONFIGFILE, "<$fileName") || Confess("Could not open option file $fileName.");                              Apr =>  3, April     =>  3, '04' =>  3,  '4' =>  3,
372          # Count the number of records read.                              May =>  4, May       =>  4, '05' =>  4,  '5' =>  4,
373          my ($records, $comments) = 0;                              Jun =>  5, June      =>  5, '06' =>  5,  '6' =>  5,
374          # Create the return hash.                              Jul =>  6, July      =>  6, '07' =>  6,  '7' =>  6,
375          my %retVal = ();                              Aug =>  7, August    =>  7, '08' =>  7,  '8' =>  7,
376          # Loop through the file, accumulating key-value pairs.                              Sep =>  8, September =>  8, '09' =>  8,  '9' =>  8,
377          while (my $line = <CONFIGFILE>) {                              Oct =>  9, October  =>   9, '10' =>  9,
378                  # Denote we've read a line.                              Nov => 10, November =>  10, '11' => 10,
379                  $records++;                              Dec => 11, December =>  11, '12' => 11
380                  # Determine the line type.                          };
                 if ($line =~ /^\s*[\n\r]/) {  
                         # A blank line is a comment.  
                         $comments++;  
                 } elsif ($line =~ /^\s*([A-Za-z0-9_\.]+)=([^;]*);/) {  
                         # Here we have an option assignment.  
                         retVal{$1} = $2;  
                 } elsif ($line =~ /^\s*;/) {  
                         # Here we have a text comment.  
                         $comments++;  
                 } else {  
                         # Here we have an invalid line.  
                         Trace("Invalid option statement in record $records.") if T(0);  
                 }  
         }  
         # Return the hash created.  
         return %retVal;  
 }  
   
 =head3 GetOptions  
   
 C<< Tracer::GetOptions(\%defaults, \%options); >>  
   
 Merge a specified set of options into a table of defaults. This method takes two hash references  
 as input and uses the data from the second to update the first. If the second does not exist,  
 there will be no effect. An error will be thrown if one of the entries in the second hash does not  
 exist in the first.  
   
 Consider the following example.  
   
 C<< my $optionTable = GetOptions({ dbType => 'mySQL', trace => 0 }, $options); >>  
   
 In this example, the variable B<$options> is expected to contain at most two options-- B<dbType> and  
 B<trace>. The default database type is C<mySQL> and the default trace level is C<0>. If the value of  
 B<$options> is C<< {dbType => 'Oracle'} >>, then the database type will be changed to C<Oracle> and  
 the trace level will remain at 0. If B<$options> is undefined, then the database type and trace level  
 will remain C<mySQL> and C<0>. If, on the other hand, B<$options> is defined as  
   
 C<< {databaseType => 'Oracle'} >>  
   
 an error will occur because the B<databaseType> option does not exist.  
   
 =over 4  
   
 =item defaults  
   
 Table of default option values.  
   
 =item options  
   
 Table of overrides, if any.  
   
 =item RETURN  
   
 Returns a reference to the default table passed in as the first parameter.  
   
 =back  
   
 =cut  
381    
382  sub GetOptions {  sub ParseDate {
383          # Get the parameters.          # Get the parameters.
384          my ($defaults, $options) = @_;      my ($dateString) = @_;
385          # Check for overrides.      # Declare the return variable.
386          if ($options) {      my $retVal;
387                  # Loop through the overrides.      # Find the month and day of month. There are two ways that can happen. We check for the
388                  while (my ($option, $setting) = each %{$options}) {      # numeric style first. That way, if the user's done something like "Sun 12/22", then we
389                          # Insure this override exists.      # won't be fooled into thinking the month is Sunday.
390                          if (!exists $defaults->{$option}) {      if ($dateString =~ m#\b(\d{1,2})/(\d{1,2})\b# || $dateString =~ m#\b(\w+)\s(\d{1,2})\b#) {
391                                  croak "Unrecognized option $option encountered.";          my ($mon, $mday) = (MONTHS->{$1}, $2);
392            # Insist that the month and day are valid.
393            if (defined($mon) && $2 >= 1 && $2 <= 31) {
394                # Find the time.
395                my ($hour, $min, $sec) = (0, 0, 0);
396                if ($dateString =~ /\b(\d{1,2}):(\d{2}):(\d{2})\b/) {
397                    ($hour, $min, $sec) = ($1, $2, $3);
398                }
399                # Find the year.
400                my $year;
401                if ($dateString =~ /\b(\d{4})\b/) {
402                    $year = $1;
403                          } else {                          } else {
404                                  # Apply the override.                  # Get the default year, which is this one. Note we must convert it to
405                                  $defaults->{$option} = $setting;                  # the four-digit value expected by "timelocal".
406                    (undef, undef, undef, undef, undef, $year) = localtime();
407                    $year += 1900;
408                          }                          }
409                $retVal = timelocal($sec, $min, $hour, $mday, $mon, $year);
410                  }                  }
411          }          }
412          # Return the merged table.      # Return the result.
413          return $defaults;      return $retVal;
414  }  }
415    
416  =head3 MergeOptions  =head3 LogErrors
417    
418  C<< Tracer::MergeOptions(\%table, \%defaults); >>      Tracer::LogErrors($fileName);
419    
420  Merge default values into a hash table. This method looks at the key-value pairs in the  Route the standard error output to a log file.
 second (default) hash, and if a matching key is not found in the first hash, the default  
 pair is copied in. The process is similar to L</GetOptions>, but there is no error-  
 checking and no return value.  
421    
422  =over 4  =over 4
423    
424  =item table  =item fileName
   
 Hash table to be updated with the default values.  
   
 =item defaults  
425    
426  Default values to be merged into the first hash table if they are not already present.  Name of the file to receive the error output.
427    
428  =back  =back
429    
430  =cut  =cut
431    
432  sub MergeOptions {  sub LogErrors {
433          # Get the parameters.      # Get the file name.
434          my ($table, $defaults) = @_;      my ($fileName) = @_;
435          # Loop through the defaults.      # Open the file as the standard error output.
436          while (my ($key, $value) = each %{$defaults}) {      open STDERR, '>', $fileName;
                 if (!exists $table->{$key}) {  
                         $table->{$key} = $value;  
                 }  
         }  
437  }  }
438    
439  =head3 Trace  =head3 Trace
440    
441  C<< Trace($message); >>      Trace($message);
442    
443  Write a trace message to the target location specified in L</TSetup>. If there has not been  Write a trace message to the target location specified in L</TSetup>. If there has not been
444  any prior call to B<TSetup>.  any prior call to B<TSetup>.
# Line 371  Line 456 
456  sub Trace {  sub Trace {
457          # Get the parameters.          # Get the parameters.
458          my ($message) = @_;          my ($message) = @_;
459        # Strip off any line terminators at the end of the message. We will add
460        # new-line stuff ourselves.
461        my $stripped = Strip($message);
462        # Compute the caller information.
463        my ($callPackage, $callFile, $callLine) = caller();
464        my $callFileTitle = basename($callFile);
465        # Check the caller.
466        my $callerInfo = ($callFileTitle ne "Tracer.pm" ? " [$callFileTitle $callLine]" : "");
467          # Get the timestamp.          # Get the timestamp.
468          my $timeStamp = Now();          my $timeStamp = Now();
469          # Format the message. Note we strip off any line terminators at the end.      # Build the prefix.
470          my $formatted = "$timeStamp <$LastCategory>: " . Strip($message);      my $level = $LevelNames[$LastLevel] || "($LastLevel)";
471        my $prefix = "[$timeStamp] [$level] [$LastCategory]$callerInfo";
472        # Format the message.
473        my $formatted = "$prefix $stripped";
474          # Process according to the destination.          # Process according to the destination.
475          if ($Destination eq "TEXT") {          if ($Destination eq "TEXT") {
476                  # Write the message to the standard output.                  # Write the message to the standard output.
477                  print "$formatted\n";                  print "$formatted\n";
478          } elsif ($Destination eq "ERROR") {          } elsif ($Destination eq "ERROR") {
479                  # Write the message to the error output.          # Write the message to the error output. Here, we want our prefix fields.
480                  print STDERR "$formatted\n";                  print STDERR "$formatted\n";
481        } elsif ($Destination eq "WARN") {
482            # Emit the message to the standard error output. It is presumed that the
483            # error logger will add its own prefix fields, the notable exception being
484            # the caller info.
485            print STDERR "$callerInfo$stripped\n";
486          } elsif ($Destination eq "QUEUE") {          } elsif ($Destination eq "QUEUE") {
487                  # Push the message into the queue.                  # Push the message into the queue.
488                  push @Queue, "$formatted";                  push @Queue, "$formatted";
489          } elsif ($Destination eq "HTML") {          } elsif ($Destination eq "HTML") {
490                  # Convert the message to HTML and write it to the standard output.                  # Convert the message to HTML and write it to the standard output.
491                  my $escapedMessage = CGI::escapeHTML($message);          my $escapedMessage = CGI::escapeHTML($stripped);
492                  print "<p>$formatted</p>\n";          print "<p>$timeStamp $LastCategory $LastLevel: $escapedMessage</p>\n";
     } elsif ($Destination eq "WARN") {  
        # Emit the message as a warning.  
        warn $message;  
493          } elsif ($Destination =~ m/^>>/) {          } elsif ($Destination =~ m/^>>/) {
494                  # Write the trace message to an output file.                  # Write the trace message to an output file.
495                  open TRACING, $Destination;          open(TRACING, $Destination) || die "Tracing open for \"$Destination\" failed: $!";
496                  print TRACING "$formatted\n";                  print TRACING "$formatted\n";
497                  close TRACING;                  close TRACING;
498            # If the Tee flag is on, echo it to the standard output.
499            if ($TeeFlag) {
500                print "$formatted\n";
501            }
502          }          }
503  }  }
504    
505  =head3 T  =head3 T
506    
507  C<< my $switch = T($category, $traceLevel); >>      my $switch = T($category, $traceLevel);
508    
509          or          or
510    
511  C<< my $switch = T($traceLevel); >>      my $switch = T($traceLevel);
512    
513  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
514  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 541 
541                  my ($category, $traceLevel) = @_;                  my ($category, $traceLevel) = @_;
542                  if (!defined $traceLevel) {                  if (!defined $traceLevel) {
543                          # 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.
544                # The calling package is normally the first parameter. If it is
545                # omitted, the first parameter will be the tracelevel. So, the
546                # first thing we do is shift the so-called category into the
547                # $traceLevel variable where it belongs.
548                          $traceLevel = $category;                          $traceLevel = $category;
549                          my ($package, $fileName, $line) = caller;                          my ($package, $fileName, $line) = caller;
550              # If there is no calling package, we default to "main".              # If there is no calling package, we default to "main".
551                          if (!$package) {                          if (!$package) {
552                  $category = "main";                  $category = "main";
553                          } else {                          } else {
554                                  $category = $package;                  my @cats = split /::/, $package;
555                    $category = $cats[$#cats];
556                          }                          }
557                  }                  }
558          # Save the category name.          # Save the category name and level.
559          $LastCategory = $category;          $LastCategory = $category;
560                  # Use the category and tracelevel to compute the result.          $LastLevel = $traceLevel;
561                  $retVal = ($traceLevel <= $TraceLevel && exists $Categories{$category});          # Convert it to lower case before we hash it.
562            $category = lc $category;
563            # Validate the trace level.
564            if (ref $traceLevel) {
565                Confess("Bad trace level.");
566            } elsif (ref $TraceLevel) {
567                Confess("Bad trace config.");
568            }
569            # Make the check. Note that level 0 shows even if the category is turned off.
570            $retVal = ($traceLevel <= $TraceLevel && ($traceLevel == 0 || $AllTrace || exists $Categories{$category}));
571      }      }
572          # Return the computed result.          # Return the computed result.
573      return $retVal;      return $retVal;
574  }  }
575    
576  =head3 ParseCommand  =head3 QTrace
   
 C<< my ($options, @arguments) = Tracer::ParseCommand(\%optionTable, @inputList); >>  
   
 Parse a command line consisting of a list of parameters. The initial parameters may be option  
 specifiers of the form C<->I<option> or C<->I<option>C<=>I<value>. The options are stripped  
 off and merged into a table of default options. The remainder of the command line is  
 returned as a list of positional arguments. For example, consider the following invocation.  
   
 C<< my ($options, @arguments) = ParseCommand({ errors => 0, logFile => 'trace.log'}, @words); >>  
   
 In this case, the list @words will be treated as a command line. There are two options available,  
 B<errors> and B<logFile>. If @words has the following format  
   
 C<< -logFile=error.log apple orange rutabaga >>  
   
 then at the end of the invocation, C<$options> will be  
   
 C<< { errors => 0, logFile => 'error.log' } >>  
   
 and C<@arguments> will contain  
577    
578  C<< apple orange rutabaga >>      my $data = QTrace($format);
579    
580  The parser allows for some escape sequences. See L</UnEscape> for a description. There is no  Return the queued trace data in the specified format.
 support for quote characters.  
581    
582  =over 4  =over 4
583    
584  =item optionTable  =item format
   
 Table of default options.  
   
 =item inputList  
   
 List of words on the command line.  
   
 =item RETURN  
585    
586  Returns a reference to the option table and a list of the positional arguments.  C<html> to format the data as an HTML list, C<text> to format it as straight text.
587    
588  =back  =back
589    
590  =cut  =cut
591    
592  sub ParseCommand {  sub QTrace {
593          # Get the parameters.      # Get the parameter.
594          my ($optionTable, @inputList) = @_;      my ($format) = @_;
595        # Create the return variable.
596        my $retVal = "";
597        # Only proceed if there is an actual queue.
598        if (@Queue) {
599            # Process according to the format.
600            if ($format =~ m/^HTML$/i) {
601                # Convert the queue into an HTML list.
602                $retVal = "<ul>\n";
603                for my $line (@Queue) {
604                    my $escapedLine = CGI::escapeHTML($line);
605                    $retVal .= "<li>$escapedLine</li>\n";
606                }
607                $retVal .= "</ul>\n";
608            } elsif ($format =~ m/^TEXT$/i) {
609                # Convert the queue into a list of text lines.
610                $retVal = join("\n", @Queue) . "\n";
611            }
612            # Clear the queue.
613            @Queue = ();
614        }
615        # Return the formatted list.
616        return $retVal;
617    }
618    
619    =head3 Confess
620    
621        Confess($message);
622    
623    Trace the call stack and abort the program with the specified message. When used with
624    the OR operator and the L</Assert> method, B<Confess> can function as a debugging assert.
625    So, for example
626    
627        Assert($recNum >= 0) || Confess("Invalid record number $recNum.");
628    
629    Will abort the program with a stack trace if the value of C<$recNum> is negative.
630    
631    =over 4
632    
633    =item message
634    
635    Message to include in the trace.
636    
637    =back
638    
639    =cut
640    
641    sub Confess {
642        # Get the parameters.
643        my ($message) = @_;
644        # Set up the category and level.
645        $LastCategory = "(confess)";
646        $LastLevel = 0;
647        if (! defined($FIG_Config::no_tool_hdr)) {
648            # Here we have a tool header. Display its length so that the user can adjust the line numbers.
649            my $toolHeaderFile = "$FIG_Config::fig_disk/dist/releases/current/$FIG_Config::arch/tool_hdr";
650            # Only proceed if the tool header file is actually present.
651            if (-f $toolHeaderFile) {
652                my $fh;
653                if (open $fh, "<$toolHeaderFile") {
654                    my @lines = <$fh>;
655                    Trace("Tool header has " . scalar(@lines) . " lines.");
656                }
657            }
658        }
659        # Trace the call stack.
660        Cluck($message);
661        # Abort the program.
662        croak(">>> $message");
663    }
664    
665    =head3 SaveCGI
666    
667        Tracer::SaveCGI($cgi);
668    
669    This method saves the CGI object but does not activate emergency tracing.
670    It is used to allow L</Warn> to work in situations where emergency
671    tracing is contra-indicated (e.g. the wiki).
672    
673    =over 4
674    
675    =item cgi
676    
677    Active CGI query object.
678    
679    =back
680    
681    =cut
682    
683    sub SaveCGI {
684        $SavedCGI = $_[0];
685    }
686    
687    =head3 Warn
688    
689        Warn($message, @options);
690    
691    This method traces an important message. If an RSS feed is configured
692    (via I<FIG_Config::error_feed>) and the tracing destination is C<WARN>,
693    then the message will be echoed to the feed. In general, a tracing
694    destination of C<WARN> indicates that the caller is running as a web
695    service in a production environment; however, this is not a requirement.
696    
697    To force warnings into the RSS feed even when the tracing destination
698    is not C<WARN>, simply specify the C<Feed> tracing module. This can be
699    configured automatically when L</StandardSetup> is used.
700    
701    The L</Cluck> method calls this one for its final message. Since
702    L</Confess> calls L</Cluck>, this means that any error which is caught
703    and confessed will put something in the feed. This insures that someone
704    will be alerted relatively quickly when a failure occurs.
705    
706    =over 4
707    
708    =item message
709    
710    Message to be traced.
711    
712    =item options
713    
714    A list containing zero or more options.
715    
716    =back
717    
718    The permissible options are as follows.
719    
720    =over 4
721    
722    =item noStack
723    
724    If specified, then the stack trace is not included in the output.
725    
726    =back
727    
728    =cut
729    
730    sub Warn {
731        # Get the parameters.
732        my $message = shift @_;
733        my %options = map { $_ => 1 } @_;
734        # Trace the message.
735        Trace($message);
736        # This will contain the lock handle. If it's defined, it means we need to unlock.
737        my $lock;
738        # Check for feed forcing.
739        my $forceFeed = exists $Categories{feed};
740        # An error here would be disastrous. Note that if debug mode is specified,
741        # we do this stuff even in a test environment.
742        eval {
743            # Do we need to put this in the RSS feed?
744            if ($FIG_Config::error_feed && ($Destination eq 'WARN' || $forceFeed)) {
745                # Yes. We now need to compute the date, the link, and the title.
746                # First, the date, in a very specific format.
747                my $date = strftime("%a, %02e %b %H:%M:%S %Y ", localtime) .
748                    (tz_local_offset() / 30);
749                # Environment data goes in here. We start with the date.
750                my $environment = "$date.  ";
751                # If we need to recap the message (because it's too long to be a title), we'll
752                # put it in here.
753                my $recap;
754                # Copy the message and remove excess space.
755                my $title = $message;
756                $title =~ s/\s+/ /gs;
757                # If it's too long, we have to split it up.
758                if (length $title > 60) {
759                    # Put the full message in the environment string.
760                    $recap = $title;
761                    # Excerpt it as the title.
762                    $title = substr($title, 0, 50) . "...";
763                }
764                # If we have a CGI object, then this is a web error. Otherwise, it's
765                # command-line.
766                if (defined $SavedCGI) {
767                    # We're in a web service. The environment is the user's IP, and the link
768                    # is the URL that got us here.
769                    my $key = $ENV{HTTP_X_FORWARDED_FOR} || $ENV{REMOTE_ADDR};
770                    $environment .= "Event Reported at IP address $key process $$.";
771                    my $url = $SavedCGI->self_url();
772                    # We need the user agent string and (if available) the referrer.
773                    # The referrer will be the link.
774                    $environment .= " User Agent $ENV{HTTP_USER_AGENT}";
775                    if ($ENV{HTTP_REFERER}) {
776                        my $link = $ENV{HTTP_REFERER};
777                        $environment .= " referred from <a href=\"$link\">$link</a>.";
778                    } else {
779                        $environment .= " referrer unknown.";
780                    }
781                    # Close off the sentence with the original link.
782                    $environment .= " URL of event is <a href=\"$url\">$url</a>.";
783                } else {
784                    # No CGI object, so we're a command-line tool. Use the tracing
785                    # key and the PID as the user identifier, and add the command.
786                    my $key = EmergencyKey();
787                    $environment .= "Event Reported by $key process $$.";
788                    if ($CommandLine) {
789                        # We're in a StandardSetup script, so we have the real command line.
790                        $environment .= "\n<pre>" . CGI::escapeHTML($CommandLine) . "</pre>\n";
791                    } elsif ($ENV{_}) {
792                        # We're in a BASH script, so the command has been stored in the _ variable.
793                        $environment .= "  Command = " . CGI::escapeHTML($ENV{_}) . "\n";
794                    }
795                }
796                # Build a GUID. We use the current time, the title, and the process ID,
797                # then digest the result.
798                my $guid = Digest::MD5::md5_base64(gettimeofday(), $title, $$);
799                # Finally, the description. This is a stack trace plus various environmental stuff.
800                # The trace is optional.
801                my $stackTrace;
802                if ($options{noStack}) {
803                    $stackTrace = "";
804                } else {
805                    my @trace = LongMess();
806                    # Only proceed if we got something back.
807                    if (scalar(@trace) > 0) {
808                        $trace[0] =~ s/Tracer::Warn.+?called/Event occurred/;
809                        $stackTrace = "Stack trace:<pre>" . join("\n", @trace, "</pre>");
810                    }
811                }
812                # We got the stack trace. Now it's time to put it all together.
813                # We have a goofy thing here in that we need to HTML-escape some sections of the description
814                # twice. They will be escaped once here, and then once when written by XML::Simple. They are
815                # unescaped once when processed by the RSS reader, and stuff in the description is treated as
816                # HTML. So, anything escaped here is treated as a literal when viewed in the RSS reader, but
817                # our <br>s and <pre>s are used to format the description.
818                $recap = (defined $recap ? "<em>" . CGI::escapeHTML($recap) . "</em><br /><br />" : "");
819                my $description = "$recap$environment  $stackTrace";
820                # Okay, we have all the pieces. Create a hash of the new event.
821                my $newItem = { title => $title,
822                                description => $description,
823                                category => $LastCategory,
824                                pubDate => $date,
825                                guid => $guid,
826                              };
827                # We need XML capability for this.
828                require XML::Simple;
829                # The RSS document goes in here.
830                my $rss;
831                # Get the name of the RSS file. It's in the FIG temporary directory.
832                my $fileName = "$FIG_Config::temp/$FIG_Config::error_feed";
833                # Open the config file and lock it.
834                $lock = Open(undef, "<$FIG_Config::fig_disk/config/FIG_Config.pm");
835                flock $lock, LOCK_EX;
836                # Does it exist?
837                if (-s $fileName) {
838                    # Slurp it in.
839                    $rss = XML::Simple::XMLin($fileName, ForceArray => ['item']);
840                } else {
841                    my $size = -s $fileName;
842                    # Create an empty channel.
843                    $rss = {
844                        channel => {
845                            title => 'NMPDR Warning Feed',
846                            link => "$FIG_Config::temp_url/$FIG_Config::error_feed",
847                            description => "Important messages regarding the status of the NMPDR.",
848                            generator => "NMPDR Trace Facility",
849                            docs => "http://blogs.law.harvard.edu/tech/rss",
850                            item => []
851                        },
852                    };
853                }
854                # Get the channel object.
855                my $channel = $rss->{channel};
856                # Update the last-build date.
857                $channel->{lastBuildDate} = $date;
858                # Get the item array.
859                my $items = $channel->{item};
860                # Insure it has only 100 entries.
861                while (scalar @{$items} > 100) {
862                    pop @{$items};
863                }
864                # Add our new item at the front.
865                unshift @{$items}, $newItem;
866                # Create the XML. Note we do not include the root or the declaration. XML Simple can't handle
867                # the requirements for those.
868                my $xml = XML::Simple::XMLout($channel, NoAttr => 1, RootName => 'channel', XmlDecl => '');
869                # Here we put in the root and declaration. The problem is that the root has to have the version attribute
870                # in it. So, we suppress the root and do it by hand, and that requires suppressing the declaration, too.
871                $xml = "<?xml version=\"1.0\" encoding=\"utf-8\"?>\n<rss version=\"2.0\">$xml\n</rss>";
872                # We don't use Open here because we can't afford an error.
873                if (open XMLOUT, ">$fileName") {
874                    print XMLOUT $xml;
875                    close XMLOUT;
876                }
877            }
878        };
879        if ($@) {
880            # If the feed failed, we need to know why. The error will be traced, but this method will not be involved
881            # (which is a good thing).
882            my $error = $@;
883            Trace("Feed Error: $error") if T(Feed => 0);
884        }
885        # Be sure to unlock.
886        if ($lock) {
887            flock $lock, LOCK_UN;
888            undef $lock;
889        }
890    }
891    
892    
893    
894    
895    =head3 Assert
896    
897        Assert($condition1, $condition2, ... $conditionN);
898    
899    Return TRUE if all the conditions are true. This method can be used in conjunction with
900    the OR operator and the L</Confess> method as a debugging assert.
901    So, for example
902    
903        Assert($recNum >= 0) || Confess("Invalid record number $recNum.");
904    
905    Will abort the program with a stack trace if the value of C<$recNum> is negative.
906    
907    =cut
908    sub Assert {
909        my $retVal = 1;
910        LOOP: for my $condition (@_) {
911            if (! $condition) {
912                $retVal = 0;
913                last LOOP;
914            }
915        }
916        return $retVal;
917    }
918    
919    =head3 Cluck
920    
921        Cluck($message);
922    
923    Trace the call stack. Note that for best results, you should qualify the call with a
924    trace condition. For example,
925    
926        Cluck("Starting record parse.") if T(3);
927    
928    will only trace the stack if the trace level for the package is 3 or more.
929    
930    =over 4
931    
932    =item message
933    
934    Message to include in the trace.
935    
936    =back
937    
938    =cut
939    
940    sub Cluck {
941        # Get the parameters.
942        my ($message) = @_;
943        # Trace what's happening.
944        Trace("Stack trace for event: $message");
945        # Get the stack trace.
946        my @trace = LongMess();
947        # Convert the trace to a series of messages.
948        for my $line (@trace) {
949            # Replace the tab at the beginning with spaces.
950            $line =~ s/^\t/    /;
951            # Trace the line.
952            Trace($line);
953        }
954        # Issue a warning. This displays the event message and inserts it into the RSS error feed.
955        Warn($message);
956    }
957    
958    =head3 LongMess
959    
960        my @lines = Tracer::LongMess();
961    
962    Return a stack trace with all tracing methods removed. The return will be in the form of a list
963    of message strings.
964    
965    =cut
966    
967    sub LongMess {
968        # Declare the return variable.
969        my @retVal = ();
970        my $confession = longmess("");
971        for my $line (split /\s*\n/, $confession) {
972            unless ($line =~ /Tracer\.pm/) {
973                # Here we have a line worth keeping. Push it onto the result list.
974                push @retVal, $line;
975            }
976        }
977        # Return the result.
978        return @retVal;
979    }
980    
981    =head3 ETracing
982    
983        ETracing($parameter);
984    
985    Set up emergency tracing. Emergency tracing is tracing that is turned
986    on automatically for any program that calls this method. The emergency
987    tracing parameters are stored in a a file identified by a tracing key.
988    If this method is called with a CGI object, then the tracing key is
989    taken from a cookie. If it is called with no parameters, then the tracing
990    key is taken from an environment variable. If it is called with a string,
991    the tracing key is that string.
992    
993    =over 4
994    
995    =item parameter
996    
997    A parameter from which the tracing key is computed. If it is a scalar,
998    that scalar is used as the tracing key. If it is a CGI object, the
999    tracing key is taken from the C<IP> cookie. If it is omitted, the
1000    tracing key is taken from the C<TRACING> environment variable. If it
1001    is a CGI object and emergency tracing is not on, the C<Trace> and
1002    C<TF> parameters will be used to determine the type of tracing.
1003    
1004    =back
1005    
1006    =cut
1007    
1008    sub ETracing {
1009        # Get the parameter.
1010        my ($parameter) = @_;
1011        # Check for CGI mode.
1012        if (defined $parameter && ref $parameter eq 'CGI') {
1013            $SavedCGI = $parameter;
1014        } else {
1015            $SavedCGI = undef;
1016        }
1017        # Default to no tracing except errors.
1018        my ($tracing, $dest) = ("0", "WARN");
1019        # Check for emergency tracing.
1020        my $tkey = EmergencyKey($parameter);
1021        my $emergencyFile = EmergencyFileName($tkey);
1022        if (-e $emergencyFile) {
1023            # We have the file. Read in the data.
1024            my @tracing = GetFile($emergencyFile);
1025            # Pull off the time limit.
1026            my $expire = shift @tracing;
1027            # Convert it to seconds.
1028            $expire *= 3600;
1029            # Check the file data.
1030            my $stat = stat($emergencyFile);
1031            my ($now) = gettimeofday;
1032            if ($now - $stat->mtime > $expire) {
1033                # Delete the expired file.
1034                unlink $emergencyFile;
1035            } else {
1036                # Emergency tracing is on. Pull off the destination and
1037                # the trace level;
1038                $dest = shift @tracing;
1039                my $level = shift @tracing;
1040                # Convert the destination to a real tracing destination.
1041                # temp directory.
1042                $dest = EmergencyTracingDest($tkey, $dest);
1043                # Insure Tracer is specified.
1044                my %moduleHash = map { $_ => 1 } @tracing;
1045                $moduleHash{Tracer} = 1;
1046                # Set the trace parameter.
1047                $tracing = join(" ", $level, sort keys %moduleHash);
1048            }
1049        } elsif (defined $SavedCGI) {
1050            # There's no emergency tracing, but we have a CGI object, so check
1051            # for tracing from the form parameters.
1052            if ($SavedCGI->param('Trace')) {
1053                # Here the user has requested tracing via a form.
1054                $dest = ($SavedCGI->param('TF') ? ">$FIG_Config::temp/Trace$$.log" : "QUEUE");
1055                $tracing = $SavedCGI->param('Trace') . " Tracer";
1056            }
1057        }
1058        # Setup the tracing we've determined from all the stuff above.
1059        TSetup($tracing, $dest);
1060        # Check to see if we're a web script.
1061        if (defined $SavedCGI) {
1062            # Yes we are. Trace the form and environment data.
1063            TraceParms($SavedCGI);
1064            # Check for RAW mode. In raw mode, we print a fake header so that we see everything
1065            # emitted by the script in its raw form.
1066            if (T(Raw => 3)) {
1067                print CGI::header(-type => 'text/plain', -tracing => 'Raw');
1068            }
1069        }
1070    }
1071    
1072    =head3 EmergencyFileName
1073    
1074        my $fileName = Tracer::EmergencyFileName($tkey);
1075    
1076    Return the emergency tracing file name. This is the file that specifies
1077    the tracing information.
1078    
1079    =over 4
1080    
1081    =item tkey
1082    
1083    Tracing key for the current program.
1084    
1085    =item RETURN
1086    
1087    Returns the name of the file to contain the emergency tracing information.
1088    
1089    =back
1090    
1091    =cut
1092    
1093    sub EmergencyFileName {
1094        # Get the parameters.
1095        my ($tkey) = @_;
1096        # Compute the emergency tracing file name.
1097        return "$FIG_Config::temp/Emergency$tkey.txt";
1098    }
1099    
1100    =head3 EmergencyFileTarget
1101    
1102        my $fileName = Tracer::EmergencyFileTarget($tkey);
1103    
1104    Return the emergency tracing target file name. This is the file that receives
1105    the tracing output for file-based tracing.
1106    
1107    =over 4
1108    
1109    =item tkey
1110    
1111    Tracing key for the current program.
1112    
1113    =item RETURN
1114    
1115    Returns the name of the file to contain the trace output.
1116    
1117    =back
1118    
1119    =cut
1120    
1121    sub EmergencyFileTarget {
1122        # Get the parameters.
1123        my ($tkey) = @_;
1124        # Compute the emergency tracing file name.
1125        return "$FIG_Config::temp/trace$tkey.log";
1126    }
1127    
1128    =head3 EmergencyTracingDest
1129    
1130        my $dest = Tracer::EmergencyTracingDest($tkey, $myDest);
1131    
1132    This method converts an emergency tracing destination to a real
1133    tracing destination. The main difference is that if the
1134    destination is C<FILE> or C<APPEND>, we convert it to file
1135    output. If the destination is C<DUAL>, we convert it to file
1136    and standard output.
1137    
1138    =over 4
1139    
1140    =item tkey
1141    
1142    Tracing key for this environment.
1143    
1144    =item myDest
1145    
1146    Destination from the emergency tracing file.
1147    
1148    =item RETURN
1149    
1150    Returns a destination that can be passed into L</TSetup>.
1151    
1152    =back
1153    
1154    =cut
1155    
1156    sub EmergencyTracingDest {
1157        # Get the parameters.
1158        my ($tkey, $myDest) = @_;
1159        # Declare the return variable.
1160        my $retVal = $myDest;
1161        # Process according to the destination value.
1162        if ($myDest eq 'FILE') {
1163            $retVal = ">" . EmergencyFileTarget($tkey);
1164        } elsif ($myDest eq 'APPEND') {
1165            $retVal = ">>" . EmergencyFileTarget($tkey);
1166        } elsif ($myDest eq 'DUAL') {
1167            $retVal = "+>" . EmergencyFileTarget($tkey);
1168        } elsif ($myDest eq 'WARN') {
1169            $retVal = "WARN";
1170        }
1171        # Return the result.
1172        return $retVal;
1173    }
1174    
1175    =head3 Emergency
1176    
1177        Emergency($key, $hours, $dest, $level, @modules);
1178    
1179    Turn on emergency tracing. This method is normally invoked over the web from
1180    a debugging console, but it can also be called by the C<trace.pl> script.
1181    The caller specifies the duration of the emergency in hours, the desired tracing
1182    destination, the trace level, and a list of the trace modules to activate.
1183    For the length of the duration, when a program in an environment with the
1184    specified tracing key active invokes a Sprout CGI script, tracing will be
1185    turned on automatically. See L</TSetup> for more about tracing setup and
1186    L</ETracing> for more about emergency tracing.
1187    
1188    =over 4
1189    
1190    =item tkey
1191    
1192    The tracing key. This is used to identify the control file and the trace file.
1193    
1194    =item hours
1195    
1196    Number of hours to keep emergency tracing alive.
1197    
1198    =item dest
1199    
1200    Tracing destination. If no path information is specified for a file
1201    destination, it is put in the FIG temporary directory.
1202    
1203    =item level
1204    
1205    Tracing level. A higher level means more trace messages.
1206    
1207    =item modules
1208    
1209    A list of the tracing modules to activate.
1210    
1211    =back
1212    
1213    =cut
1214    
1215    sub Emergency {
1216        # Get the parameters.
1217        my ($tkey, $hours, $dest, $level, @modules) = @_;
1218        # Create the emergency file.
1219        my $specFile = EmergencyFileName($tkey);
1220        my $outHandle = Open(undef, ">$specFile");
1221        print $outHandle join("\n", $hours, $dest, $level, @modules, "");
1222    }
1223    
1224    =head3 EmergencyKey
1225    
1226        my $tkey = EmergencyKey($parameter);
1227    
1228    Return the Key to be used for emergency tracing. This could be an IP address,
1229     a session ID, or a user name, depending on the environment.
1230    
1231    =over 4
1232    
1233    =item parameter
1234    
1235    Parameter defining the method for finding the tracing key. If it is a scalar,
1236    then it is presumed to be the tracing key itself. If it is a CGI object, then
1237    the tracing key is taken from the C<IP> cookie. Otherwise, the tracing key is
1238    taken from the C<TRACING> environment variable.
1239    
1240    =item RETURN
1241    
1242    Returns the key to be used for labels in emergency tracing.
1243    
1244    =back
1245    
1246    =cut
1247    
1248    sub EmergencyKey {
1249        # Get the parameters.
1250        my ($parameter) = @_;
1251        # Declare the return variable.
1252        my $retVal;
1253        # Determine the parameter type.
1254        if (! defined $parameter) {
1255            # Here we're supposed to check the environment. If that fails, we
1256            # get the effective login ID.
1257            $retVal = $ENV{TRACING} || scalar getpwuid($<);
1258        } else {
1259            my $ptype = ref $parameter;
1260            if ($ptype eq 'CGI') {
1261                # Here we were invoked from a web page. Look for a cookie.
1262                $retVal = $parameter->cookie('IP');
1263            } elsif (! $ptype) {
1264                # Here the key was passed in.
1265                $retVal = $parameter;
1266            }
1267        }
1268        # If no luck finding a key, use the PID.
1269        if (! defined $retVal) {
1270            $retVal = $$;
1271        }
1272        # Return the result.
1273        return $retVal;
1274    }
1275    
1276    
1277    =head3 TraceParms
1278    
1279        Tracer::TraceParms($cgi);
1280    
1281    Trace the CGI parameters at trace level CGI => 3 and the environment variables
1282    at level CGI => 4. A self-referencing URL is traced at level CGI => 2.
1283    
1284    =over 4
1285    
1286    =item cgi
1287    
1288    CGI query object containing the parameters to trace.
1289    
1290    =back
1291    
1292    =cut
1293    
1294    sub TraceParms {
1295        # Get the parameters.
1296        my ($cgi) = @_;
1297        if (T(CGI => 2)) {
1298            # Here we trace the GET-style URL for the script.
1299            Trace("[URL] " . $cgi->url(-relative => 1, -query => 1));
1300        }
1301        if (T(CGI => 3)) {
1302            # Here we want to trace the parameter data.
1303            my @names = $cgi->param;
1304            for my $parmName (sort @names) {
1305                # Note we skip the Trace parameters, which are for our use only.
1306                if ($parmName ne 'Trace' && $parmName ne 'TF') {
1307                    my @values = $cgi->param($parmName);
1308                    Trace("[CGI] $parmName = " . join(", ", @values));
1309                }
1310            }
1311            # Display the request method.
1312            my $method = $cgi->request_method();
1313            Trace("Method: $method");
1314        }
1315        if (T(CGI => 4)) {
1316            # Here we want the environment data too.
1317            for my $envName (sort keys %ENV) {
1318                Trace("[ENV] $envName = $ENV{$envName}");
1319            }
1320        }
1321    }
1322    
1323    =head3 TraceImages
1324    
1325        Tracer::TraceImages($htmlString);
1326    
1327    Trace information about all of an html document's images. The tracing
1328    will be for type "IMG" at level 3. The image's source string
1329    will be displayed. This is generally either the URL of the image or
1330    raw data for the image itself. If the source is too long, only the first 300
1331    characters will be shown at trace level 3. The entire source will be shown,
1332    however, at trace level 4. This method is not very smart, and might catch
1333    Javascript code, but it is still useful when debugging the arcane
1334    behavior of images in multiple browser environments.
1335    
1336    =over 4
1337    
1338    =item htmlString
1339    
1340    HTML text for an outgoing web page.
1341    
1342    =back
1343    
1344    =cut
1345    
1346    sub TraceImages {
1347        # Only proceed if we're at the proper trace level.
1348        if (T(IMG => 3)) {
1349            # For performance reasons we're manipulating $_[0] instead of retrieving the string
1350            # into a variable called "$htmlString". This is because we expect html strings to be
1351            # long, and don't want to copy them any more than we have to.
1352            Trace(length($_[0]) . " characters in web page.");
1353            # Loop through the HTML, culling image tags.
1354            while ($_[0] =~ /<img\s+[^>]+?src="([^"]+)"/sgi) {
1355                # Extract the source string and determine whether or not it's too long.
1356                my $srcString = $1;
1357                my $pos = pos($_[0]) - length($srcString);
1358                my $excess = length($srcString) - 300;
1359                # We'll put the display string in here.
1360                my $srcDisplay = $srcString;
1361                # If it's a data string, split it at the comma.
1362                $srcDisplay =~ s/^(data[^,]+,)/$1\n/;
1363                # If there's no excess or we're at trace level 4, we're done. At level 3 with
1364                # a long string, however, we only show the first 300 characters.
1365                if ($excess > 0 && ! T(IMG => 4)) {
1366                    $srcDisplay = substr($srcDisplay,0,300) . "\nplus $excess characters.";
1367                }
1368                # Output the trace message.
1369                Trace("Image tag at position $pos:\n$srcDisplay");
1370            }
1371        }
1372    }
1373    
1374    =head2 Command-Line Utility Methods
1375    
1376    =head3 SendSMS
1377    
1378        my $msgID = Tracer::SendSMS($phoneNumber, $msg);
1379    
1380    Send a text message to a phone number using Clickatell. The FIG_Config file must contain the
1381    user name, password, and API ID for the relevant account in the hash reference variable
1382    I<$FIG_Config::phone>, using the keys C<user>, C<password>, and C<api_id>. For
1383    example, if the user name is C<BruceTheHumanPet>, the password is C<silly>, and the API ID
1384    is C<2561022>, then the FIG_Config file must contain
1385    
1386        $phone =  { user => 'BruceTheHumanPet',
1387                    password => 'silly',
1388                    api_id => '2561022' };
1389    
1390    The original purpose of this method was to insure Bruce would be notified immediately when the
1391    Sprout Load terminates. Care should be taken if you do not wish Bruce to be notified immediately
1392    when you call this method.
1393    
1394    The message ID will be returned if successful, and C<undef> if an error occurs.
1395    
1396    =over 4
1397    
1398    =item phoneNumber
1399    
1400    Phone number to receive the message, in international format. A United States phone number
1401    would be prefixed by "1". A British phone number would be prefixed by "44".
1402    
1403    =item msg
1404    
1405    Message to send to the specified phone.
1406    
1407    =item RETURN
1408    
1409    Returns the message ID if successful, and C<undef> if the message could not be sent.
1410    
1411    =back
1412    
1413    =cut
1414    
1415    sub SendSMS {
1416        # Get the parameters.
1417        my ($phoneNumber, $msg) = @_;
1418        # Declare the return variable. If we do not change it, C<undef> will be returned.
1419        my $retVal;
1420        # Only proceed if we have phone support.
1421        if (! defined $FIG_Config::phone) {
1422            Trace("Phone support not present in FIG_Config.") if T(1);
1423        } else {
1424            # Get the phone data.
1425            my $parms = $FIG_Config::phone;
1426            # Get the Clickatell URL.
1427            my $url = "http://api.clickatell.com/http/";
1428            # Create the user agent.
1429            my $ua = LWP::UserAgent->new;
1430            # Request a Clickatell session.
1431            my $resp = $ua->post("$url/sendmsg", { user => $parms->{user},
1432                                         password => $parms->{password},
1433                                         api_id => $parms->{api_id},
1434                                         to => $phoneNumber,
1435                                         text => $msg});
1436            # Check for an error.
1437            if (! $resp->is_success) {
1438                Trace("Alert failed.") if T(1);
1439            } else {
1440                # Get the message ID.
1441                my $rstring = $resp->content;
1442                if ($rstring =~ /^ID:\s+(.*)$/) {
1443                    $retVal = $1;
1444                } else {
1445                    Trace("Phone attempt failed with $rstring") if T(1);
1446                }
1447            }
1448        }
1449        # Return the result.
1450        return $retVal;
1451    }
1452    
1453    =head3 StandardSetup
1454    
1455        my ($options, @parameters) = StandardSetup(\@categories, \%options, $parmHelp, @ARGV);
1456    
1457    This method performs standard command-line parsing and tracing setup. The return
1458    values are a hash of the command-line options and a list of the positional
1459    parameters. Tracing is automatically set up and the command-line options are
1460    validated.
1461    
1462    This is a complex method that does a lot of grunt work. The parameters can
1463    be more easily understood, however, once they are examined individually.
1464    
1465    The I<categories> parameter is the most obtuse. It is a reference to a list of
1466    special-purpose tracing categories. Most tracing categories are PERL package
1467    names. So, for example, if you wanted to turn on tracing inside the B<Sprout>,
1468    B<ERDB>, and B<SproutLoad> packages, you would specify the categories
1469    
1470        ["Sprout", "SproutLoad", "ERDB"]
1471    
1472    This would cause trace messages in the specified three packages to appear in
1473    the output. There are two special tracing categories that are automatically
1474    handled by this method. In other words, if you used L</TSetup> you would need
1475    to include these categories manually, but if you use this method they are turned
1476    on automatically.
1477    
1478    =over 4
1479    
1480    =item SQL
1481    
1482    Traces SQL commands and activity.
1483    
1484    =item Tracer
1485    
1486    Traces error messages and call stacks.
1487    
1488    =back
1489    
1490    C<SQL> is only turned on if the C<-sql> option is specified in the command line.
1491    The trace level is specified using the C<-trace> command-line option. For example,
1492    the following command line for C<TransactFeatures> turns on SQL tracing and runs
1493    all tracing at level 3.
1494    
1495        TransactFeatures -trace=3 -sql register ../xacts IDs.tbl
1496    
1497    Standard tracing is output to the standard output and echoed to the file
1498    C<trace>I<$$>C<.log> in the FIG temporary directory, where I<$$> is the
1499    process ID. You can also specify the C<user> parameter to put a user ID
1500    instead of a process ID in the trace file name. So, for example
1501    
1502    The default trace level is 2. To get all messages, specify a trace level of 4.
1503    For a genome-by-genome update, use 3.
1504    
1505        TransactFeatures -trace=3 -sql -user=Bruce register ../xacts IDs.tbl
1506    
1507    would send the trace output to C<traceBruce.log> in the temporary directory.
1508    
1509    The I<options> parameter is a reference to a hash containing the command-line
1510    options, their default values, and an explanation of what they mean. Command-line
1511    options may be in the form of switches or keywords. In the case of a switch, the
1512    option value is 1 if it is specified and 0 if it is not specified. In the case
1513    of a keyword, the value is separated from the option name by an equal sign. You
1514    can see this last in the command-line example above.
1515    
1516    You can specify a different default trace level by setting C<$options->{trace}>
1517    prior to calling this method.
1518    
1519    An example at this point would help. Consider, for example, the command-line utility
1520    C<TransactFeatures>. It accepts a list of positional parameters plus the options
1521    C<safe>, C<noAlias>, C<start>, and C<tblFiles>. To start up this command, we execute
1522    the following code.
1523    
1524        my ($options, @parameters) = Tracer::StandardSetup(["DocUtils"],
1525                            { safe => [0, "use database transactions"],
1526                              noAlias => [0, "do not expect aliases in CHANGE transactions"],
1527                              start => [' ', "start with this genome"],
1528                              tblFiles => [0, "output TBL files containing the corrected IDs"] },
1529                            "<command> <transactionDirectory> <IDfile>",
1530                          @ARGV);
1531    
1532    
1533    The call to C<ParseCommand> specifies the default values for the options and
1534    stores the actual options in a hash that is returned as C<$options>. The
1535    positional parameters are returned in C<@parameters>.
1536    
1537    The following is a sample command line for C<TransactFeatures>.
1538    
1539        TransactFeatures -trace=2 -noAlias register ../xacts IDs.tbl
1540    
1541    Single and double hyphens are equivalent. So, you could also code the
1542    above command as
1543    
1544        TransactFeatures --trace=2 --noAlias register ../xacts IDs.tbl
1545    
1546    In this case, C<register>, C<../xacts>, and C<IDs.tbl> are the positional
1547    parameters, and would find themselves in I<@parameters> after executing the
1548    above code fragment. The tracing would be set to level 2, and the categories
1549    would be C<Tracer>, and <DocUtils>. C<Tracer> is standard,
1550    and C<DocUtils> was included because it came in within the first parameter
1551    to this method. The I<$options> hash would be
1552    
1553        { trace => 2, sql => 0, safe => 0,
1554          noAlias => 1, start => ' ', tblFiles => 0 }
1555    
1556    Use of C<StandardSetup> in this way provides a simple way of performing
1557    standard tracing setup and command-line parsing. Note that the caller is
1558    not even aware of the command-line switches C<-trace> and C<-sql>, which
1559    are used by this method to control the tracing. If additional tracing features
1560    need to be added in the future, they can be processed by this method without
1561    upsetting the command-line utilities.
1562    
1563    If the C<background> option is specified on the command line, then the
1564    standard and error outputs will be directed to files in the temporary
1565    directory, using the same suffix as the trace file. So, if the command
1566    line specified
1567    
1568        -user=Bruce -background
1569    
1570    then the trace output would go to C<traceBruce.log>, the standard output to
1571    C<outBruce.log>, and the error output to C<errBruce.log>. This is designed to
1572    simplify starting a command in the background.
1573    
1574    The user name is also used as the tracing key for L</Emergency Tracing>.
1575    Specifying a value of C<E> for the trace level causes emergency tracing to
1576    be used instead of custom tracing. If the user name is not specified,
1577    the tracing key is taken from the C<Tracing> environment variable. If there
1578    is no value for that variable, the tracing key will be computed from the active
1579    login ID.
1580    
1581    Since the default situation in StandardSetup is to trace to the standard
1582    output, errors that occur in command-line scripts will not generate
1583    RSS events. To force the events, use the C<warn> option.
1584    
1585        TransactFeatures -background -warn register ../xacts IDs.tbl
1586    
1587    Finally, if the special option C<-help> is specified, the option
1588    names will be traced at level 0 and the program will exit without processing.
1589    This provides a limited help capability. For example, if the user enters
1590    
1591        TransactFeatures -help
1592    
1593    he would see the following output.
1594    
1595        TransactFeatures [options] <command> <transactionDirectory> <IDfile>
1596            -trace    tracing level (default E)
1597            -sql      trace SQL commands
1598            -safe     use database transactions
1599            -noAlias  do not expect aliases in CHANGE transactions
1600            -start    start with this genome
1601            -tblFiles output TBL files containing the corrected IDs
1602    
1603    The caller has the option of modifying the tracing scheme by placing a value
1604    for C<trace> in the incoming options hash. The default value can be overridden,
1605    or the tracing to the standard output can be turned off by suffixing a minus
1606    sign to the trace level. So, for example,
1607    
1608        { trace => [0, "tracing level (default 0)"],
1609           ...
1610    
1611    would set the default trace level to 0 instead of E, while
1612    
1613        { trace => ["2-", "tracing level (default 2)"],
1614           ...
1615    
1616    would set the default to 2, but trace only to the log file, not to the
1617    standard output.
1618    
1619    The parameters to this method are as follows.
1620    
1621    =over 4
1622    
1623    =item categories
1624    
1625    Reference to a list of tracing category names. These should be names of
1626    packages whose internal workings will need to be debugged to get the
1627    command working.
1628    
1629    =item options
1630    
1631    Reference to a hash containing the legal options for the current command mapped
1632    to their default values and descriptions. The user can override the defaults
1633    by specifying the options as command-line switches prefixed by a hyphen.
1634    Tracing-related options may be added to this hash. If the C<-h> option is
1635    specified on the command line, the option descriptions will be used to
1636    explain the options. To turn off tracing to the standard output, add a
1637    minus sign to the value for C<trace> (see above).
1638    
1639    =item parmHelp
1640    
1641    A string that vaguely describes the positional parameters. This is used
1642    if the user specifies the C<-h> option.
1643    
1644    =item argv
1645    
1646    List of command line parameters, including the option switches, which must
1647    precede the positional parameters and be prefixed by a hyphen.
1648    
1649    =item RETURN
1650    
1651    Returns a list. The first element of the list is the reference to a hash that
1652    maps the command-line option switches to their values. These will either be the
1653    default values or overrides specified on the command line. The remaining
1654    elements of the list are the position parameters, in order.
1655    
1656    =back
1657    
1658    =cut
1659    
1660    sub StandardSetup {
1661        # Get the parameters.
1662        my ($categories, $options, $parmHelp, @argv) = @_;
1663        # Get the default tracing key.
1664        my $tkey = EmergencyKey();
1665        # Save the command line.
1666        $CommandLine = join(" ", $0, map { $_ =~ /\s/ ? "\"$_\"" : $_ } @argv);
1667        # Add the tracing options.
1668        if (! exists $options->{trace}) {
1669            $options->{trace} = ['2', "tracing level (E for emergency tracing)"];
1670        }
1671        $options->{sql} = [0, "turn on SQL tracing"];
1672        $options->{help} = [0, "display command-line options"];
1673        $options->{user} = [$tkey, "tracing key"];
1674        $options->{background} = [0, "spool standard and error output"];
1675        $options->{warn} = [0, "send errors to RSS feed"];
1676        # Create a parsing hash from the options hash. The parsing hash
1677        # contains the default values rather than the default value
1678        # and the description. While we're at it, we'll memorize the
1679        # length of the longest option name.
1680        my $longestName = 0;
1681        my %parseOptions = ();
1682        for my $key (keys %{$options}) {
1683            if (length $key > $longestName) {
1684                $longestName = length $key;
1685            }
1686            $parseOptions{$key} = $options->{$key}->[0];
1687        }
1688        # Parse the command line.
1689        my ($retOptions, @retParameters) = ParseCommand(\%parseOptions, @argv);
1690        # Get the logfile suffix.
1691        my $suffix = $retOptions->{user};
1692        # Check for background mode.
1693        if ($retOptions->{background}) {
1694            my $outFileName = "$FIG_Config::temp/out$suffix.log";
1695            my $errFileName = "$FIG_Config::temp/err$suffix.log";
1696            open STDOUT, ">$outFileName";
1697            open STDERR, ">$errFileName";
1698            # Check for phone support. If we have phone support and a phone number,
1699            # we want to turn it on.
1700            if ($ENV{PHONE} && defined($FIG_Config::phone)) {
1701                $retOptions->{phone} = $ENV{PHONE};
1702            }
1703        }
1704        # Now we want to set up tracing. First, we need to know if the user
1705        # wants emergency tracing.
1706        if ($retOptions->{trace} eq 'E') {
1707            ETracing($retOptions->{user});
1708        } else {
1709            # Here the tracing is controlled from the command line.
1710            my @cats = @{$categories};
1711            if ($retOptions->{sql}) {
1712                push @cats, "SQL";
1713            }
1714            if ($retOptions->{warn}) {
1715                push @cats, "Feed";
1716            }
1717            # Add the default categories.
1718            push @cats, "Tracer";
1719            # Next, we create the category string by joining the categories.
1720            my $cats = join(" ", @cats);
1721            # Check to determine whether or not the caller wants to turn off tracing
1722            # to the standard output.
1723            my $traceLevel = $retOptions->{trace};
1724            my $textOKFlag = 1;
1725            if ($traceLevel =~ /^(.)-/) {
1726                $traceLevel = $1;
1727                $textOKFlag = 0;
1728            }
1729            # Now we set up the trace mode.
1730            my $traceMode;
1731            # Verify that we can open a file in the FIG temporary directory.
1732            my $traceFileName = "$FIG_Config::temp/trace$suffix.log";
1733            if (open TESTTRACE, ">$traceFileName") {
1734                # Here we can trace to a file.
1735                $traceMode = ">$traceFileName";
1736                if ($textOKFlag) {
1737                    # Echo to standard output if the text-OK flag is set.
1738                    $traceMode = "+$traceMode";
1739                }
1740                # Close the test file.
1741                close TESTTRACE;
1742            } else {
1743                # Here we can't trace to a file. Complain about this.
1744                warn "Could not open trace file $traceFileName: $!\n";
1745                # We trace to the standard output if it's
1746                # okay, and the error log otherwise.
1747                if ($textOKFlag) {
1748                    $traceMode = "TEXT";
1749                } else {
1750                    $traceMode = "WARN";
1751                }
1752            }
1753            # Now set up the tracing.
1754            TSetup("$traceLevel $cats", $traceMode);
1755        }
1756        # Check for the "help" option. If it is specified, dump the command-line
1757        # options and exit the program.
1758        if ($retOptions->{help}) {
1759            $0 =~ m#[/\\](\w+)(\.pl)?$#i;
1760            print "$1 [options] $parmHelp\n";
1761            for my $key (sort keys %{$options}) {
1762                my $name = Pad($key, $longestName, 0, ' ');
1763                my $desc = $options->{$key}->[1];
1764                if ($options->{$key}->[0]) {
1765                    $desc .= " (default " . $options->{$key}->[0] . ")";
1766                }
1767                print "  $name $desc\n";
1768            }
1769            exit(0);
1770        }
1771        # Trace the options, if applicable.
1772        if (T(3)) {
1773            my @parms = grep { $retOptions->{$_} } keys %{$retOptions};
1774            Trace("Selected options: " . join(", ", sort @parms) . ".");
1775        }
1776        # Return the parsed parameters.
1777        return ($retOptions, @retParameters);
1778    }
1779    
1780    =head3 ReadOptions
1781    
1782        my %options = Tracer::ReadOptions($fileName);
1783    
1784    Read a set of options from a file. Each option is encoded in a line of text that has the
1785    format
1786    
1787    I<optionName>C<=>I<optionValue>C<; >I<comment>
1788    
1789    The option name must consist entirely of letters, digits, and the punctuation characters
1790    C<.> and C<_>, and is case sensitive. Blank lines and lines in which the first nonblank
1791    character is a semi-colon will be ignored. The return hash will map each option name to
1792    the corresponding option value.
1793    
1794    =over 4
1795    
1796    =item fileName
1797    
1798    Name of the file containing the option data.
1799    
1800    =item RETURN
1801    
1802    Returns a hash mapping the option names specified in the file to their corresponding option
1803    value.
1804    
1805    =back
1806    
1807    =cut
1808    
1809    sub ReadOptions {
1810        # Get the parameters.
1811        my ($fileName) = @_;
1812        # Open the file.
1813        (open CONFIGFILE, "<$fileName") || Confess("Could not open option file $fileName.");
1814        # Count the number of records read.
1815        my ($records, $comments) = 0;
1816        # Create the return hash.
1817        my %retVal = ();
1818        # Loop through the file, accumulating key-value pairs.
1819        while (my $line = <CONFIGFILE>) {
1820            # Denote we've read a line.
1821            $records++;
1822            # Determine the line type.
1823            if ($line =~ /^\s*[\n\r]/) {
1824                # A blank line is a comment.
1825                $comments++;
1826            } elsif ($line =~ /^\s*([A-Za-z0-9_\.]+)=([^;]*);/) {
1827                # Here we have an option assignment.
1828                retVal{$1} = $2;
1829            } elsif ($line =~ /^\s*;/) {
1830                # Here we have a text comment.
1831                $comments++;
1832            } else {
1833                # Here we have an invalid line.
1834                Trace("Invalid option statement in record $records.") if T(0);
1835            }
1836        }
1837        # Return the hash created.
1838        return %retVal;
1839    }
1840    
1841    =head3 GetOptions
1842    
1843        Tracer::GetOptions(\%defaults, \%options);
1844    
1845    Merge a specified set of options into a table of defaults. This method takes two hash references
1846    as input and uses the data from the second to update the first. If the second does not exist,
1847    there will be no effect. An error will be thrown if one of the entries in the second hash does not
1848    exist in the first.
1849    
1850    Consider the following example.
1851    
1852        my $optionTable = GetOptions({ dbType => 'mySQL', trace => 0 }, $options);
1853    
1854    In this example, the variable B<$options> is expected to contain at most two options-- B<dbType> and
1855    B<trace>. The default database type is C<mySQL> and the default trace level is C<0>. If the value of
1856    B<$options> is C<< {dbType => 'Oracle'} >>, then the database type will be changed to C<Oracle> and
1857    the trace level will remain at 0. If B<$options> is undefined, then the database type and trace level
1858    will remain C<mySQL> and C<0>. If, on the other hand, B<$options> is defined as
1859    
1860        {databaseType => 'Oracle'}
1861    
1862    an error will occur because the B<databaseType> option does not exist.
1863    
1864    =over 4
1865    
1866    =item defaults
1867    
1868    Table of default option values.
1869    
1870    =item options
1871    
1872    Table of overrides, if any.
1873    
1874    =item RETURN
1875    
1876    Returns a reference to the default table passed in as the first parameter.
1877    
1878    =back
1879    
1880    =cut
1881    
1882    sub GetOptions {
1883        # Get the parameters.
1884        my ($defaults, $options) = @_;
1885        # Check for overrides.
1886        if ($options) {
1887            # Loop through the overrides.
1888            while (my ($option, $setting) = each %{$options}) {
1889                # Insure this override exists.
1890                if (!exists $defaults->{$option}) {
1891                    croak "Unrecognized option $option encountered.";
1892                } else {
1893                    # Apply the override.
1894                    $defaults->{$option} = $setting;
1895                }
1896            }
1897        }
1898        # Return the merged table.
1899        return $defaults;
1900    }
1901    
1902    =head3 MergeOptions
1903    
1904        Tracer::MergeOptions(\%table, \%defaults);
1905    
1906    Merge default values into a hash table. This method looks at the key-value pairs in the
1907    second (default) hash, and if a matching key is not found in the first hash, the default
1908    pair is copied in. The process is similar to L</GetOptions>, but there is no error-
1909    checking and no return value.
1910    
1911    =over 4
1912    
1913    =item table
1914    
1915    Hash table to be updated with the default values.
1916    
1917    =item defaults
1918    
1919    Default values to be merged into the first hash table if they are not already present.
1920    
1921    =back
1922    
1923    =cut
1924    
1925    sub MergeOptions {
1926        # Get the parameters.
1927        my ($table, $defaults) = @_;
1928        # Loop through the defaults.
1929        while (my ($key, $value) = each %{$defaults}) {
1930            if (!exists $table->{$key}) {
1931                $table->{$key} = $value;
1932            }
1933        }
1934    }
1935    
1936    =head3 ParseCommand
1937    
1938        my ($options, @arguments) = Tracer::ParseCommand(\%optionTable, @inputList);
1939    
1940    Parse a command line consisting of a list of parameters. The initial parameters may be option
1941    specifiers of the form C<->I<option> or C<->I<option>C<=>I<value>. The options are stripped
1942    off and merged into a table of default options. The remainder of the command line is
1943    returned as a list of positional arguments. For example, consider the following invocation.
1944    
1945        my ($options, @arguments) = ParseCommand({ errors => 0, logFile => 'trace.log'}, @words);
1946    
1947    In this case, the list @words will be treated as a command line and there are two options available,
1948    B<errors> and B<logFile>. If @words has the following format
1949    
1950        -logFile=error.log apple orange rutabaga
1951    
1952    then at the end of the invocation, C<$options> will be
1953    
1954        { errors => 0, logFile => 'error.log' }
1955    
1956    and C<@arguments> will contain
1957    
1958        apple orange rutabaga
1959    
1960    The parser allows for some escape sequences. See L</UnEscape> for a description. There is no
1961    support for quote characters. Options can be specified with single or double hyphens.
1962    
1963    =over 4
1964    
1965    =item optionTable
1966    
1967    Table of default options.
1968    
1969    =item inputList
1970    
1971    List of words on the command line.
1972    
1973    =item RETURN
1974    
1975    Returns a reference to the option table and a list of the positional arguments.
1976    
1977    =back
1978    
1979    =cut
1980    
1981    sub ParseCommand {
1982        # Get the parameters.
1983        my ($optionTable, @inputList) = @_;
1984          # Process any options in the input list.          # Process any options in the input list.
1985          my %overrides = ();          my %overrides = ();
1986          while ((@inputList > 0) && ($inputList[0] =~ /^-/)) {      while ((@inputList > 0) && ($inputList[0] =~ /^--?/)) {
1987                  # Get the current option.                  # Get the current option.
1988                  my $arg = shift @inputList;                  my $arg = shift @inputList;
1989                  # Pull out the option name.                  # Pull out the option name.
1990                  $arg =~ /^-([^=]*)/g;          $arg =~ /^--?([^=]*)/g;
1991                  my $name = $1;                  my $name = $1;
1992                  # Check for an option value.                  # Check for an option value.
1993                  if ($arg =~ /\G=(.*)$/g) {                  if ($arg =~ /\G=(.*)$/g) {
1994                          # Here we have a value for the option.                          # Here we have a value for the option.
1995                          $overrides{$name} = UnEscape($1);                          $overrides{$name} = UnEscape($1);
1996                  } else {                  } else {
1997                          # Here there is no value, so we use 1.              # Here there is no value, so we use 1.
1998                          $overrides{$name} = 1;              $overrides{$name} = 1;
1999            }
2000        }
2001        # Merge the options into the defaults.
2002        GetOptions($optionTable, \%overrides);
2003        # Translate the remaining parameters.
2004        my @retVal = ();
2005        for my $inputParm (@inputList) {
2006            push @retVal, UnEscape($inputParm);
2007        }
2008        # Return the results.
2009        return ($optionTable, @retVal);
2010    }
2011    
2012    
2013    =head2 File Utility Methods
2014    
2015    =head3 GetFile
2016    
2017        my @fileContents = Tracer::GetFile($fileName);
2018    
2019        or
2020    
2021        my $fileContents = Tracer::GetFile($fileName);
2022    
2023    Return the entire contents of a file. In list context, line-ends are removed and
2024    each line is a list element. In scalar context, line-ends are replaced by C<\n>.
2025    
2026    =over 4
2027    
2028    =item fileName
2029    
2030    Name of the file to read.
2031    
2032    =item RETURN
2033    
2034    In a list context, returns the entire file as a list with the line terminators removed.
2035    In a scalar context, returns the entire file as a string. If an error occurs opening
2036    the file, an empty list will be returned.
2037    
2038    =back
2039    
2040    =cut
2041    
2042    sub GetFile {
2043        # Get the parameters.
2044        my ($fileName) = @_;
2045        # Declare the return variable.
2046        my @retVal = ();
2047        # Open the file for input.
2048        my $handle = Open(undef, "<$fileName");
2049        # Read the whole file into the return variable, stripping off any terminator
2050        # characters.
2051        my $lineCount = 0;
2052        while (my $line = <$handle>) {
2053            $lineCount++;
2054            $line = Strip($line);
2055            push @retVal, $line;
2056        }
2057        # Close it.
2058        close $handle;
2059        my $actualLines = @retVal;
2060        Trace("$actualLines lines read from file $fileName.") if T(File => 2);
2061        # Return the file's contents in the desired format.
2062        if (wantarray) {
2063            return @retVal;
2064        } else {
2065            return join "\n", @retVal;
2066        }
2067    }
2068    
2069    =head3 PutFile
2070    
2071        Tracer::PutFile($fileName, \@lines);
2072    
2073    Write out a file from a list of lines of text.
2074    
2075    =over 4
2076    
2077    =item fileName
2078    
2079    Name of the output file.
2080    
2081    =item lines
2082    
2083    Reference to a list of text lines. The lines will be written to the file in order, with trailing
2084    new-line characters. Alternatively, may be a string, in which case the string will be written without
2085    modification.
2086    
2087    =back
2088    
2089    =cut
2090    
2091    sub PutFile {
2092        # Get the parameters.
2093        my ($fileName, $lines) = @_;
2094        # Open the output file.
2095        my $handle = Open(undef, ">$fileName");
2096        # Count the lines written.
2097        if (ref $lines ne 'ARRAY') {
2098            # Here we have a scalar, so we write it raw.
2099            print $handle $lines;
2100            Trace("Scalar put to file $fileName.") if T(File => 3);
2101        } else {
2102            # Write the lines one at a time.
2103            my $count = 0;
2104            for my $line (@{$lines}) {
2105                print $handle "$line\n";
2106                $count++;
2107            }
2108            Trace("$count lines put to file $fileName.") if T(File => 3);
2109        }
2110        # Close the output file.
2111        close $handle;
2112    }
2113    
2114    =head3 ParseRecord
2115    
2116        my @fields = Tracer::ParseRecord($line);
2117    
2118    Parse a tab-delimited data line. The data line is split into field values. Embedded tab
2119    and new-line characters in the data line must be represented as C<\t> and C<\n>, respectively.
2120    These will automatically be converted.
2121    
2122    =over 4
2123    
2124    =item line
2125    
2126    Line of data containing the tab-delimited fields.
2127    
2128    =item RETURN
2129    
2130    Returns a list of the fields found in the data line.
2131    
2132    =back
2133    
2134    =cut
2135    
2136    sub ParseRecord {
2137        # Get the parameter.
2138        my ($line) = @_;
2139        # Remove the trailing new-line, if any.
2140        chomp $line;
2141        # Split the line read into pieces using the tab character.
2142        my @retVal = split /\t/, $line;
2143        # Trim and fix the escapes in each piece.
2144        for my $value (@retVal) {
2145            # Trim leading whitespace.
2146            $value =~ s/^\s+//;
2147            # Trim trailing whitespace.
2148            $value =~ s/\s+$//;
2149            # Delete the carriage returns.
2150            $value =~ s/\r//g;
2151            # Convert the escapes into their real values.
2152            $value =~ s/\\t/"\t"/ge;
2153            $value =~ s/\\n/"\n"/ge;
2154        }
2155        # Return the result.
2156        return @retVal;
2157    }
2158    
2159    =head3 Merge
2160    
2161        my @mergedList = Tracer::Merge(@inputList);
2162    
2163    Sort a list of strings and remove duplicates.
2164    
2165    =over 4
2166    
2167    =item inputList
2168    
2169    List of scalars to sort and merge.
2170    
2171    =item RETURN
2172    
2173    Returns a list containing the same elements sorted in ascending order with duplicates
2174    removed.
2175    
2176    =back
2177    
2178    =cut
2179    
2180    sub Merge {
2181        # Get the input list in sort order.
2182        my @inputList = sort @_;
2183        # Only proceed if the list has at least two elements.
2184        if (@inputList > 1) {
2185            # Now we want to move through the list splicing out duplicates.
2186            my $i = 0;
2187            while ($i < @inputList) {
2188                # Get the current entry.
2189                my $thisEntry = $inputList[$i];
2190                # Find out how many elements duplicate the current entry.
2191                my $j = $i + 1;
2192                my $dup1 = $i + 1;
2193                while ($j < @inputList && $inputList[$j] eq $thisEntry) { $j++; };
2194                # If the number is nonzero, splice out the duplicates found.
2195                if ($j > $dup1) {
2196                    splice @inputList, $dup1, $j - $dup1;
2197                }
2198                # Now the element at position $dup1 is different from the element before it
2199                # at position $i. We push $i forward one position and start again.
2200                $i++;
2201            }
2202        }
2203        # Return the merged list.
2204        return @inputList;
2205    }
2206    
2207    =head3 Open
2208    
2209        my $handle = Open($fileHandle, $fileSpec, $message);
2210    
2211    Open a file.
2212    
2213    The I<$fileSpec> is essentially the second argument of the PERL C<open>
2214    function. The mode is specified using Unix-like shell information. So, for
2215    example,
2216    
2217        Open(\*LOGFILE, '>>/usr/spool/news/twitlog', "Could not open twit log.");
2218    
2219    would open for output appended to the specified file, and
2220    
2221        Open(\*DATASTREAM, "| sort -u >$outputFile", "Could not open $outputFile.");
2222    
2223    would open a pipe that sorts the records written and removes duplicates. Note
2224    the use of file handle syntax in the Open call. To use anonymous file handles,
2225    code as follows.
2226    
2227        my $logFile = Open(undef, '>>/usr/spool/news/twitlog', "Could not open twit log.");
2228    
2229    The I<$message> parameter is used if the open fails. If it is set to C<0>, then
2230    the open returns TRUE if successful and FALSE if an error occurred. Otherwise, a
2231    failed open will throw an exception and the third parameter will be used to construct
2232    an error message. If the parameter is omitted, a standard message is constructed
2233    using the file spec.
2234    
2235        Could not open "/usr/spool/news/twitlog"
2236    
2237    Note that the mode characters are automatically cleaned from the file name.
2238    The actual error message from the file system will be captured and appended to the
2239    message in any case.
2240    
2241        Could not open "/usr/spool/news/twitlog": file not found.
2242    
2243    In some versions of PERL the only error message we get is a number, which
2244    corresponds to the C++ C<errno> value.
2245    
2246        Could not open "/usr/spool/news/twitlog": 6.
2247    
2248    =over 4
2249    
2250    =item fileHandle
2251    
2252    File handle. If this parameter is C<undef>, a file handle will be generated
2253    and returned as the value of this method.
2254    
2255    =item fileSpec
2256    
2257    File name and mode, as per the PERL C<open> function.
2258    
2259    =item message (optional)
2260    
2261    Error message to use if the open fails. If omitted, a standard error message
2262    will be generated. In either case, the error information from the file system
2263    is appended to the message. To specify a conditional open that does not throw
2264    an error if it fails, use C<0>.
2265    
2266    =item RETURN
2267    
2268    Returns the name of the file handle assigned to the file, or C<undef> if the
2269    open failed.
2270    
2271    =back
2272    
2273    =cut
2274    
2275    sub Open {
2276        # Get the parameters.
2277        my ($fileHandle, $fileSpec, $message) = @_;
2278        # Attempt to open the file.
2279        my $rv = open $fileHandle, $fileSpec;
2280        # If the open failed, generate an error message.
2281        if (! $rv) {
2282            # Save the system error message.
2283            my $sysMessage = $!;
2284            # See if we need a default message.
2285            if (!$message) {
2286                # Clean any obvious mode characters and leading spaces from the
2287                # filename.
2288                my ($fileName) = FindNamePart($fileSpec);
2289                $message = "Could not open \"$fileName\"";
2290            }
2291            # Terminate with an error using the supplied message and the
2292            # error message from the file system.
2293            Confess("$message: $!");
2294        }
2295        # Return the file handle.
2296        return $fileHandle;
2297    }
2298    
2299    =head3 FindNamePart
2300    
2301        my ($fileName, $start, $len) = Tracer::FindNamePart($fileSpec);
2302    
2303    Extract the portion of a file specification that contains the file name.
2304    
2305    A file specification is the string passed to an C<open> call. It specifies the file
2306    mode and name. In a truly complex situation, it can specify a pipe sequence. This
2307    method assumes that the file name is whatever follows the first angle bracket
2308    sequence.  So, for example, in the following strings the file name is
2309    C</usr/fig/myfile.txt>.
2310    
2311        >>/usr/fig/myfile.txt
2312        </usr/fig/myfile.txt
2313        | sort -u > /usr/fig/myfile.txt
2314    
2315    If the method cannot find a file name using its normal methods, it will return the
2316    whole incoming string.
2317    
2318    =over 4
2319    
2320    =item fileSpec
2321    
2322    File specification string from which the file name is to be extracted.
2323    
2324    =item RETURN
2325    
2326    Returns a three-element list. The first element contains the file name portion of
2327    the specified string, or the whole string if a file name cannot be found via normal
2328    methods. The second element contains the start position of the file name portion and
2329    the third element contains the length.
2330    
2331    =back
2332    
2333    =cut
2334    #: Return Type $;
2335    sub FindNamePart {
2336        # Get the parameters.
2337        my ($fileSpec) = @_;
2338        # Default to the whole input string.
2339        my ($retVal, $pos, $len) = ($fileSpec, 0, length $fileSpec);
2340        # Parse out the file name if we can.
2341        if ($fileSpec =~ m/(<|>>?)(.+?)(\s*)$/) {
2342            $retVal = $2;
2343            $len = length $retVal;
2344            $pos = (length $fileSpec) - (length $3) - $len;
2345        }
2346        # Return the result.
2347        return ($retVal, $pos, $len);
2348    }
2349    
2350    =head3 OpenDir
2351    
2352        my @files = OpenDir($dirName, $filtered, $flag);
2353    
2354    Open a directory and return all the file names. This function essentially performs
2355    the functions of an C<opendir> and C<readdir>. If the I<$filtered> parameter is
2356    set to TRUE, all filenames beginning with a period (C<.>), dollar sign (C<$>),
2357    or pound sign (C<#>) and all filenames ending with a tilde C<~>) will be
2358    filtered out of the return list. If the directory does not open and I<$flag> is not
2359    set, an exception is thrown. So, for example,
2360    
2361        my @files = OpenDir("/Volumes/fig/contigs", 1);
2362    
2363    is effectively the same as
2364    
2365        opendir(TMP, "/Volumes/fig/contigs") || Confess("Could not open /Volumes/fig/contigs.");
2366        my @files = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir(TMP);
2367    
2368    Similarly, the following code
2369    
2370        my @files = grep { $_ =~ /^\d/ } OpenDir("/Volumes/fig/orgs", 0, 1);
2371    
2372    Returns the names of all files in C</Volumes/fig/orgs> that begin with digits and
2373    automatically returns an empty list if the directory fails to open.
2374    
2375    =over 4
2376    
2377    =item dirName
2378    
2379    Name of the directory to open.
2380    
2381    =item filtered
2382    
2383    TRUE if files whose names begin with a period (C<.>) should be automatically removed
2384    from the list, else FALSE.
2385    
2386    =item flag
2387    
2388    TRUE if a failure to open is okay, else FALSE
2389    
2390    =back
2391    
2392    =cut
2393    #: Return Type @;
2394    sub OpenDir {
2395        # Get the parameters.
2396        my ($dirName, $filtered, $flag) = @_;
2397        # Declare the return variable.
2398        my @retVal = ();
2399        # Open the directory.
2400        if (opendir(my $dirHandle, $dirName)) {
2401            # The directory opened successfully. Get the appropriate list according to the
2402            # strictures of the filter parameter.
2403            if ($filtered) {
2404                @retVal = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir $dirHandle;
2405            } else {
2406                @retVal = readdir $dirHandle;
2407            }
2408        } elsif (! $flag) {
2409            # Here the directory would not open and it's considered an error.
2410            Confess("Could not open directory $dirName.");
2411        }
2412        # Return the result.
2413        return @retVal;
2414    }
2415    
2416    
2417    =head3 Insure
2418    
2419        Insure($dirName, $chmod);
2420    
2421    Insure a directory is present.
2422    
2423    =over 4
2424    
2425    =item dirName
2426    
2427    Name of the directory to check. If it does not exist, it will be created.
2428    
2429    =item chmod (optional)
2430    
2431    Security privileges to be given to the directory if it is created.
2432    
2433    =back
2434    
2435    =cut
2436    
2437    sub Insure {
2438        my ($dirName, $chmod) = @_;
2439        if (! -d $dirName) {
2440            Trace("Creating $dirName directory.") if T(2);
2441            eval {
2442                mkpath $dirName;
2443                # If we have permissions specified, set them here.
2444                if (defined($chmod)) {
2445                    chmod $chmod, $dirName;
2446                }
2447            };
2448            if ($@) {
2449                Confess("Error creating $dirName: $@");
2450            }
2451        }
2452    }
2453    
2454    =head3 ChDir
2455    
2456        ChDir($dirName);
2457    
2458    Change to the specified directory.
2459    
2460    =over 4
2461    
2462    =item dirName
2463    
2464    Name of the directory to which we want to change.
2465    
2466    =back
2467    
2468    =cut
2469    
2470    sub ChDir {
2471        my ($dirName) = @_;
2472        if (! -d $dirName) {
2473            Confess("Cannot change to directory $dirName: no such directory.");
2474        } else {
2475            Trace("Changing to directory $dirName.") if T(File => 4);
2476            my $okFlag = chdir $dirName;
2477            if (! $okFlag) {
2478                Confess("Error switching to directory $dirName.");
2479            }
2480        }
2481    }
2482    
2483    =head3 SetPermissions
2484    
2485        Tracer::SetPermissions($dirName, $group, $mask, %otherMasks);
2486    
2487    Set the permissions for a directory and all the files and folders inside it.
2488    In addition, the group ownership will be changed to the specified value.
2489    
2490    This method is more vulnerable than most to permission and compatability
2491    problems, so it does internal error recovery.
2492    
2493    =over 4
2494    
2495    =item dirName
2496    
2497    Name of the directory to process.
2498    
2499    =item group
2500    
2501    Name of the group to be assigned.
2502    
2503    =item mask
2504    
2505    Permission mask. Bits that are C<1> in this mask will be ORed into the
2506    permission bits of any file or directory that does not already have them
2507    set to 1.
2508    
2509    =item otherMasks
2510    
2511    Map of search patterns to permission masks. If a directory name matches
2512    one of the patterns, that directory and all its members and subdirectories
2513    will be assigned the new pattern. For example, the following would
2514    assign 01664 to most files, but would use 01777 for directories named C<tmp>.
2515    
2516        Tracer::SetPermissions($dirName, 'fig', 01664, '^tmp$' => 01777);
2517    
2518    The list is ordered, so the following would use 0777 for C<tmp1> and
2519    0666 for C<tmp>, C<tmp2>, or C<tmp3>.
2520    
2521        Tracer::SetPermissions($dirName, 'fig', 01664, '^tmp1' => 0777,
2522                                                       '^tmp' => 0666);
2523    
2524    Note that the pattern matches are all case-insensitive, and only directory
2525    names are matched, not file names.
2526    
2527    =back
2528    
2529    =cut
2530    
2531    sub SetPermissions {
2532        # Get the parameters.
2533        my ($dirName, $group, $mask, @otherMasks) = @_;
2534        # Set up for error recovery.
2535        eval {
2536            # Switch to the specified directory.
2537            ChDir($dirName);
2538            # Get the group ID.
2539            my $gid = getgrnam($group);
2540            # Get the mask for tracing.
2541            my $traceMask = sprintf("%04o", $mask) . "($mask)";
2542            Trace("Fixing permissions for directory $dirName using group $group($gid) and mask $traceMask.") if T(File => 2);
2543            my $fixCount = 0;
2544            my $lookCount = 0;
2545            # @dirs will be a stack of directories to be processed.
2546            my @dirs = (getcwd());
2547            while (scalar(@dirs) > 0) {
2548                # Get the current directory.
2549                my $dir = pop @dirs;
2550                # Check for a match to one of the specified directory names. To do
2551                # that, we need to pull the individual part of the name off of the
2552                # whole path.
2553                my $simpleName = $dir;
2554                if ($dir =~ m!/([^/]+)$!) {
2555                    $simpleName = $1;
2556                }
2557                Trace("Simple directory name for $dir is $simpleName.") if T(File => 4);
2558                # Search for a match.
2559                my $match = 0;
2560                my $i;
2561                for ($i = 0; $i < $#otherMasks && ! $match; $i += 2) {
2562                    my $pattern = $otherMasks[$i];
2563                    if ($simpleName =~ /$pattern/i) {
2564                        $match = 1;
2565                    }
2566                }
2567                # Check for a match. Note we use $i-1 because the loop added 2
2568                # before terminating due to the match.
2569                if ($match && $otherMasks[$i-1] != $mask) {
2570                    # This directory matches one of the incoming patterns, and it's
2571                    # a different mask, so we process it recursively with that mask.
2572                    SetPermissions($dir, $group, $otherMasks[$i-1], @otherMasks);
2573                } else {
2574                    # Here we can process normally. Get all of the non-hidden members.
2575                    my @submems = OpenDir($dir, 1);
2576                    for my $submem (@submems) {
2577                        # Get the full name.
2578                        my $thisMem = "$dir/$submem";
2579                        Trace("Checking member $thisMem.") if T(4);
2580                        $lookCount++;
2581                        if ($lookCount % 1000 == 0) {
2582                            Trace("$lookCount members examined. Current is $thisMem. Mask is $traceMask") if T(File => 3);
2583                        }
2584                        # Fix the group.
2585                        chown -1, $gid, $thisMem;
2586                        # Insure this member is not a symlink.
2587                        if (! -l $thisMem) {
2588                            # Get its info.
2589                            my $fileInfo = stat $thisMem;
2590                            # Only proceed if we got the info. Otherwise, it's a hard link
2591                            # and we want to skip it anyway.
2592                            if ($fileInfo) {
2593                                my $fileMode = $fileInfo->mode;
2594                                if (($fileMode & $mask) != $mask) {
2595                                    # Fix this member.
2596                                    $fileMode |= $mask;
2597                                    chmod $fileMode, $thisMem;
2598                                    $fixCount++;
2599                                }
2600                                # If it's a subdirectory, stack it.
2601                                if (-d $thisMem) {
2602                                    push @dirs, $thisMem;
2603                                }
2604                            }
2605                        }
2606                    }
2607                }
2608            }
2609            Trace("$lookCount files and directories processed, $fixCount fixed.") if T(File => 2);
2610        };
2611        # Check for an error.
2612        if ($@) {
2613            Confess("SetPermissions error: $@");
2614        }
2615    }
2616    
2617    =head3 GetLine
2618    
2619        my @data = Tracer::GetLine($handle);
2620    
2621    Read a line of data from a tab-delimited file.
2622    
2623    =over 4
2624    
2625    =item handle
2626    
2627    Open file handle from which to read.
2628    
2629    =item RETURN
2630    
2631    Returns a list of the fields in the record read. The fields are presumed to be
2632    tab-delimited. If we are at the end of the file, then an empty list will be
2633    returned. If an empty line is read, a single list item consisting of a null
2634    string will be returned.
2635    
2636    =back
2637    
2638    =cut
2639    
2640    sub GetLine {
2641        # Get the parameters.
2642        my ($handle) = @_;
2643        # Declare the return variable.
2644        my @retVal = ();
2645        Trace("File position is " . tell($handle) . ". EOF flag is " . eof($handle) . ".") if T(File => 4);
2646        # Read from the file.
2647        my $line = <$handle>;
2648        # Only proceed if we found something.
2649        if (defined $line) {
2650            # Remove the new-line. We are a bit over-cautious here because the file may be coming in via an
2651            # upload control and have a nonstandard EOL combination.
2652            $line =~ s/(\r|\n)+$//;
2653            # Here we do some fancy tracing to help in debugging complicated EOL marks.
2654            if (T(File => 4)) {
2655                my $escapedLine = $line;
2656                $escapedLine =~ s/\n/\\n/g;
2657                $escapedLine =~ s/\r/\\r/g;
2658                $escapedLine =~ s/\t/\\t/g;
2659                Trace("Line read: -->$escapedLine<--");
2660            }
2661            # If the line is empty, return a single empty string; otherwise, parse
2662            # it into fields.
2663            if ($line eq "") {
2664                push @retVal, "";
2665            } else {
2666                push @retVal, split /\t/,$line;
2667            }
2668        } else {
2669            # Trace the reason the read failed.
2670            Trace("End of file: $!") if T(File => 3);
2671        }
2672        # Return the result.
2673        return @retVal;
2674    }
2675    
2676    =head3 PutLine
2677    
2678        Tracer::PutLine($handle, \@fields, $eol);
2679    
2680    Write a line of data to a tab-delimited file. The specified field values will be
2681    output in tab-separated form, with a trailing new-line.
2682    
2683    =over 4
2684    
2685    =item handle
2686    
2687    Output file handle.
2688    
2689    =item fields
2690    
2691    List of field values.
2692    
2693    =item eol (optional)
2694    
2695    End-of-line character (default is "\n").
2696    
2697    =back
2698    
2699    =cut
2700    
2701    sub PutLine {
2702        # Get the parameters.
2703        my ($handle, $fields, $eol) = @_;
2704        # Write the data.
2705        print $handle join("\t", @{$fields}) . ($eol || "\n");
2706    }
2707    
2708    
2709    =head3 PrintLine
2710    
2711        Tracer::PrintLine($line);
2712    
2713    Print a line of text with a trailing new-line.
2714    
2715    =over 4
2716    
2717    =item line
2718    
2719    Line of text to print.
2720    
2721    =back
2722    
2723    =cut
2724    
2725    sub PrintLine {
2726        # Get the parameters.
2727        my ($line) = @_;
2728        # Print the line.
2729        print "$line\n";
2730    }
2731    
2732    
2733    =head2 Other Useful Methods
2734    
2735    =head3 ParseParm
2736    
2737        my $listValue = Tracer::ParseParm($string);
2738    
2739    Convert a parameter into a list reference. If the parameter is undefined,
2740    an undefined value will be returned. Otherwise, it will be parsed as a
2741    comma-separated list of values.
2742    
2743    =over 4
2744    
2745    =item string
2746    
2747    Incoming string.
2748    
2749    =item RETURN
2750    
2751    Returns a reference to a list of values, or C<undef> if the incoming value
2752    was undefined.
2753    
2754    =back
2755    
2756    =cut
2757    
2758    sub ParseParm {
2759        # Get the parameters.
2760        my ($string) = @_;
2761        # Declare the return variable.
2762        my $retVal;
2763        # Check for data.
2764        if (defined $string) {
2765            # We have some, so split it into a list.
2766            $retVal = [ split /\s*,\s*/, $string];
2767        }
2768        # Return the result.
2769        return $retVal;
2770    }
2771    
2772    =head3 Now
2773    
2774        my $string = Tracer::Now();
2775    
2776    Return a displayable time stamp containing the local time. Whatever format this
2777    method produces must be parseable by L</ParseDate>.
2778    
2779    =cut
2780    
2781    sub Now {
2782        return DisplayTime(time);
2783                  }                  }
2784    
2785    =head3 DisplayTime
2786    
2787        my $string = Tracer::DisplayTime($time);
2788    
2789    Convert a time value to a displayable time stamp. Whatever format this
2790    method produces must be parseable by L</ParseDate>.
2791    
2792    =over 4
2793    
2794    =item time
2795    
2796    Time to display, in seconds since the epoch, or C<undef> if the time is unknown.
2797    
2798    =item RETURN
2799    
2800    Returns a displayable time, or C<(n/a)> if the incoming time is undefined.
2801    
2802    =back
2803    
2804    =cut
2805    
2806    sub DisplayTime {
2807        my ($time) = @_;
2808        my $retVal = "(n/a)";
2809        if (defined $time) {
2810            my ($sec,$min,$hour,$mday,$mon,$year,$wday,$yday,$isdst) = localtime($time);
2811            $retVal = _p2($mon+1) . "/" . _p2($mday) . "/" . ($year + 1900) . " " .
2812                      _p2($hour) . ":" . _p2($min) . ":" . _p2($sec);
2813          }          }
2814          # Merge the options into the defaults.      return $retVal;
         GetOptions($optionTable, \%overrides);  
         # Translate the remaining parameters.  
         my @retVal = ();  
         for my $inputParm (@inputList) {  
                 push @retVal, UnEscape($inputParm);  
2815          }          }
2816          # Return the results.  
2817          return ($optionTable, @retVal);  # Pad a number to 2 digits.
2818    sub _p2 {
2819        my ($value) = @_;
2820        $value = "0$value" if ($value < 10);
2821        return $value;
2822  }  }
2823    
2824  =head3 Escape  =head3 Escape
2825    
2826  C<< my $codedString = Tracer::Escape($realString); >>      my $codedString = Tracer::Escape($realString);
2827    
2828  Escape a string for use in a command length. Spaces will be replaced by C<\b>,  Escape a string for use in a command. Tabs will be replaced by C<\t>, new-lines
2829  tabs replaced by C<\t>, new-lines replaced by C<\n>, and backslashes will be  replaced by C<\n>, carriage returns will be deleted, and backslashes will be doubled. The
2830  doubled. The effect is to exactly reverse the effect of L</UnEscape>.  result is to reverse the effect of L</UnEscape>.
2831    
2832  =over 4  =over 4
2833    
# Line 563  Line 2851 
2851          # Loop through the parameter string, looking for sequences to escape.          # Loop through the parameter string, looking for sequences to escape.
2852          while (length $realString > 0) {          while (length $realString > 0) {
2853                  # Look for the first sequence to escape.                  # Look for the first sequence to escape.
2854                  if ($realString =~ /^(.*?)([ \n\t\\])/) {          if ($realString =~ /^(.*?)([\n\t\r\\])/) {
2855                          # Here we found it. The text preceding the sequence is in $1. The sequence                          # Here we found it. The text preceding the sequence is in $1. The sequence
2856                          # itself is in $2. First, move the clear text to the return variable.                          # itself is in $2. First, move the clear text to the return variable.
2857                          $retVal .= $1;                          $retVal .= $1;
2858                          $realString = substr $realString, (length $2 + length $1);              # Strip the processed section off the real string.
2859                          # Encode the escape sequence.              $realString = substr $realString, (length $2) + (length $1);
2860                # Get the matched character.
2861                          my $char = $2;                          my $char = $2;
2862                          $char =~ tr/ \t\n/btn/;              # If we have a CR, we are done.
2863                if ($char ne "\r") {
2864                    # It's not a CR, so encode the escape sequence.
2865                    $char =~ tr/\t\n/tn/;
2866                          $retVal .= "\\" . $char;                          $retVal .= "\\" . $char;
2867                }
2868                  } else {                  } else {
2869                          # Here there are no more escape sequences. The rest of the string is                          # Here there are no more escape sequences. The rest of the string is
2870                          # transferred unmodified.                          # transferred unmodified.
# Line 585  Line 2878 
2878    
2879  =head3 UnEscape  =head3 UnEscape
2880    
2881  C<< my $realString = Tracer::UnEscape($codedString); >>      my $realString = Tracer::UnEscape($codedString);
2882    
2883  Replace escape sequences with their actual equivalents. C<\b> will be replaced by a space,  Replace escape sequences with their actual equivalents. C<\t> will be replaced by
2884  C<\t> by a tab, C<\n> by a new-line character, and C<\\> by a back-slash.  a tab, C<\n> by a new-line character, and C<\\> by a backslash. C<\r> codes will
2885    be deleted.
2886    
2887  =over 4  =over 4
2888    
# Line 613  Line 2907 
2907          # Only proceed if the incoming string is nonempty.          # Only proceed if the incoming string is nonempty.
2908          if (defined $codedString) {          if (defined $codedString) {
2909                  # Loop through the parameter string, looking for escape sequences. We can't do                  # Loop through the parameter string, looking for escape sequences. We can't do
2910                  # translating because it causes problems with the escaped slash. ("\\b" becomes          # translating because it causes problems with the escaped slash. ("\\t" becomes
2911                  # "\ " no matter what we do.)          # "\<tab>" no matter what we do.)
2912                  while (length $codedString > 0) {                  while (length $codedString > 0) {
2913                          # Look for the first escape sequence.                          # Look for the first escape sequence.
2914                          if ($codedString =~ /^(.*?)\\(\\|b|n|t)/) {              if ($codedString =~ /^(.*?)\\(\\|n|t|r)/) {
2915                                  # Here we found it. The text preceding the sequence is in $1. The sequence                                  # Here we found it. The text preceding the sequence is in $1. The sequence
2916                                  # itself is in $2. First, move the clear text to the return variable.                                  # itself is in $2. First, move the clear text to the return variable.
2917                                  $retVal .= $1;                                  $retVal .= $1;
2918                                  $codedString = substr $codedString, (2 + length $1);                                  $codedString = substr $codedString, (2 + length $1);
2919                                  # Decode the escape sequence.                  # Get the escape value.
2920                                  my $char = $2;                                  my $char = $2;
2921                                  $char =~ tr/\\btn/\\ \t\n/;                  # If we have a "\r", we are done.
2922                    if ($char ne 'r') {
2923                        # Here it's not an 'r', so we convert it.
2924                        $char =~ tr/\\tn/\\\t\n/;
2925                                  $retVal .= $char;                                  $retVal .= $char;
2926                    }
2927                          } else {                          } else {
2928                                  # Here there are no more escape sequences. The rest of the string is                                  # Here there are no more escape sequences. The rest of the string is
2929                                  # transferred unmodified.                                  # transferred unmodified.
# Line 638  Line 2936 
2936          return $retVal;          return $retVal;
2937  }  }
2938    
2939  =head3 ParseRecord  =head3 Percent
2940    
2941  C<< my @fields = Tracer::ParseRecord($line); >>      my $percent = Tracer::Percent($number, $base);
2942    
2943  Parse a tab-delimited data line. The data line is split into field values. Embedded tab  Returns the percent of the base represented by the given number. If the base
2944  and new-line characters in the data line must be represented as C<\t> and C<\n>, respectively.  is zero, returns zero.
 These will automatically be converted.  
2945    
2946  =over 4  =over 4
2947    
2948  =item line  =item number
2949    
2950  Line of data containing the tab-delimited fields.  Percent numerator.
2951    
2952    =item base
2953    
2954    Percent base.
2955    
2956  =item RETURN  =item RETURN
2957    
2958  Returns a list of the fields found in the data line.  Returns the percentage of the base represented by the numerator.
2959    
2960  =back  =back
2961    
2962  =cut  =cut
2963    
2964  sub ParseRecord {  sub Percent {
2965          # Get the parameter.      # Get the parameters.
2966          my ($line) = @_;      my ($number, $base) = @_;
2967          # Remove the trailing new-line, if any.      # Declare the return variable.
2968          chomp $line;      my $retVal = 0;
2969          # Split the line read into pieces using the tab character.      # Compute the percent.
2970          my @retVal = split /\t/, $line;      if ($base != 0) {
2971          # Trim and fix the escapes in each piece.          $retVal = $number * 100 / $base;
         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;  
2972          }          }
2973          # Return the result.          # Return the result.
2974          return @retVal;      return $retVal;
2975  }  }
2976    
2977  =head3 Merge  =head3 Constrain
2978    
2979  C<< my @mergedList = Tracer::Merge(@inputList); >>      my $constrained = Constrain($value, $min, $max);
2980    
2981  Sort a list of strings and remove duplicates.  Modify a numeric value to bring it to a point in between a maximum and a minimum.
2982    
2983  =over 4  =over 4
2984    
2985  =item inputList  =item value
2986    
2987  List of scalars to sort and merge.  Value to constrain.
2988    
2989    =item min (optional)
2990    
2991    Minimum permissible value. If this parameter is undefined, no minimum constraint will be applied.
2992    
2993    =item max (optional)
2994    
2995    Maximum permissible value. If this parameter is undefined, no maximum constraint will be applied.
2996    
2997  =item RETURN  =item RETURN
2998    
2999  Returns a list containing the same elements sorted in ascending order with duplicates  Returns the incoming value, constrained according to the other parameters.
 removed.  
3000    
3001  =back  =back
3002    
3003  =cut  =cut
3004    
3005  sub Merge {  sub Constrain {
3006          # Get the input list in sort order.      # Get the parameters.
3007          my @inputList = sort @_;      my ($value, $min, $max) = @_;
3008          # Only proceed if the list has at least two elements.      # Declare the return variable.
3009          if (@inputList > 1) {      my $retVal = $value;
3010                  # Now we want to move through the list splicing out duplicates.      # Apply the minimum constraint.
3011                  my $i = 0;      if (defined $min && $retVal < $min) {
3012                  while ($i < @inputList) {          $retVal = $min;
3013                          # Get the current entry.      }
3014                          my $thisEntry = $inputList[$i];      # Apply the maximum constraint.
3015                          # Find out how many elements duplicate the current entry.      if (defined $max && $retVal > $max) {
3016                          my $j = $i + 1;          $retVal = $max;
3017                          my $dup1 = $i + 1;      }
3018                          while ($j < @inputList && $inputList[$j] eq $thisEntry) { $j++; };      # Return the result.
3019                          # If the number is nonzero, splice out the duplicates found.      return $retVal;
3020                          if ($j > $dup1) {  }
3021                                  splice @inputList, $dup1, $j - $dup1;  
3022    =head3 Min
3023    
3024        my $min = Min($value1, $value2, ... $valueN);
3025    
3026    Return the minimum argument. The arguments are treated as numbers.
3027    
3028    =over 4
3029    
3030    =item $value1, $value2, ... $valueN
3031    
3032    List of numbers to compare.
3033    
3034    =item RETURN
3035    
3036    Returns the lowest number in the list.
3037    
3038    =back
3039    
3040    =cut
3041    
3042    sub Min {
3043        # Get the parameters. Note that we prime the return value with the first parameter.
3044        my ($retVal, @values) = @_;
3045        # Loop through the remaining parameters, looking for the lowest.
3046        for my $value (@values) {
3047            if ($value < $retVal) {
3048                $retVal = $value;
3049            }
3050        }
3051        # Return the minimum found.
3052        return $retVal;
3053    }
3054    
3055    =head3 Max
3056    
3057        my $max = Max($value1, $value2, ... $valueN);
3058    
3059    Return the maximum argument. The arguments are treated as numbers.
3060    
3061    =over 4
3062    
3063    =item $value1, $value2, ... $valueN
3064    
3065    List of numbers to compare.
3066    
3067    =item RETURN
3068    
3069    Returns the highest number in the list.
3070    
3071    =back
3072    
3073    =cut
3074    
3075    sub Max {
3076        # Get the parameters. Note that we prime the return value with the first parameter.
3077        my ($retVal, @values) = @_;
3078        # Loop through the remaining parameters, looking for the highest.
3079        for my $value (@values) {
3080            if ($value > $retVal) {
3081                $retVal = $value;
3082            }
3083        }
3084        # Return the maximum found.
3085        return $retVal;
3086    }
3087    
3088    =head3 Strip
3089    
3090        my $string = Tracer::Strip($line);
3091    
3092    Strip all line terminators off a string. This is necessary when dealing with files
3093    that may have been transferred back and forth several times among different
3094    operating environments.
3095    
3096    =over 4
3097    
3098    =item line
3099    
3100    Line of text to be stripped.
3101    
3102    =item RETURN
3103    
3104    The same line of text with all the line-ending characters chopped from the end.
3105    
3106    =back
3107    
3108    =cut
3109    
3110    sub Strip {
3111        # Get a copy of the parameter string.
3112        my ($string) = @_;
3113        my $retVal = (defined $string ? $string : "");
3114        # Strip the line terminator characters.
3115        $retVal =~ s/(\r|\n)+$//g;
3116        # Return the result.
3117        return $retVal;
3118    }
3119    
3120    =head3 Pad
3121    
3122        my $paddedString = Tracer::Pad($string, $len, $left, $padChar);
3123    
3124    Pad a string to a specified length. The pad character will be a
3125    space, and the padding will be on the right side unless specified
3126    in the third parameter.
3127    
3128    =over 4
3129    
3130    =item string
3131    
3132    String to be padded.
3133    
3134    =item len
3135    
3136    Desired length of the padded string.
3137    
3138    =item left (optional)
3139    
3140    TRUE if the string is to be left-padded; otherwise it will be padded on the right.
3141    
3142    =item padChar (optional)
3143    
3144    Character to use for padding. The default is a space.
3145    
3146    =item RETURN
3147    
3148    Returns a copy of the original string with the pad character added to the
3149    specified end so that it achieves the desired length.
3150    
3151    =back
3152    
3153    =cut
3154    
3155    sub Pad {
3156        # Get the parameters.
3157        my ($string, $len, $left, $padChar) = @_;
3158        # Compute the padding character.
3159        if (! defined $padChar) {
3160            $padChar = " ";
3161        }
3162        # Compute the number of spaces needed.
3163        my $needed = $len - length $string;
3164        # Copy the string into the return variable.
3165        my $retVal = $string;
3166        # Only proceed if padding is needed.
3167        if ($needed > 0) {
3168            # Create the pad string.
3169            my $pad = $padChar x $needed;
3170            # Affix it to the return value.
3171            if ($left) {
3172                $retVal = $pad . $retVal;
3173            } else {
3174                $retVal .= $pad;
3175                          }                          }
                         # Now the element at position $dup1 is different from the element before it  
                         # at position $i. We push $i forward one position and start again.  
                         $i++;  
3176                  }                  }
3177        # Return the result.
3178        return $retVal;
3179          }          }
3180          # Return the merged list.  
3181          return @inputList;  =head3 EOF
3182    
3183    This is a constant that is lexically greater than any useful string.
3184    
3185    =cut
3186    
3187    sub EOF {
3188        return "\xFF\xFF\xFF\xFF\xFF";
3189  }  }
3190    
3191  =head3 GetFile  =head3 TICK
3192    
3193  C<< my @fileContents = Tracer::GetFile($fileName); >>      my @results = TICK($commandString);
3194    
3195  Return the entire contents of a file.  Perform a back-tick operation on a command. If this is a Windows environment, any leading
3196    dot-slash (C<./> will be removed. So, for example, if you were doing
3197    
3198        `./protein.cgi`
3199    
3200    from inside a CGI script, it would work fine in Unix, but would issue an error message
3201    in Windows complaining that C<'.'> is not a valid command. If instead you code
3202    
3203        TICK("./protein.cgi")
3204    
3205    it will work correctly in both environments.
3206    
3207  =over 4  =over 4
3208    
3209  =item fileName  =item commandString
3210    
3211  Name of the file to read.  The command string to pass to the system.
3212    
3213  =item RETURN  =item RETURN
3214    
3215  In a list context, returns the entire file as a list with the line terminators removed.  Returns the standard output from the specified command, as a list.
 In a scalar context, returns the entire file as a string.  
3216    
3217  =back  =back
3218    
3219  =cut  =cut
3220    #: Return Type @;
3221  sub GetFile {  sub TICK {
3222          # Get the parameters.          # Get the parameters.
3223          my ($fileName) = @_;      my ($commandString) = @_;
3224          # Declare the return variable.      # Chop off the dot-slash if this is Windows.
3225          my @retVal = ();      if ($FIG_Config::win_mode) {
3226          # Open the file for input.          $commandString =~ s!^\./!!;
         my $ok = open INPUTFILE, "<$fileName";  
         if (!$ok) {  
                 # If we had an error, trace it. We will automatically return a null value.  
                 Trace("Could not open \"$fileName\" for input.") if T(0);  
         } else {  
                 # Read the whole file into the return variable, stripping off any terminator  
         # characters.  
         my $lineCount = 0;  
                 while (my $line = <INPUTFILE>) {  
             $lineCount++;  
             $line = Strip($line);  
                         push @retVal, $line;  
                 }  
                 # Close it.  
                 close INPUTFILE;  
         my $actualLines = @retVal;  
         Trace("$lineCount lines read from $fileName. $actualLines processed.") if T(3);  
         }  
         # Return the file's contents in the desired format.  
     if (wantarray) {  
             return @retVal;  
     } else {  
         return join "\n", @retVal;  
3227      }      }
3228        # Activate the command and return the result.
3229        return `$commandString`;
3230  }  }
3231    
 =head3 QTrace  
3232    
3233  C<< my $data = QTrace($format); >>  =head3 CommaFormat
3234    
3235  Return the queued trace data in the specified format.      my $formatted = Tracer::CommaFormat($number);
3236    
3237    Insert commas into a number.
3238    
3239  =over 4  =over 4
3240    
3241  =item format  =item number
3242    
3243  C<html> to format the data as an HTML list, C<text> to format it as straight text.  A sequence of digits.
3244    
3245    =item RETURN
3246    
3247    Returns the same digits with commas strategically inserted.
3248    
3249  =back  =back
3250    
3251  =cut  =cut
3252    
3253  sub QTrace {  sub CommaFormat {
3254          # Get the parameter.      # Get the parameters.
3255          my ($format) = @_;      my ($number) = @_;
3256          # Create the return variable.      # Pad the length up to a multiple of three.
3257          my $retVal = "";      my $padded = "$number";
3258          # Process according to the format.      $padded = " " . $padded while length($padded) % 3 != 0;
3259          if ($format =~ m/^HTML$/i) {      # This is a fancy PERL trick. The parentheses in the SPLIT pattern
3260                  # Convert the queue into an HTML list.      # cause the delimiters to be included in the output stream. The
3261                  $retVal = "<ul>\n";      # GREP removes the empty strings in between the delimiters.
3262                  for my $line (@Queue) {      my $retVal = join(",", grep { $_ ne '' } split(/(...)/, $padded));
3263                          my $escapedLine = CGI::escapeHTML($line);      # Clean out the spaces.
3264                          $retVal .= "<li>$escapedLine</li>\n";      $retVal =~ s/ //g;
3265                  }      # Return the result.
                 $retVal .= "</ul>\n";  
         } elsif ($format =~ m/^TEXT$/i) {  
                 # Convert the queue into a list of text lines.  
                 $retVal = join("\n", @Queue) . "\n";  
         }  
         # Clear the queue.  
         @Queue = ();  
         # Return the formatted list.  
3266          return $retVal;          return $retVal;
3267  }  }
3268    
 =head3 Confess  
   
 C<< Confess($message); >>  
3269    
3270  Trace the call stack and abort the program with the specified message. The stack  =head3 CompareLists
 trace will only appear if the trace level for this package is 1 or more. When used with  
 the OR operator and the L</Assert> method, B<Confess> can function as a debugging assert.  
 So, for example  
3271    
3272  C<< Assert($recNum >= 0) || Confess("Invalid record number $recNum."); >>      my ($inserted, $deleted) = Tracer::CompareLists(\@newList, \@oldList, $keyIndex);
3273    
3274  Will abort the program with a stack trace if the value of C<$recNum> is negative.  Compare two lists of tuples, and return a hash analyzing the differences. The lists
3275    are presumed to be sorted alphabetically by the value in the $keyIndex column.
3276    The return value contains a list of items that are only in the new list
3277    (inserted) and only in the old list (deleted).
3278    
3279  =over 4  =over 4
3280    
3281  =item message  =item newList
   
 Message to include in the trace.  
3282    
3283  =back  Reference to a list of new tuples.
3284    
3285  =cut  =item oldList
3286    
3287  sub Confess {  Reference to a list of old tuples.
         # Get the parameters.  
         my ($message) = @_;  
         # Trace the call stack.  
         Cluck($message) if T(1);  
         # Abort the program.  
         croak(">>> $message");  
 }  
3288    
3289  =head3 Assert  =item keyIndex (optional)
3290    
3291  C<< Assert($condition1, $condition2, ... $conditionN); >>  Index into each tuple of its key field. The default is 0.
3292    
3293  Return TRUE if all the conditions are true. This method can be used in conjunction with  =item RETURN
 the OR operator and the L</Confess> method, B<Assert> can function as a debugging assert.  
 So, for example  
3294    
3295  C<< Assert($recNum >= 0) || Confess("Invalid record number $recNum."); >>  Returns a 2-tuple consisting of a reference to the list of items that are only in the new
3296    list (inserted) followed by a reference to the list of items that are only in the old
3297    list (deleted).
3298    
3299  Will abort the program with a stack trace if the value of C<$recNum> is negative.  =back
3300    
3301  =cut  =cut
3302  sub Assert {  
3303      my $retVal = 1;  sub CompareLists {
3304      LOOP: for my $condition (@_) {      # Get the parameters.
3305          if (! $condition) {      my ($newList, $oldList, $keyIndex) = @_;
3306              $retVal = 0;      if (! defined $keyIndex) {
3307              last LOOP;          $keyIndex = 0;
3308        }
3309        # Declare the return variables.
3310        my ($inserted, $deleted) = ([], []);
3311        # Loop through the two lists simultaneously.
3312        my ($newI, $oldI) = (0, 0);
3313        my ($newN, $oldN) = (scalar @{$newList}, scalar @{$oldList});
3314        while ($newI < $newN || $oldI < $oldN) {
3315            # Get the current object in each list. Note that if one
3316            # of the lists is past the end, we'll get undef.
3317            my $newItem = $newList->[$newI];
3318            my $oldItem = $oldList->[$oldI];
3319            if (! defined($newItem) || defined($oldItem) && $newItem->[$keyIndex] gt $oldItem->[$keyIndex]) {
3320                # The old item is not in the new list, so mark it deleted.
3321                push @{$deleted}, $oldItem;
3322                $oldI++;
3323            } elsif (! defined($oldItem) || $oldItem->[$keyIndex] gt $newItem->[$keyIndex]) {
3324                # The new item is not in the old list, so mark it inserted.
3325                push @{$inserted}, $newItem;
3326                $newI++;
3327            } else {
3328                # The item is in both lists, so push forward.
3329                $oldI++;
3330                $newI++;
3331          }          }
3332      }      }
3333      return $retVal;      # Return the result.
3334        return ($inserted, $deleted);
3335  }  }
3336    
3337  =head3 Cluck  =head3 Cmp
3338    
3339  C<< Cluck($message); >>      my $cmp = Tracer::Cmp($a, $b);
3340    
3341  Trace the call stack. Note that for best results, you should qualify the call with a  This method performs a universal sort comparison. Each value coming in is
3342  trace condition. For example,  separated into a leading text part and a trailing number part. The text
3343    part is string compared, and if both parts are equal, then the number
3344    parts are compared numerically. A stream of just numbers or a stream of
3345    just strings will sort correctly, and a mixed stream will sort with the
3346    numbers first. Strings with a label and a number will sort in the
3347    expected manner instead of lexically.
3348    
3349  C<< Cluck("Starting record parse.") if T(3); >>  =over 4
3350    
3351  will only trace the stack if the trace level for the package is 3 or more.  =item a
3352    
3353  =over 4  First item to compare.
3354    
3355  =item message  =item b
3356    
3357  Message to include in the trace.  Second item to compare.
3358    
3359    =item RETURN
3360    
3361    Returns a negative number if the first item should sort first (is less), a positive
3362    number if the first item should sort second (is greater), and a zero if the items are
3363    equal.
3364    
3365  =back  =back
3366    
3367  =cut  =cut
3368    
3369  sub Cluck {  sub Cmp {
3370          # Get the parameters.          # Get the parameters.
3371          my ($message) = @_;      my ($a, $b) = @_;
3372      # Trace what's happening.      # Declare the return value.
3373      Trace("Stack trace for event: $message");      my $retVal;
3374          my $confession = longmess($message);      # Check for nulls.
3375          # Convert the confession to a series of trace messages. Note we skip any      if (! defined($a)) {
3376      # messages relating to calls into Tracer.          $retVal = (! defined($b) ? 0 : -1);
3377          for my $line (split /\s*\n/, $confession) {      } elsif (! defined($b)) {
3378                  Trace($line) if ($line !~ /Tracer\.pm/);          $retVal = 1;
3379        } else {
3380            # Here we have two real values. Parse the two strings.
3381            $a =~ /^(\D*)(\d*)$/;
3382            my $aParsed = [$1, $2];
3383            $b =~ /^(\D*)(\d*)$/;
3384            my $bParsed = [$1, $2];
3385            # Compare the string parts.
3386            $retVal = $aParsed->[0] cmp $bParsed->[0];
3387            if (! $retVal) {
3388                $retVal = $aParsed->[1] <=> $bParsed->[1];
3389            }
3390          }          }
3391        # Return the result.
3392        return $retVal;
3393  }  }
3394    
3395  =head3 Min  =head2 CGI Script Utilities
3396    
3397  C<< my $min = Min($value1, $value2, ... $valueN); >>  =head3 ScriptSetup (deprecated)
3398    
3399  Return the minimum argument. The arguments are treated as numbers.      my ($cgi, $varHash) = ScriptSetup($noTrace);
3400    
3401    Perform standard tracing and debugging setup for scripts. The value returned is
3402    the CGI object followed by a pre-built variable hash. At the end of the script,
3403    the client should call L</ScriptFinish> to output the web page.
3404    
3405    This method calls L</ETracing> to configure tracing, which allows the tracing
3406    to be configured via the emergency tracing form on the debugging control panel.
3407    Tracing will then be turned on automatically for all programs that use the L</ETracing>
3408    method, which includes every program that uses this method or L</StandardSetup>.
3409    
3410  =over 4  =over 4
3411    
3412  =item $value1, $value2, ... $valueN  =item noTrace (optional)
3413    
3414  List of numbers to compare.  If specified, tracing will be suppressed. This is useful if the script wants to set up
3415    tracing manually.
3416    
3417  =item RETURN  =item RETURN
3418    
3419  Returns the lowest number in the list.  Returns a two-element list consisting of a CGI query object and a variable hash for
3420    the output page.
3421    
3422  =back  =back
3423    
3424  =cut  =cut
3425    
3426  sub Min {  sub ScriptSetup {
3427          # Get the parameters. Note that we prime the return value with the first parameter.      # Get the parameters.
3428          my ($retVal, @values) = @_;      my ($noTrace) = @_;
3429          # Loop through the remaining parameters, looking for the lowest.      # Get the CGI query object.
3430          for my $value (@values) {      my $cgi = CGI->new();
3431                  if ($value < $retVal) {      # Set up tracing if it's not suppressed.
3432                          $retVal = $value;      ETracing($cgi) unless $noTrace;
3433                  }      # Create the variable hash.
3434          }      my $varHash = { results => '' };
3435          # Return the minimum found.      # Return the query object and variable hash.
3436          return $retVal;      return ($cgi, $varHash);
3437    }
3438    
3439    =head3 ScriptFinish (deprecated)
3440    
3441        ScriptFinish($webData, $varHash);
3442    
3443    Output a web page at the end of a script. Either the string to be output or the
3444    name of a template file can be specified. If the second parameter is omitted,
3445    it is assumed we have a string to be output; otherwise, it is assumed we have the
3446    name of a template file. The template should have the variable C<DebugData>
3447    specified in any form that invokes a standard script. If debugging mode is turned
3448    on, a form field will be put in that allows the user to enter tracing data.
3449    Trace messages will be placed immediately before the terminal C<BODY> tag in
3450    the output, formatted as a list.
3451    
3452    A typical standard script would loook like the following.
3453    
3454        BEGIN {
3455            # Print the HTML header.
3456            print "CONTENT-TYPE: text/html\n\n";
3457  }  }
3458        use Tracer;
3459        use CGI;
3460        use FIG;
3461        # ... more uses ...
3462    
3463  =head3 Max      my ($cgi, $varHash) = ScriptSetup();
3464        eval {
3465  C<< my $max = Max($value1, $value2, ... $valueN); >>          # ... get data from $cgi, put it in $varHash ...
3466        };
3467        if ($@) {
3468            Trace("Script Error: $@") if T(0);
3469        }
3470        ScriptFinish("Html/MyTemplate.html", $varHash);
3471    
3472  Return the maximum argument. The arguments are treated as numbers.  The idea here is that even if the script fails, you'll see trace messages and
3473    useful output.
3474    
3475  =over 4  =over 4
3476    
3477  =item $value1, $value2, ... $valueN  =item webData
3478    
3479  List of numbers to compare.  A string containing either the full web page to be written to the output or the
3480    name of a template file from which the page is to be constructed. If the name
3481    of a template file is specified, then the second parameter must be present;
3482    otherwise, it must be absent.
3483    
3484  =item RETURN  =item varHash (optional)
3485    
3486  Returns the highest number in the list.  If specified, then a reference to a hash mapping variable names for a template
3487    to their values. The template file will be read into memory, and variable markers
3488    will be replaced by data in this hash reference.
3489    
3490  =back  =back
3491    
3492  =cut  =cut
3493    
3494  sub Max {  sub ScriptFinish {
3495          # Get the parameters. Note that we prime the return value with the first parameter.      # Get the parameters.
3496          my ($retVal, @values) = @_;      my ($webData, $varHash) = @_;
3497          # Loop through the remaining parameters, looking for the highest.      # Check for a template file situation.
3498          for my $value (@values) {      my $outputString;
3499                  if ($value > $retVal) {      if (defined $varHash) {
3500                          $retVal = $value;          # Here we have a template file. We need to determine the template type.
3501            my $template;
3502            if ($FIG_Config::template_url && $webData =~ /\.php$/) {
3503                $template = "$FIG_Config::template_url/$webData";
3504            } else {
3505                $template = "<<$webData";
3506                  }                  }
3507            $outputString = PageBuilder::Build($template, $varHash, "Html");
3508        } else {
3509            # Here the user gave us a raw string.
3510            $outputString = $webData;
3511          }          }
3512          # Return the maximum found.      # Check for trace messages.
3513          return $retVal;      if ($Destination ne "NONE" && $TraceLevel > 0) {
3514            # We have trace messages, so we want to put them at the end of the body. This
3515            # is either at the end of the whole string or at the beginning of the BODY
3516            # end-tag.
3517            my $pos = length $outputString;
3518            if ($outputString =~ m#</body>#gi) {
3519                $pos = (pos $outputString) - 7;
3520            }
3521            # If the trace messages were queued, we unroll them. Otherwise, we display the
3522            # destination.
3523            my $traceHtml;
3524            if ($Destination eq "QUEUE") {
3525                $traceHtml = QTrace('Html');
3526            } elsif ($Destination =~ /^>>(.+)$/) {
3527                # Here the tracing output it to a file. We code it as a hyperlink so the user
3528                # can copy the file name into the clipboard easily.
3529                my $actualDest = $1;
3530                $traceHtml = "<p>Tracing output to $actualDest.</p>\n";
3531            } else {
3532                # Here we have one of the special destinations.
3533                $traceHtml = "<P>Tracing output type is $Destination.</p>\n";
3534            }
3535            substr $outputString, $pos, 0, $traceHtml;
3536  }  }
3537        # Write the output string.
3538        print $outputString;
3539    }
3540    
3541    =head3 GenerateURL
3542    
3543  =head3 AddToListMap      my $queryUrl = Tracer::GenerateURL($page, %parameters);
3544    
3545  C<< Tracer::AddToListMap(\%hash, $key, $value); >>  Generate a GET-style URL for the specified page with the specified parameter
3546    names and values. The values will be URL-escaped automatically. So, for
3547    example
3548    
3549  Add a key-value pair to a hash of lists. If no value exists for the key, a singleton list      Tracer::GenerateURL("form.cgi", type => 1, string => "\"high pass\" or highway")
3550  is created for the key. Otherwise, the new value is pushed onto the list.  
3551    would return
3552    
3553        form.cgi?type=1;string=%22high%20pass%22%20or%20highway
3554    
3555  =over 4  =over 4
3556    
3557  =item hash  =item page
3558    
3559  Reference to the target hash.  Page URL.
3560    
3561  =item key  =item parameters
3562    
3563  Key for which the value is to be added.  Hash mapping parameter names to parameter values.
3564    
3565  =item value  =item RETURN
3566    
3567  Value to add to the key's value list.  Returns a GET-style URL that goes to the specified page and passes in the
3568    specified parameters and values.
3569    
3570  =back  =back
3571    
3572  =cut  =cut
3573    
3574  sub AddToListMap {  sub GenerateURL {
3575      # Get the parameters.      # Get the parameters.
3576      my ($hash, $key, $value) = @_;      my ($page, %parameters) = @_;
3577      # Process according to whether or not the key already has a value.      # Prime the return variable with the page URL.
3578      if (! exists $hash->{$key}) {      my $retVal = $page;
3579          $hash->{$key} = [$value];      # Loop through the parameters, creating parameter elements in a list.
3580      } else {      my @parmList = map { "$_=" . uri_escape($parameters{$_}) } keys %parameters;
3581          push @{$hash->{$key}}, $value;      # If the list is nonempty, tack it on.
3582        if (@parmList) {
3583            $retVal .= "?" . join(";", @parmList);