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1    # -*- perl -*-
2    ########################################################################
3    # Copyright (c) 2003-2006 University of Chicago and Fellowship
4    # for Interpretations of Genomes. All Rights Reserved.
5    #
6    # This file is part of the SEED Toolkit.
7    #
8    # The SEED Toolkit is free software. You can redistribute
9    # it and/or modify it under the terms of the SEED Toolkit
10    # Public License.
11    #
12    # You should have received a copy of the SEED Toolkit Public License
13    # along with this program; if not write to the University of Chicago
14    # at info@ci.uchicago.edu or the Fellowship for Interpretation of
15    # Genomes at veronika@thefig.info or download a copy from
16    # http://www.theseed.org/LICENSE.TXT.
17    ########################################################################
18    
19  package Tracer;  package Tracer;
20    
21          require Exporter;          require Exporter;
22          @ISA = ('Exporter');          @ISA = ('Exporter');
23          @EXPORT = qw(Trace T TSetup QTrace Confess Cluck Min Max Assert);      @EXPORT = qw(Trace T TSetup QTrace Confess Cluck Min Max Assert Open OpenDir TICK StandardSetup EmergencyKey ETracing Constrain Insure ChDir Emergency Warn);
24          @EXPORT_OK = qw(GetFile GetOptions Merge MergeOptions ParseCommand ParseRecord UnEscape);      @EXPORT_OK = qw(GetFile GetOptions Merge MergeOptions ParseCommand ParseRecord UnEscape Escape PrintLine PutLine);
25          use strict;          use strict;
26          use Carp qw(longmess croak);      use Carp qw(longmess croak carp);
27          use CGI;          use CGI;
28        use Cwd;
29        use FIG_Config;
30        use PageBuilder;
31        use Digest::MD5;
32        use File::Basename;
33        use File::Path;
34        use File::stat;
35        use LWP::UserAgent;
36        use Time::HiRes 'gettimeofday';
37        use URI::Escape;
38        use Time::Local;
39        use POSIX qw(strftime);
40        use Time::Zone;
41    
42    
43  =head1 Tracing and Debugging Helpers  =head1 Tracing and Debugging Helpers
44    
45  =head2 Introduction  =head2 Tracing
46    
47  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
48  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.
49  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,
50  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
51  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
52  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
53  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
54  appear. To generate a trace message, use the following syntax.  appear.
55    
56    =head3 Putting Trace Messages in Your Code
57    
58    To generate a trace message, use the following syntax.
59    
60  C<< Trace($message) if T(errors => 4); >>      Trace($message) if T(errors => 4);
61    
62  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>
63  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
64    
65  C<< Trace($message) if T(main => 4); >>      Trace($message) if T(main => 4);
66    
67  will trace if the trace level is 4 or more.  will trace if the trace level is 4 or more.
68    
# Line 34  Line 70 
70  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
71  active and the trace level is 2 or more.  active and the trace level is 2 or more.
72    
73  C<< Trace($message) if T(2); >>      Trace($message) if T(2);
74    
75  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>.
76  of category names, and a set of options. The trace level and list of category names are  
77    =head3 Custom Tracing
78    
79    Many programs have customized tracing configured using the L</TSetup> method. This is no longer
80    the preferred method, but a knowledge of how custom tracing works can make the more modern
81    L</Emergency Tracing> easier to understand.
82    
83    To set up custom tracing, you call the L</TSetup> method. The method takes as input a trace level,
84    a list of category names, and a destination. The trace level and list of category names are
85  specified as a space-delimited string. Thus  specified as a space-delimited string. Thus
86    
87  C<< TSetup('3 errors Sprout ERDB', 'HTML'); >>      TSetup('3 errors Sprout ERDB', 'TEXT');
88    
89    sets the trace level to 3, activates the C<errors>, C<Sprout>, and C<ERDB> categories, and
90    specifies that messages should be sent to the standard output.
91    
92  sets the trace level to 3, activated the C<errors>, C<Sprout>, and C<ERDB> categories, and  To turn on tracing for ALL categories, use an asterisk. The call below sets every category to
93  specifies that messages should be output as HTML paragraphs. The idea is to make it easier to  level 3 and writes the output to the standard error output. This sort of thing might be
94  input tracing configuration on a web form.  useful in a CGI environment.
95    
96  In addition to HTML and file output for trace messages, you can specify that the trace messages      TSetup('3 *', 'WARN');
97    
98    In addition standard error and file output for trace messages, you can specify that the trace messages
99  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
100  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
101  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
102  it easier to debug page formatting problems.  it easier to debug page formatting problems.
103    
104  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
105    a file at the same time. To trace to a file, specify the filename with an output character in front
106    of it.
107    
108        TSetup('4 SQL', ">$fileName");
109    
110    To trace to the standard output and a file at the same time, put a C<+> in front of the angle
111    bracket.
112    
113        TSetup('3 *', "+>$fileName");
114    
115  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>.
116  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.
117  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
118  being used out in the field.  being used out in the field.
119    
120    =head3 Trace Levels
121    
122    There is no hard and fast rule on how to use trace levels. The following is therefore only
123    a suggestion.
124    
125    =over 4
126    
127    =item Error 0
128    
129    Message indicates an error that may lead to incorrect results or that has stopped the
130    application entirely.
131    
132    =item Warning 1
133    
134    Message indicates something that is unexpected but that probably did not interfere
135    with program execution.
136    
137    =item Notice 2
138    
139    Message indicates the beginning or end of a major task.
140    
141    =item Information 3
142    
143    Message indicates a subtask. In the FIG system, a subtask generally relates to a single
144    genome. This would be a big loop that is not expected to execute more than 500 times or so.
145    
146    =item Detail 4
147    
148    Message indicates a low-level loop iteration.
149    
150    =back
151    
152    The format of trace messages is important because some utilities analyze trace files.
153    There are three fields-- the time stamp, the category name, and the text.
154    The time stamp is between square brackets and the category name between angle brackets.
155    After the category name there is a colon (C<:>) followed by the message text.
156    If the square brackets or angle brackets are missing, then the trace management
157    utilities assume that they are encountering a set of pre-formatted lines.
158    
159    Note, however, that this formatting is done automatically by the tracing functions. You
160    only need to know about it if you want to parse a trace file.
161    
162    =head3 Emergency Tracing
163    
164    Sometimes, you need a way for tracing to happen automatically without putting parameters
165    in a form or on the command line. Emergency tracing does this. You invoke emergency tracing
166    from the debug form, which is accessed from the [[DebugConsole]]. Emergency tracing requires
167    that you specify a tracing key. For command-line tools, the key is
168    taken from the C<TRACING> environment variable. For web services, the key is taken from
169    a cookie. Either way, the key tells the tracing facility who you are, so that you control
170    the tracing in your environment without stepping on other users.
171    
172    The key can be anything you want. If you don't have a key, the C<SetPassword> page will
173    generate one for you.
174    
175    You can activate and de-activate emergency tracing from the debugging control panel, as
176    well as display the trace file itself.
177    
178    To enable emergency tracing in your code, call
179    
180        ETracing($cgi)
181    
182    from a web script and
183    
184        ETracing()
185    
186    from a command-line script.
187    
188    The web script will look for the tracing key in the cookies, and the command-line
189    script will look for it in the C<TRACING> environment variable. If you are
190    using the L</StandardSetup> method or a [[WebApplication]], emergency tracing
191    will be configured automatically.
192    
193  =cut  =cut
194    
195  # Declare the configuration variables.  # Declare the configuration variables.
196    
197  my $Destination = "NONE";       # Description of where to send the trace output.  my $Destination = "WARN";   # Description of where to send the trace output.
198    my $TeeFlag = 0;            # TRUE if output is going to a file and to the
199                                # standard output
200  my %Categories = ( main => 1 );  my %Categories = ( main => 1 );
201                                                          # hash of active category names                                                          # hash of active category names
202    my @LevelNames = qw(error warn notice info detail);
203  my $TraceLevel = 0;                     # trace level; a higher trace level produces more  my $TraceLevel = 0;                     # trace level; a higher trace level produces more
204                                                          # messages                                                          # messages
205  my @Queue = ();                         # queued list of trace messages.  my @Queue = ();                         # queued list of trace messages.
206    my $LastCategory = "main";  # name of the last category interrogated
207    my $LastLevel = 0;          # level of the last test call
208    my $SetupCount = 0;         # number of times TSetup called
209    my $AllTrace = 0;           # TRUE if we are tracing all categories.
210    my $SavedCGI;               # CGI object passed to ETracing
211    umask 2;                    # Fix the damn umask so everything is group-writable.
212    
213  =head2 Public Methods  =head2 Tracing Methods
214    
215    =head3 Setups
216    
217        my $count = Tracer::Setups();
218    
219    Return the number of times L</TSetup> has been called.
220    
221    This method allows for the creation of conditional tracing setups where, for example, we
222    may want to set up tracing if nobody else has done it before us.
223    
224    =cut
225    
226    sub Setups {
227        return $SetupCount;
228    }
229    
230  =head3 TSetup  =head3 TSetup
231    
232  C<< TSetup($categoryList, $target); >>      TSetup($categoryList, $target);
233    
234  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
235  and interrogated by the L</Trace> and L</T> methods.  and interrogated by the L</Trace> and L</T> methods.
# Line 90  Line 245 
245    
246  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
247  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
248  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 ">"
249  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
250  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
251    cause tracing to the standard output with each line formatted as an HTML paragraph. C<TEXT>
252  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
253  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
254  messages to be stored in a queue for later retrieval by the L</QTrace> method. C<WARN> will  messages to be stored in a queue for later retrieval by the L</QTrace> method. C<WARN> will
# Line 110  Line 266 
266          my @categoryData = split /\s+/, $categoryList;          my @categoryData = split /\s+/, $categoryList;
267          # Extract the trace level.          # Extract the trace level.
268          $TraceLevel = shift @categoryData;          $TraceLevel = shift @categoryData;
269          # Build the category hash.      # Presume category-based tracing until we learn otherwise.
270        $AllTrace = 0;
271        # Build the category hash. Note that if we find a "*", we turn on non-category
272        # tracing. We must also clear away any pre-existing data.
273        %Categories = ( main => 1 );
274          for my $category (@categoryData) {          for my $category (@categoryData) {
275                  $Categories{$category} = 1;          if ($category eq '*') {
276                $AllTrace = 1;
277            } else {
278                $Categories{lc $category} = 1;
279            }
280          }          }
281          # Now we need to process the destination information. The most important special          # Now we need to process the destination information. The most important special
282          # case is the single ">", which requires we clear the file first. After doing      # case is when we're writing to a file. This is indicated by ">" (overwrite) and
283          # so, we tack on another ">" sign so that future trace messages are appended.      # ">>" (append). A leading "+" for either indicates that we are also writing to
284        # the standard output (tee mode).
285        if ($target =~ m/^\+?>>?/) {
286            if ($target =~ m/^\+/) {
287                $TeeFlag = 1;
288                $target = substr($target, 1);
289            }
290          if ($target =~ m/^>[^>]/) {          if ($target =~ m/^>[^>]/) {
291                # We need to initialize the file (which clears it).
292                  open TRACEFILE, $target;                  open TRACEFILE, $target;
293                  print TRACEFILE Now() . " Tracing initialized.\n";              print TRACEFILE "[" . Now() . "] [notice] [Tracer] Tracing initialized.\n";
294                  close TRACEFILE;                  close TRACEFILE;
295                # Set to append mode now that the file has been cleared.
296                  $Destination = ">$target";                  $Destination = ">$target";
297          } else {          } else {
298                $Destination = $target;
299            }
300        } else {
301                  $Destination = uc($target);                  $Destination = uc($target);
302          }          }
303        # Increment the setup counter.
304        $SetupCount++;
305  }  }
306    
307  =head3 SetLevel  =head3 SetLevel
308    
309  C<< Tracer::SetLevel($newLevel); >>      Tracer::SetLevel($newLevel);
310    
311  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.
312    
# Line 147  Line 324 
324      $TraceLevel = $_[0];      $TraceLevel = $_[0];
325  }  }
326    
327  =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  
328    
329  =cut      my $time = Tracer::ParseDate($dateString);
330    
331  sub LogErrors {  Convert a date into a PERL time number. This method expects a date-like string
332          # Get the file name.  and parses it into a number. The string must be vaguely date-like or it will
333          my ($fileName) = @_;  return an undefined value. Our requirement is that a month and day be
334          # Open the file as the standard error output.  present and that three pieces of the date string (time of day, month and day,
335          open STDERR, '>', $fileName;  year) be separated by likely delimiters, such as spaces, commas, and such-like.
 }  
336    
337  =head3 ReadOptions  If a time of day is present, it must be in military time with two digits for
338    everything but the hour.
339    
340  C<< my %options = Tracer::ReadOptions($fileName); >>  The year must be exactly four digits.
341    
342  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
343  format  equally innocuous. This means, however, that a sufficiently long sentence with date-like
344    parts in it may be interpreted as a date. Hopefully this will not be a problem.
345    
346  I<optionName>C<=>I<optionValue>C<; >I<comment>  It should be guaranteed that this method will parse the output of the L</Now> function.
347    
348  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.  
349    
350  =over 4  =over 4
351    
352  =item fileName  =item dateString
353    
354  Name of the file containing the option data.  The date string to convert.
355    
356  =item RETURN  =item RETURN
357    
358  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
359  value.  the date string is invalid. A valid date string must contain a month and day.
360    
361  =back  =back
362    
363  =cut  =cut
364    
365  sub ReadOptions {  # Universal month conversion table.
366          # Get the parameters.  use constant MONTHS => {    Jan =>  0, January   =>  0, '01' =>  0,  '1' =>  0,
367          my ($fileName) = @_;                              Feb =>  1, February  =>  1, '02' =>  1,  '2' =>  1,
368          # Open the file.                              Mar =>  2, March     =>  2, '03' =>  2,  '3' =>  2,
369          (open CONFIGFILE, "<$fileName") || Confess("Could not open option file $fileName.");                              Apr =>  3, April     =>  3, '04' =>  3,  '4' =>  3,
370          # Count the number of records read.                              May =>  4, May       =>  4, '05' =>  4,  '5' =>  4,
371          my ($records, $comments) = 0;                              Jun =>  5, June      =>  5, '06' =>  5,  '6' =>  5,
372          # Create the return hash.                              Jul =>  6, July      =>  6, '07' =>  6,  '7' =>  6,
373          my %retVal = ();                              Aug =>  7, August    =>  7, '08' =>  7,  '8' =>  7,
374          # Loop through the file, accumulating key-value pairs.                              Sep =>  8, September =>  8, '09' =>  8,  '9' =>  8,
375          while (my $line = <CONFIGFILE>) {                              Oct =>  9, October  =>   9, '10' =>  9,
376                  # Denote we've read a line.                              Nov => 10, November =>  10, '11' => 10,
377                  $records++;                              Dec => 11, December =>  11, '12' => 11
378                  # Determine the line type.                          };
                 if ($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  
379    
380  sub GetOptions {  sub ParseDate {
381          # Get the parameters.          # Get the parameters.
382          my ($defaults, $options) = @_;      my ($dateString) = @_;
383          # Check for overrides.      # Declare the return variable.
384          if ($options) {      my $retVal;
385                  # Loop through the overrides.      # Find the month and day of month. There are two ways that can happen. We check for the
386                  while (my ($option, $setting) = each %{$options}) {      # numeric style first. That way, if the user's done something like "Sun 12/22", then we
387                          # Insure this override exists.      # won't be fooled into thinking the month is Sunday.
388                          if (!exists $defaults->{$option}) {      if ($dateString =~ m#\b(\d{1,2})/(\d{1,2})\b# || $dateString =~ m#\b(\w+)\s(\d{1,2})\b#) {
389                                  croak "Unrecognized option $option encountered.";          my ($mon, $mday) = (MONTHS->{$1}, $2);
390            # Insist that the month and day are valid.
391            if (defined($mon) && $2 >= 1 && $2 <= 31) {
392                # Find the time.
393                my ($hour, $min, $sec) = (0, 0, 0);
394                if ($dateString =~ /\b(\d{1,2}):(\d{2}):(\d{2})\b/) {
395                    ($hour, $min, $sec) = ($1, $2, $3);
396                }
397                # Find the year.
398                my $year;
399                if ($dateString =~ /\b(\d{4})\b/) {
400                    $year = $1;
401                          } else {                          } else {
402                                  # Apply the override.                  # Get the default year, which is this one. Note we must convert it to
403                                  $defaults->{$option} = $setting;                  # the four-digit value expected by "timelocal".
404                    (undef, undef, undef, undef, undef, $year) = localtime();
405                    $year += 1900;
406                          }                          }
407                $retVal = timelocal($sec, $min, $hour, $mday, $mon, $year);
408                  }                  }
409          }          }
410          # Return the merged table.      # Return the result.
411          return $defaults;      return $retVal;
412  }  }
413    
414  =head3 MergeOptions  =head3 LogErrors
415    
416  C<< Tracer::MergeOptions(\%table, \%defaults); >>      Tracer::LogErrors($fileName);
417    
418  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.  
419    
420  =over 4  =over 4
421    
422  =item table  =item fileName
   
 Hash table to be updated with the default values.  
   
 =item defaults  
423    
424  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.
425    
426  =back  =back
427    
428  =cut  =cut
429    
430  sub MergeOptions {  sub LogErrors {
431          # Get the parameters.      # Get the file name.
432          my ($table, $defaults) = @_;      my ($fileName) = @_;
433          # Loop through the defaults.      # Open the file as the standard error output.
434          while (my ($key, $value) = each %{$defaults}) {      open STDERR, '>', $fileName;
                 if (!exists $table->{$key}) {  
                         $table->{$key} = $value;  
                 }  
         }  
435  }  }
436    
437  =head3 Trace  =head3 Trace
438    
439  C<< Trace($message); >>      Trace($message);
440    
441  Write a trace message to the target location specified in L</TSetup>. If there has not been  Write a trace message to the target location specified in L</TSetup>. If there has not been
442  any prior call to B<TSetup>.  any prior call to B<TSetup>.
# Line 368  Line 454 
454  sub Trace {  sub Trace {
455          # Get the parameters.          # Get the parameters.
456          my ($message) = @_;          my ($message) = @_;
457        # Strip off any line terminators at the end of the message. We will add
458        # new-line stuff ourselves.
459        my $stripped = Strip($message);
460        # Compute the caller information.
461        my ($callPackage, $callFile, $callLine) = caller();
462        my $callFileTitle = basename($callFile);
463        # Check the caller.
464        my $callerInfo = ($callFileTitle ne "Tracer.pm" ? " [$callFileTitle $callLine]" : "");
465          # Get the timestamp.          # Get the timestamp.
466          my $timeStamp = Now();          my $timeStamp = Now();
467        # Build the prefix.
468        my $level = $LevelNames[$LastLevel] || "($LastLevel)";
469        my $prefix = "[$timeStamp] [$level] [$LastCategory]$callerInfo";
470          # Format the message.          # Format the message.
471          my $formatted = "$timeStamp $message";      my $formatted = "$prefix $stripped";
472          # Process according to the destination.          # Process according to the destination.
473          if ($Destination eq "TEXT") {          if ($Destination eq "TEXT") {
474                  # Write the message to the standard output.                  # Write the message to the standard output.
475                  print "$formatted\n";                  print "$formatted\n";
476          } elsif ($Destination eq "ERROR") {          } elsif ($Destination eq "ERROR") {
477                  # Write the message to the error output.          # Write the message to the error output. Here, we want our prefix fields.
478                  print STDERR "$formatted\n";                  print STDERR "$formatted\n";
479        } elsif ($Destination eq "WARN") {
480            # Emit the message to the standard error output. It is presumed that the
481            # error logger will add its own prefix fields, the notable exception being
482            # the caller info.
483            print STDERR "$callerInfo$stripped\n";
484          } elsif ($Destination eq "QUEUE") {          } elsif ($Destination eq "QUEUE") {
485                  # Push the message into the queue.                  # Push the message into the queue.
486                  push @Queue, "$formatted";                  push @Queue, "$formatted";
487          } elsif ($Destination eq "HTML") {          } elsif ($Destination eq "HTML") {
488                  # Convert the message to HTML and write it to the standard output.                  # Convert the message to HTML and write it to the standard output.
489                  my $escapedMessage = CGI::escapeHTML($message);          my $escapedMessage = CGI::escapeHTML($stripped);
490                  print "<p>$formatted</p>\n";          print "<p>$timeStamp $LastCategory $LastLevel: $escapedMessage</p>\n";
     } elsif ($Destination eq "WARN") {  
        # Emit the message as a warning.  
        warn $message;  
491          } elsif ($Destination =~ m/^>>/) {          } elsif ($Destination =~ m/^>>/) {
492                  # Write the trace message to an output file.                  # Write the trace message to an output file.
493                  open TRACING, $Destination;          open(TRACING, $Destination) || die "Tracing open for \"$Destination\" failed: $!";
494                  print TRACING "$formatted\n";                  print TRACING "$formatted\n";
495                  close TRACING;                  close TRACING;
496            # If the Tee flag is on, echo it to the standard output.
497            if ($TeeFlag) {
498                print "$formatted\n";
499            }
500          }          }
501  }  }
502    
503  =head3 T  =head3 T
504    
505  C<< my $switch = T($category, $traceLevel); >>      my $switch = T($category, $traceLevel);
506    
507          or          or
508    
509  C<< my $switch = T($traceLevel); >>      my $switch = T($traceLevel);
510    
511  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
512  is active, else FALSE. If no category is specified, the caller's package name is used.  is active, else FALSE. If no category is specified, the caller's package name is used.
# Line 436  Line 539 
539                  my ($category, $traceLevel) = @_;                  my ($category, $traceLevel) = @_;
540                  if (!defined $traceLevel) {                  if (!defined $traceLevel) {
541                          # 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.
542                # The calling package is normally the first parameter. If it is
543                # omitted, the first parameter will be the tracelevel. So, the
544                # first thing we do is shift the so-called category into the
545                # $traceLevel variable where it belongs.
546                          $traceLevel = $category;                          $traceLevel = $category;
547                          my ($package, $fileName, $line) = caller;                          my ($package, $fileName, $line) = caller;
548              # If there is no calling package, we default to "main".              # If there is no calling package, we default to "main".
549                          if (!$package) {                          if (!$package) {
550                  $category = "main";                  $category = "main";
551                          } else {                          } else {
552                                  $category = $package;                  my @cats = split /::/, $package;
553                    $category = $cats[$#cats];
554                          }                          }
555                  }                  }
556                  # Use the package and tracelevel to compute the result.          # Save the category name and level.
557                  $retVal = ($traceLevel <= $TraceLevel && exists $Categories{$category});          $LastCategory = $category;
558            $LastLevel = $traceLevel;
559            # Convert it to lower case before we hash it.
560            $category = lc $category;
561            # Validate the trace level.
562            if (ref $traceLevel) {
563                Confess("Bad trace level.");
564            } elsif (ref $TraceLevel) {
565                Confess("Bad trace config.");
566            }
567            # Make the check. Note that level 0 shows even if the category is turned off.
568            $retVal = ($traceLevel <= $TraceLevel && ($traceLevel == 0 || $AllTrace || exists $Categories{$category}));
569      }      }
570          # Return the computed result.          # Return the computed result.
571      return $retVal;      return $retVal;
572  }  }
573    
574  =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  
575    
576  C<< apple orange rutabaga >>      my $data = QTrace($format);
577    
578  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.  
579    
580  =over 4  =over 4
581    
582  =item optionTable  =item format
   
 Table of default options.  
   
 =item inputList  
   
 List of words on the command line.  
   
 =item RETURN  
583    
584  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.
585    
586  =back  =back
587    
588  =cut  =cut
589    
590  sub ParseCommand {  sub QTrace {
591          # Get the parameters.      # Get the parameter.
592          my ($optionTable, @inputList) = @_;      my ($format) = @_;
593          # Process any options in the input list.      # Create the return variable.
594        my $retVal = "";
595        # Only proceed if there is an actual queue.
596        if (@Queue) {
597            # Process according to the format.
598            if ($format =~ m/^HTML$/i) {
599                # Convert the queue into an HTML list.
600                $retVal = "<ul>\n";
601                for my $line (@Queue) {
602                    my $escapedLine = CGI::escapeHTML($line);
603                    $retVal .= "<li>$escapedLine</li>\n";
604                }
605                $retVal .= "</ul>\n";
606            } elsif ($format =~ m/^TEXT$/i) {
607                # Convert the queue into a list of text lines.
608                $retVal = join("\n", @Queue) . "\n";
609            }
610            # Clear the queue.
611            @Queue = ();
612        }
613        # Return the formatted list.
614        return $retVal;
615    }
616    
617    =head3 Confess
618    
619        Confess($message);
620    
621    Trace the call stack and abort the program with the specified message. When used with
622    the OR operator and the L</Assert> method, B<Confess> can function as a debugging assert.
623    So, for example
624    
625        Assert($recNum >= 0) || Confess("Invalid record number $recNum.");
626    
627    Will abort the program with a stack trace if the value of C<$recNum> is negative.
628    
629    =over 4
630    
631    =item message
632    
633    Message to include in the trace.
634    
635    =back
636    
637    =cut
638    
639    sub Confess {
640        # Get the parameters.
641        my ($message) = @_;
642        # Set up the category and level.
643        $LastCategory = "(confess)";
644        $LastLevel = 0;
645        if (! defined($FIG_Config::no_tool_hdr)) {
646            # Here we have a tool header. Display its length so that the user can adjust the line numbers.
647            my $toolHeaderFile = "$FIG_Config::fig_disk/dist/releases/current/$FIG_Config::arch/tool_hdr";
648            # Only proceed if the tool header file is actually present.
649            if (-f $toolHeaderFile) {
650                my $fh;
651                if (open $fh, "<$toolHeaderFile") {
652                    my @lines = <$fh>;
653                    Trace("Tool header has " . scalar(@lines) . " lines.");
654                }
655            }
656        }
657        # Trace the call stack.
658        Cluck($message);
659        # Abort the program.
660        croak(">>> $message");
661    }
662    
663    =head3 Warn
664    
665        Warn($message);
666    
667    This method traces an important message. If an RSS feed is configured
668    (via I<FIG_Config::error_feed>) and the tracing destination is C<WARN>,
669    then the message will be echoed to the feed. In general, a tracing
670    destination of C<WARN> indicates that the caller is running as a web
671    service in a production environment; however, this is not a requirement.
672    
673    The L</Cluck> method calls this one for its final message. Since
674    L</Confess> calls L</Cluck>, this means that any error which is caught
675    and confessed will put something in the feed. This insures that someone
676    will be alerted relatively quickly when a failure occurs.
677    
678    =over 4
679    
680    =item message
681    
682    Message to be traced.
683    
684    =back
685    
686    =cut
687    
688    sub Warn {
689        # Get the parameters.
690        my ($message) = @_;
691        # Trace the message.
692        Trace($message);
693        # An error here would be disastrous. Note, however, that we aren't too worried
694        # about losing events. The error log is always available for the occasions where
695        # we mess up.
696        eval {
697            # Do we need to put this in the RSS feed?
698            if ($FIG_Config::error_feed && $Destination eq 'WARN') {
699                # Yes. We now need to compute the date, the link, and the title.
700                # First, the date, in a very specific format.
701                my $date = strftime("%a, %02e %b %H:%M:%S %Y ", localtime) .
702                    (tz_local_offset() / 30);
703                # We'll put the link and title in here.
704                my ($link, $title);
705                # Environment data goes in here.
706                my $environment;
707                # HTML-escape the message.
708                my $escaped = CGI::escapeHTML($message);
709                # If we have a CGI object, then this is a web error. Otherwise, it's
710                # command-line.
711                if (defined $SavedCGI) {
712                    # We're in a web service. The title is the user's IP, and the link
713                    # is the URL that got us here.
714                    my $key = $ENV{HTTP_X_FORWARDED_FOR} || $ENV{REMOTE_ADDR};
715                    $title = "Event Reported at IP address $key: $escaped";
716                    $link = $SavedCGI->url(-full => 1, -query => 1);
717                    # We need the user agent string and (if available) the referrer.
718                    $environment = "User Agent $ENV{HTTP_USER_AGENT}";
719                    if ($ENV{HTTP_REFERER}) {
720                        $environment .= " referred from $ENV{HTTP_REFERER}"
721                    }
722                    # Close off the sentence.
723                    $environment .= ". ";
724                } else {
725                    # No CGI object, so we're a command-line tool. Use the tracing
726                    # key and the PID as the user identifier.
727                    my $key = EmergencyKey();
728                    $title = "Event Reported by $key Process $$: $escaped";
729                    # Set the link to the development NMPDR. There is really no good
730                    # choice here.
731                    $link = "http://$FIG_Config::dev_server";
732                    # We need the command
733                    $environment = "Command $ENV{_}.";
734                }
735                # Build a GUID. We use the current time, the title, and the process ID,
736                # then digest the result.
737                my $guid = Digest::MD5::md5_base64(gettimeofday(), $title, $$);
738                # Finally, the description. This is a stack trace plus various environmental stuff.
739                my @trace = LongMess();
740                my $trace = join "; ", @trace;
741                my $description = CGI::escapeHTML("$environment Stack trace: $trace");
742                # Okay, we have all the pieces. Create a hash of the new event.
743                my $newItem = { title => $title,
744                                description => $description,
745                                link => $link,
746                                category => $LastCategory,
747                                pubDate => $date,
748                                guid => $guid,
749                               };
750                # We need XML capability for this.
751                require XML::Simple;
752                # The RSS document goes in here.
753                my $rss;
754                # Get the name of the RSS file. It's in the FIG temporary directory.
755                my $fileName = "$FIG_Config::temp/$FIG_Config::error_feed";
756                # Does it exist?
757                if (-s $fileName) {
758                    # Slurp it in.
759                    $rss = XML::Simple::XMLin($fileName, ForceArray => ['item']);
760                } else {
761                    my $size = -s $fileName;
762                    # Create an empty channel.
763                    $rss = {
764                        channel => {
765                            title => 'NMPDR Warning Feed',
766                            link => "$FIG_Config::temp_url/$FIG_Config::error_feed",
767                            description => "Important messages regarding the status of the NMPDR.",
768                            generator => "NMPDR Trace Facility",
769                            docs => "http://blogs.law.harvard.edu/tech/rss",
770                            item => []
771                        },
772                    };
773                }
774                # Get the channel object.
775                my $channel = $rss->{channel};
776                # Update the last-build date.
777                $channel->{lastBuildDate} = $date;
778                # Get the item array.
779                my $items = $channel->{item};
780                # Insure it has only 100 entries.
781                while (scalar @{$items} > 100) {
782                    pop @{$items};
783                }
784                # Add our new item at the front.
785                unshift @{$items}, $newItem;
786                # Replace the file.
787                my $xml = XML::Simple::XMLout($rss, NoAttr => 1, RootName => 'rss', XmlDecl => '<?xml version="1.0" encoding="utf-8"?>',
788                                              NoEscape => 1);
789                # We don't use Open here because we can't afford an error.
790                if (open XMLOUT, ">$fileName") {
791                    print XMLOUT $xml;
792                    close XMLOUT;
793                }
794            }
795        };
796        # There's no "if ($@)" here, because putting an error message in the log
797        # saying that we missed putting an error message in the feed of messages
798        # in the log is not going to help anybody.
799    }
800    
801    =head3 Assert
802    
803        Assert($condition1, $condition2, ... $conditionN);
804    
805    Return TRUE if all the conditions are true. This method can be used in conjunction with
806    the OR operator and the L</Confess> method as a debugging assert.
807    So, for example
808    
809        Assert($recNum >= 0) || Confess("Invalid record number $recNum.");
810    
811    Will abort the program with a stack trace if the value of C<$recNum> is negative.
812    
813    =cut
814    sub Assert {
815        my $retVal = 1;
816        LOOP: for my $condition (@_) {
817            if (! $condition) {
818                $retVal = 0;
819                last LOOP;
820            }
821        }
822        return $retVal;
823    }
824    
825    =head3 Cluck
826    
827        Cluck($message);
828    
829    Trace the call stack. Note that for best results, you should qualify the call with a
830    trace condition. For example,
831    
832        Cluck("Starting record parse.") if T(3);
833    
834    will only trace the stack if the trace level for the package is 3 or more.
835    
836    =over 4
837    
838    =item message
839    
840    Message to include in the trace.
841    
842    =back
843    
844    =cut
845    
846    sub Cluck {
847        # Get the parameters.
848        my ($message) = @_;
849        # Trace what's happening.
850        Trace("Stack trace for event: $message");
851        # Get the stack trace.
852        my @trace = LongMess();
853        # Convert the trace to a series of messages.
854        for my $line (@trace) {
855            # Replace the tab at the beginning with spaces.
856            $line =~ s/^\t/    /;
857            # Trace the line.
858            Trace($line);
859        }
860        # Issue a warning. This displays the event message and inserts it into the RSS error feed.
861        Warn($message);
862    }
863    
864    =head3 LongMess
865    
866        my @lines = Tracer::LongMess();
867    
868    Return a stack trace with all tracing methods removed. The return will be in the form of a list
869    of message strings.
870    
871    =cut
872    
873    sub LongMess {
874        # Declare the return variable.
875        my @retVal = ();
876        my $confession = longmess("");
877        for my $line (split /\s*\n/, $confession) {
878            unless ($line =~ /Tracer\.pm/) {
879                # Here we have a line worth keeping. Push it onto the result list.
880                push @retVal, $line;
881            }
882        }
883        # Return the result.
884        return @retVal;
885    }
886    
887    =head3 ScriptSetup (deprecated)
888    
889        my ($cgi, $varHash) = ScriptSetup($noTrace);
890    
891    Perform standard tracing and debugging setup for scripts. The value returned is
892    the CGI object followed by a pre-built variable hash. At the end of the script,
893    the client should call L</ScriptFinish> to output the web page.
894    
895    This method calls L</ETracing> to configure tracing, which allows the tracing
896    to be configured via the emergency tracing form on the debugging control panel.
897    Tracing will then be turned on automatically for all programs that use the L</ETracing>
898    method, which includes every program that uses this method or L</StandardSetup>.
899    
900    =over 4
901    
902    =item noTrace (optional)
903    
904    If specified, tracing will be suppressed. This is useful if the script wants to set up
905    tracing manually.
906    
907    =item RETURN
908    
909    Returns a two-element list consisting of a CGI query object and a variable hash for
910    the output page.
911    
912    =back
913    
914    =cut
915    
916    sub ScriptSetup {
917        # Get the parameters.
918        my ($noTrace) = @_;
919        # Get the CGI query object.
920        my $cgi = CGI->new();
921        # Set up tracing if it's not suppressed.
922        ETracing($cgi) unless $noTrace;
923        # Create the variable hash.
924        my $varHash = { results => '' };
925        # Return the query object and variable hash.
926        return ($cgi, $varHash);
927    }
928    
929    =head3 ETracing
930    
931        ETracing($parameter);
932    
933    Set up emergency tracing. Emergency tracing is tracing that is turned
934    on automatically for any program that calls this method. The emergency
935    tracing parameters are stored in a a file identified by a tracing key.
936    If this method is called with a CGI object, then the tracing key is
937    taken from a cookie. If it is called with no parameters, then the tracing
938    key is taken from an environment variable. If it is called with a string,
939    the tracing key is that string.
940    
941    =over 4
942    
943    =item parameter
944    
945    A parameter from which the tracing key is computed. If it is a scalar,
946    that scalar is used as the tracing key. If it is a CGI object, the
947    tracing key is taken from the C<IP> cookie. If it is omitted, the
948    tracing key is taken from the C<TRACING> environment variable. If it
949    is a CGI object and emergency tracing is not on, the C<Trace> and
950    C<TF> parameters will be used to determine the type of tracing.
951    
952    =back
953    
954    =cut
955    
956    sub ETracing {
957        # Get the parameter.
958        my ($parameter) = @_;
959        # Check for CGI mode.
960        if (defined $parameter && ref $parameter eq 'CGI') {
961            $SavedCGI = $parameter;
962        } else {
963            $SavedCGI = undef;
964        }
965        # Default to no tracing except errors.
966        my ($tracing, $dest) = ("0", "WARN");
967        # Check for emergency tracing.
968        my $tkey = EmergencyKey($parameter);
969        my $emergencyFile = EmergencyFileName($tkey);
970        if (-e $emergencyFile) {
971            # We have the file. Read in the data.
972            my @tracing = GetFile($emergencyFile);
973            # Pull off the time limit.
974            my $expire = shift @tracing;
975            # Convert it to seconds.
976            $expire *= 3600;
977            # Check the file data.
978            my $stat = stat($emergencyFile);
979            my ($now) = gettimeofday;
980            if ($now - $stat->mtime > $expire) {
981                # Delete the expired file.
982                unlink $emergencyFile;
983            } else {
984                # Emergency tracing is on. Pull off the destination and
985                # the trace level;
986                $dest = shift @tracing;
987                my $level = shift @tracing;
988                # Convert the destination to a real tracing destination.
989                # temp directory.
990                $dest = EmergencyTracingDest($tkey, $dest);
991                # Insure Tracer is specified.
992                my %moduleHash = map { $_ => 1 } @tracing;
993                $moduleHash{Tracer} = 1;
994                # Set the trace parameter.
995                $tracing = join(" ", $level, sort keys %moduleHash);
996            }
997        } elsif (defined $SavedCGI) {
998            # There's no emergency tracing, but we have a CGI object, so check
999            # for tracing from the form parameters.
1000            if ($SavedCGI->param('Trace')) {
1001                # Here the user has requested tracing via a form.
1002                $dest = ($SavedCGI->param('TF') ? ">$FIG_Config::temp/Trace$$.log" : "QUEUE");
1003                $tracing = $SavedCGI->param('Trace') . " Tracer";
1004            }
1005        }
1006        # Setup the tracing we've determined from all the stuff above.
1007        TSetup($tracing, $dest);
1008        # Check to see if we're a web script.
1009        if (defined $SavedCGI) {
1010            # Yes we are. Trace the form and environment data.
1011            TraceParms($SavedCGI);
1012            # Check for RAW mode. In raw mode, we print a fake header so that we see everything
1013            # emitted by the script in its raw form.
1014            if (T(Raw => 3)) {
1015                print CGI::header(-type => 'text/plain', -tracing => 'Raw');
1016            }
1017        }
1018    }
1019    
1020    =head3 EmergencyFileName
1021    
1022        my $fileName = Tracer::EmergencyFileName($tkey);
1023    
1024    Return the emergency tracing file name. This is the file that specifies
1025    the tracing information.
1026    
1027    =over 4
1028    
1029    =item tkey
1030    
1031    Tracing key for the current program.
1032    
1033    =item RETURN
1034    
1035    Returns the name of the file to contain the emergency tracing information.
1036    
1037    =back
1038    
1039    =cut
1040    
1041    sub EmergencyFileName {
1042        # Get the parameters.
1043        my ($tkey) = @_;
1044        # Compute the emergency tracing file name.
1045        return "$FIG_Config::temp/Emergency$tkey.txt";
1046    }
1047    
1048    =head3 EmergencyFileTarget
1049    
1050        my $fileName = Tracer::EmergencyFileTarget($tkey);
1051    
1052    Return the emergency tracing target file name. This is the file that receives
1053    the tracing output for file-based tracing.
1054    
1055    =over 4
1056    
1057    =item tkey
1058    
1059    Tracing key for the current program.
1060    
1061    =item RETURN
1062    
1063    Returns the name of the file to contain the trace output.
1064    
1065    =back
1066    
1067    =cut
1068    
1069    sub EmergencyFileTarget {
1070        # Get the parameters.
1071        my ($tkey) = @_;
1072        # Compute the emergency tracing file name.
1073        return "$FIG_Config::temp/trace$tkey.log";
1074    }
1075    
1076    =head3 EmergencyTracingDest
1077    
1078        my $dest = Tracer::EmergencyTracingDest($tkey, $myDest);
1079    
1080    This method converts an emergency tracing destination to a real
1081    tracing destination. The main difference is that if the
1082    destination is C<FILE> or C<APPEND>, we convert it to file
1083    output. If the destination is C<DUAL>, we convert it to file
1084    and standard output.
1085    
1086    =over 4
1087    
1088    =item tkey
1089    
1090    Tracing key for this environment.
1091    
1092    =item myDest
1093    
1094    Destination from the emergency tracing file.
1095    
1096    =item RETURN
1097    
1098    Returns a destination that can be passed into L</TSetup>.
1099    
1100    =back
1101    
1102    =cut
1103    
1104    sub EmergencyTracingDest {
1105        # Get the parameters.
1106        my ($tkey, $myDest) = @_;
1107        # Declare the return variable.
1108        my $retVal = $myDest;
1109        # Process according to the destination value.
1110        if ($myDest eq 'FILE') {
1111            $retVal = ">" . EmergencyFileTarget($tkey);
1112        } elsif ($myDest eq 'APPEND') {
1113            $retVal = ">>" . EmergencyFileTarget($tkey);
1114        } elsif ($myDest eq 'DUAL') {
1115            $retVal = "+>" . EmergencyFileTarget($tkey);
1116        } elsif ($myDest eq 'WARN') {
1117            $retVal = "WARN";
1118        }
1119        # Return the result.
1120        return $retVal;
1121    }
1122    
1123    =head3 Emergency
1124    
1125        Emergency($key, $hours, $dest, $level, @modules);
1126    
1127    Turn on emergency tracing. This method is normally invoked over the web from
1128    a debugging console, but it can also be called by the C<trace.pl> script.
1129    The caller specifies the duration of the emergency in hours, the desired tracing
1130    destination, the trace level, and a list of the trace modules to activate.
1131    For the length of the duration, when a program in an environment with the
1132    specified tracing key active invokes a Sprout CGI script, tracing will be
1133    turned on automatically. See L</TSetup> for more about tracing setup and
1134    L</ETracing> for more about emergency tracing.
1135    
1136    =over 4
1137    
1138    =item tkey
1139    
1140    The tracing key. This is used to identify the control file and the trace file.
1141    
1142    =item hours
1143    
1144    Number of hours to keep emergency tracing alive.
1145    
1146    =item dest
1147    
1148    Tracing destination. If no path information is specified for a file
1149    destination, it is put in the FIG temporary directory.
1150    
1151    =item level
1152    
1153    Tracing level. A higher level means more trace messages.
1154    
1155    =item modules
1156    
1157    A list of the tracing modules to activate.
1158    
1159    =back
1160    
1161    =cut
1162    
1163    sub Emergency {
1164        # Get the parameters.
1165        my ($tkey, $hours, $dest, $level, @modules) = @_;
1166        # Create the emergency file.
1167        my $specFile = EmergencyFileName($tkey);
1168        my $outHandle = Open(undef, ">$specFile");
1169        print $outHandle join("\n", $hours, $dest, $level, @modules, "");
1170    }
1171    
1172    =head3 EmergencyKey
1173    
1174        my $tkey = EmergencyKey($parameter);
1175    
1176    Return the Key to be used for emergency tracing. This could be an IP address,
1177     a session ID, or a user name, depending on the environment.
1178    
1179    =over 4
1180    
1181    =item parameter
1182    
1183    Parameter defining the method for finding the tracing key. If it is a scalar,
1184    then it is presumed to be the tracing key itself. If it is a CGI object, then
1185    the tracing key is taken from the C<IP> cookie. Otherwise, the tracing key is
1186    taken from the C<TRACING> environment variable.
1187    
1188    =item RETURN
1189    
1190    Returns the key to be used for labels in emergency tracing.
1191    
1192    =back
1193    
1194    =cut
1195    
1196    sub EmergencyKey {
1197        # Get the parameters.
1198        my ($parameter) = @_;
1199        # Declare the return variable.
1200        my $retVal;
1201        # Determine the parameter type.
1202        if (! defined $parameter) {
1203            # Here we're supposed to check the environment. If that fails, we
1204            # get the effective login ID.
1205            $retVal = $ENV{TRACING} || scalar getpwuid($<);
1206        } else {
1207            my $ptype = ref $parameter;
1208            if ($ptype eq 'CGI') {
1209                # Here we were invoked from a web page. Look for a cookie.
1210                $retVal = $parameter->cookie('IP');
1211            } elsif (! $ptype) {
1212                # Here the key was passed in.
1213                $retVal = $parameter;
1214            }
1215        }
1216        # If no luck finding a key, use the PID.
1217        if (! defined $retVal) {
1218            $retVal = $$;
1219        }
1220        # Return the result.
1221        return $retVal;
1222    }
1223    
1224    
1225    =head3 TraceParms
1226    
1227        Tracer::TraceParms($cgi);
1228    
1229    Trace the CGI parameters at trace level CGI => 3 and the environment variables
1230    at level CGI => 4. A self-referencing URL is traced at level CGI => 2.
1231    
1232    =over 4
1233    
1234    =item cgi
1235    
1236    CGI query object containing the parameters to trace.
1237    
1238    =back
1239    
1240    =cut
1241    
1242    sub TraceParms {
1243        # Get the parameters.
1244        my ($cgi) = @_;
1245        if (T(CGI => 2)) {
1246            # Here we trace the GET-style URL for the script.
1247            Trace("[URL] " . $cgi->url(-relative => 1, -query => 1));
1248        }
1249        if (T(CGI => 3)) {
1250            # Here we want to trace the parameter data.
1251            my @names = $cgi->param;
1252            for my $parmName (sort @names) {
1253                # Note we skip the Trace parameters, which are for our use only.
1254                if ($parmName ne 'Trace' && $parmName ne 'TF') {
1255                    my @values = $cgi->param($parmName);
1256                    Trace("[CGI] $parmName = " . join(", ", @values));
1257                }
1258            }
1259            # Display the request method.
1260            my $method = $cgi->request_method();
1261            Trace("Method: $method");
1262        }
1263        if (T(CGI => 4)) {
1264            # Here we want the environment data too.
1265            for my $envName (sort keys %ENV) {
1266                Trace("[ENV] $envName = $ENV{$envName}");
1267            }
1268        }
1269    }
1270    
1271    =head3 TraceImages
1272    
1273        Tracer::TraceImages($htmlString);
1274    
1275    Trace information about all of an html document's images. The tracing
1276    will be for type "IMG" at level 3. The image's source string
1277    will be displayed. This is generally either the URL of the image or
1278    raw data for the image itself. If the source is too long, only the first 300
1279    characters will be shown at trace level 3. The entire source will be shown,
1280    however, at trace level 4. This method is not very smart, and might catch
1281    Javascript code, but it is still useful when debugging the arcane
1282    behavior of images in multiple browser environments.
1283    
1284    =over 4
1285    
1286    =item htmlString
1287    
1288    HTML text for an outgoing web page.
1289    
1290    =back
1291    
1292    =cut
1293    
1294    sub TraceImages {
1295        # Only proceed if we're at the proper trace level.
1296        if (T(IMG => 3)) {
1297            # For performance reasons we're manipulating $_[0] instead of retrieving the string
1298            # into a variable called "$htmlString". This is because we expect html strings to be
1299            # long, and don't want to copy them any more than we have to.
1300            Trace(length($_[0]) . " characters in web page.");
1301            # Loop through the HTML, culling image tags.
1302            while ($_[0] =~ /<img\s+[^>]+?src="([^"]+)"/sgi) {
1303                # Extract the source string and determine whether or not it's too long.
1304                my $srcString = $1;
1305                my $pos = pos($_[0]) - length($srcString);
1306                my $excess = length($srcString) - 300;
1307                # We'll put the display string in here.
1308                my $srcDisplay = $srcString;
1309                # If it's a data string, split it at the comma.
1310                $srcDisplay =~ s/^(data[^,]+,)/$1\n/;
1311                # If there's no excess or we're at trace level 4, we're done. At level 3 with
1312                # a long string, however, we only show the first 300 characters.
1313                if ($excess > 0 && ! T(IMG => 4)) {
1314                    $srcDisplay = substr($srcDisplay,0,300) . "\nplus $excess characters.";
1315                }
1316                # Output the trace message.
1317                Trace("Image tag at position $pos:\n$srcDisplay");
1318            }
1319        }
1320    }
1321    
1322    
1323    =head3 ScriptFinish (deprecated)
1324    
1325        ScriptFinish($webData, $varHash);
1326    
1327    Output a web page at the end of a script. Either the string to be output or the
1328    name of a template file can be specified. If the second parameter is omitted,
1329    it is assumed we have a string to be output; otherwise, it is assumed we have the
1330    name of a template file. The template should have the variable C<DebugData>
1331    specified in any form that invokes a standard script. If debugging mode is turned
1332    on, a form field will be put in that allows the user to enter tracing data.
1333    Trace messages will be placed immediately before the terminal C<BODY> tag in
1334    the output, formatted as a list.
1335    
1336    A typical standard script would loook like the following.
1337    
1338        BEGIN {
1339            # Print the HTML header.
1340            print "CONTENT-TYPE: text/html\n\n";
1341        }
1342        use Tracer;
1343        use CGI;
1344        use FIG;
1345        # ... more uses ...
1346    
1347        my ($cgi, $varHash) = ScriptSetup();
1348        eval {
1349            # ... get data from $cgi, put it in $varHash ...
1350        };
1351        if ($@) {
1352            Trace("Script Error: $@") if T(0);
1353        }
1354        ScriptFinish("Html/MyTemplate.html", $varHash);
1355    
1356    The idea here is that even if the script fails, you'll see trace messages and
1357    useful output.
1358    
1359    =over 4
1360    
1361    =item webData
1362    
1363    A string containing either the full web page to be written to the output or the
1364    name of a template file from which the page is to be constructed. If the name
1365    of a template file is specified, then the second parameter must be present;
1366    otherwise, it must be absent.
1367    
1368    =item varHash (optional)
1369    
1370    If specified, then a reference to a hash mapping variable names for a template
1371    to their values. The template file will be read into memory, and variable markers
1372    will be replaced by data in this hash reference.
1373    
1374    =back
1375    
1376    =cut
1377    
1378    sub ScriptFinish {
1379        # Get the parameters.
1380        my ($webData, $varHash) = @_;
1381        # Check for a template file situation.
1382        my $outputString;
1383        if (defined $varHash) {
1384            # Here we have a template file. We need to determine the template type.
1385            my $template;
1386            if ($FIG_Config::template_url && $webData =~ /\.php$/) {
1387                $template = "$FIG_Config::template_url/$webData";
1388            } else {
1389                $template = "<<$webData";
1390            }
1391            $outputString = PageBuilder::Build($template, $varHash, "Html");
1392        } else {
1393            # Here the user gave us a raw string.
1394            $outputString = $webData;
1395        }
1396        # Check for trace messages.
1397        if ($Destination ne "NONE" && $TraceLevel > 0) {
1398            # We have trace messages, so we want to put them at the end of the body. This
1399            # is either at the end of the whole string or at the beginning of the BODY
1400            # end-tag.
1401            my $pos = length $outputString;
1402            if ($outputString =~ m#</body>#gi) {
1403                $pos = (pos $outputString) - 7;
1404            }
1405            # If the trace messages were queued, we unroll them. Otherwise, we display the
1406            # destination.
1407            my $traceHtml;
1408            if ($Destination eq "QUEUE") {
1409                $traceHtml = QTrace('Html');
1410            } elsif ($Destination =~ /^>>(.+)$/) {
1411                # Here the tracing output it to a file. We code it as a hyperlink so the user
1412                # can copy the file name into the clipboard easily.
1413                my $actualDest = $1;
1414                $traceHtml = "<p>Tracing output to $actualDest.</p>\n";
1415            } else {
1416                # Here we have one of the special destinations.
1417                $traceHtml = "<P>Tracing output type is $Destination.</p>\n";
1418            }
1419            substr $outputString, $pos, 0, $traceHtml;
1420        }
1421        # Write the output string.
1422        print $outputString;
1423    }
1424    
1425    =head2 Command-Line Utility Methods
1426    
1427    =head3 SendSMS
1428    
1429        my $msgID = Tracer::SendSMS($phoneNumber, $msg);
1430    
1431    Send a text message to a phone number using Clickatell. The FIG_Config file must contain the
1432    user name, password, and API ID for the relevant account in the hash reference variable
1433    I<$FIG_Config::phone>, using the keys C<user>, C<password>, and C<api_id>. For
1434    example, if the user name is C<BruceTheHumanPet>, the password is C<silly>, and the API ID
1435    is C<2561022>, then the FIG_Config file must contain
1436    
1437        $phone =  { user => 'BruceTheHumanPet',
1438                    password => 'silly',
1439                    api_id => '2561022' };
1440    
1441    The original purpose of this method was to insure Bruce would be notified immediately when the
1442    Sprout Load terminates. Care should be taken if you do not wish Bruce to be notified immediately
1443    when you call this method.
1444    
1445    The message ID will be returned if successful, and C<undef> if an error occurs.
1446    
1447    =over 4
1448    
1449    =item phoneNumber
1450    
1451    Phone number to receive the message, in international format. A United States phone number
1452    would be prefixed by "1". A British phone number would be prefixed by "44".
1453    
1454    =item msg
1455    
1456    Message to send to the specified phone.
1457    
1458    =item RETURN
1459    
1460    Returns the message ID if successful, and C<undef> if the message could not be sent.
1461    
1462    =back
1463    
1464    =cut
1465    
1466    sub SendSMS {
1467        # Get the parameters.
1468        my ($phoneNumber, $msg) = @_;
1469        # Declare the return variable. If we do not change it, C<undef> will be returned.
1470        my $retVal;
1471        # Only proceed if we have phone support.
1472        if (! defined $FIG_Config::phone) {
1473            Trace("Phone support not present in FIG_Config.") if T(1);
1474        } else {
1475            # Get the phone data.
1476            my $parms = $FIG_Config::phone;
1477            # Get the Clickatell URL.
1478            my $url = "http://api.clickatell.com/http/";
1479            # Create the user agent.
1480            my $ua = LWP::UserAgent->new;
1481            # Request a Clickatell session.
1482            my $resp = $ua->post("$url/sendmsg", { user => $parms->{user},
1483                                         password => $parms->{password},
1484                                         api_id => $parms->{api_id},
1485                                         to => $phoneNumber,
1486                                         text => $msg});
1487            # Check for an error.
1488            if (! $resp->is_success) {
1489                Trace("Alert failed.") if T(1);
1490            } else {
1491                # Get the message ID.
1492                my $rstring = $resp->content;
1493                if ($rstring =~ /^ID:\s+(.*)$/) {
1494                    $retVal = $1;
1495                } else {
1496                    Trace("Phone attempt failed with $rstring") if T(1);
1497                }
1498            }
1499        }
1500        # Return the result.
1501        return $retVal;
1502    }
1503    
1504    =head3 StandardSetup
1505    
1506        my ($options, @parameters) = StandardSetup(\@categories, \%options, $parmHelp, @ARGV);
1507    
1508    This method performs standard command-line parsing and tracing setup. The return
1509    values are a hash of the command-line options and a list of the positional
1510    parameters. Tracing is automatically set up and the command-line options are
1511    validated.
1512    
1513    This is a complex method that does a lot of grunt work. The parameters can
1514    be more easily understood, however, once they are examined individually.
1515    
1516    The I<categories> parameter is the most obtuse. It is a reference to a list of
1517    special-purpose tracing categories. Most tracing categories are PERL package
1518    names. So, for example, if you wanted to turn on tracing inside the B<Sprout>,
1519    B<ERDB>, and B<SproutLoad> packages, you would specify the categories
1520    
1521        ["Sprout", "SproutLoad", "ERDB"]
1522    
1523    This would cause trace messages in the specified three packages to appear in
1524    the output. There are two special tracing categories that are automatically
1525    handled by this method. In other words, if you used L</TSetup> you would need
1526    to include these categories manually, but if you use this method they are turned
1527    on automatically.
1528    
1529    =over 4
1530    
1531    =item SQL
1532    
1533    Traces SQL commands and activity.
1534    
1535    =item Tracer
1536    
1537    Traces error messages and call stacks.
1538    
1539    =back
1540    
1541    C<SQL> is only turned on if the C<-sql> option is specified in the command line.
1542    The trace level is specified using the C<-trace> command-line option. For example,
1543    the following command line for C<TransactFeatures> turns on SQL tracing and runs
1544    all tracing at level 3.
1545    
1546        TransactFeatures -trace=3 -sql register ../xacts IDs.tbl
1547    
1548    Standard tracing is output to the standard output and echoed to the file
1549    C<trace>I<$$>C<.log> in the FIG temporary directory, where I<$$> is the
1550    process ID. You can also specify the C<user> parameter to put a user ID
1551    instead of a process ID in the trace file name. So, for example
1552    
1553    The default trace level is 2. To get all messages, specify a trace level of 4.
1554    For a genome-by-genome update, use 3.
1555    
1556        TransactFeatures -trace=3 -sql -user=Bruce register ../xacts IDs.tbl
1557    
1558    would send the trace output to C<traceBruce.log> in the temporary directory.
1559    
1560    The I<options> parameter is a reference to a hash containing the command-line
1561    options, their default values, and an explanation of what they mean. Command-line
1562    options may be in the form of switches or keywords. In the case of a switch, the
1563    option value is 1 if it is specified and 0 if it is not specified. In the case
1564    of a keyword, the value is separated from the option name by an equal sign. You
1565    can see this last in the command-line example above.
1566    
1567    You can specify a different default trace level by setting C<$options->{trace}>
1568    prior to calling this method.
1569    
1570    An example at this point would help. Consider, for example, the command-line utility
1571    C<TransactFeatures>. It accepts a list of positional parameters plus the options
1572    C<safe>, C<noAlias>, C<start>, and C<tblFiles>. To start up this command, we execute
1573    the following code.
1574    
1575        my ($options, @parameters) = Tracer::StandardSetup(["DocUtils"],
1576                            { safe => [0, "use database transactions"],
1577                              noAlias => [0, "do not expect aliases in CHANGE transactions"],
1578                              start => [' ', "start with this genome"],
1579                              tblFiles => [0, "output TBL files containing the corrected IDs"] },
1580                            "<command> <transactionDirectory> <IDfile>",
1581                          @ARGV);
1582    
1583    
1584    The call to C<ParseCommand> specifies the default values for the options and
1585    stores the actual options in a hash that is returned as C<$options>. The
1586    positional parameters are returned in C<@parameters>.
1587    
1588    The following is a sample command line for C<TransactFeatures>.
1589    
1590        TransactFeatures -trace=2 -noAlias register ../xacts IDs.tbl
1591    
1592    Single and double hyphens are equivalent. So, you could also code the
1593    above command as
1594    
1595        TransactFeatures --trace=2 --noAlias register ../xacts IDs.tbl
1596    
1597    In this case, C<register>, C<../xacts>, and C<IDs.tbl> are the positional
1598    parameters, and would find themselves in I<@parameters> after executing the
1599    above code fragment. The tracing would be set to level 2, and the categories
1600    would be C<Tracer>, and <DocUtils>. C<Tracer> is standard,
1601    and C<DocUtils> was included because it came in within the first parameter
1602    to this method. The I<$options> hash would be
1603    
1604        { trace => 2, sql => 0, safe => 0,
1605          noAlias => 1, start => ' ', tblFiles => 0 }
1606    
1607    Use of C<StandardSetup> in this way provides a simple way of performing
1608    standard tracing setup and command-line parsing. Note that the caller is
1609    not even aware of the command-line switches C<-trace> and C<-sql>, which
1610    are used by this method to control the tracing. If additional tracing features
1611    need to be added in the future, they can be processed by this method without
1612    upsetting the command-line utilities.
1613    
1614    If the C<background> option is specified on the command line, then the
1615    standard and error outputs will be directed to files in the temporary
1616    directory, using the same suffix as the trace file. So, if the command
1617    line specified
1618    
1619        -user=Bruce -background
1620    
1621    then the trace output would go to C<traceBruce.log>, the standard output to
1622    C<outBruce.log>, and the error output to C<errBruce.log>. This is designed to
1623    simplify starting a command in the background.
1624    
1625    The user name is also used as the tracing key for L</Emergency Tracing>.
1626    Specifying a value of C<E> for the trace level causes emergency tracing to
1627    be used instead of custom tracing. If the user name is not specified,
1628    the tracing key is taken from the C<Tracing> environment variable. If there
1629    is no value for that variable, the tracing key will be computed from the PID.
1630    
1631    Finally, if the special option C<-help> is specified, the option
1632    names will be traced at level 0 and the program will exit without processing.
1633    This provides a limited help capability. For example, if the user enters
1634    
1635        TransactFeatures -help
1636    
1637    he would see the following output.
1638    
1639        TransactFeatures [options] <command> <transactionDirectory> <IDfile>
1640            -trace    tracing level (default E)
1641            -sql      trace SQL commands
1642            -safe     use database transactions
1643            -noAlias  do not expect aliases in CHANGE transactions
1644            -start    start with this genome
1645            -tblFiles output TBL files containing the corrected IDs
1646    
1647    The caller has the option of modifying the tracing scheme by placing a value
1648    for C<trace> in the incoming options hash. The default value can be overridden,
1649    or the tracing to the standard output can be turned off by suffixing a minus
1650    sign to the trace level. So, for example,
1651    
1652        { trace => [0, "tracing level (default 0)"],
1653           ...
1654    
1655    would set the default trace level to 0 instead of E, while
1656    
1657        { trace => ["2-", "tracing level (default 2)"],
1658           ...
1659    
1660    would set the default to 2, but trace only to the log file, not to the
1661    standard output.
1662    
1663    The parameters to this method are as follows.
1664    
1665    =over 4
1666    
1667    =item categories
1668    
1669    Reference to a list of tracing category names. These should be names of
1670    packages whose internal workings will need to be debugged to get the
1671    command working.
1672    
1673    =item options
1674    
1675    Reference to a hash containing the legal options for the current command mapped
1676    to their default values and descriptions. The user can override the defaults
1677    by specifying the options as command-line switches prefixed by a hyphen.
1678    Tracing-related options may be added to this hash. If the C<-h> option is
1679    specified on the command line, the option descriptions will be used to
1680    explain the options. To turn off tracing to the standard output, add a
1681    minus sign to the value for C<trace> (see above).
1682    
1683    =item parmHelp
1684    
1685    A string that vaguely describes the positional parameters. This is used
1686    if the user specifies the C<-h> option.
1687    
1688    =item argv
1689    
1690    List of command line parameters, including the option switches, which must
1691    precede the positional parameters and be prefixed by a hyphen.
1692    
1693    =item RETURN
1694    
1695    Returns a list. The first element of the list is the reference to a hash that
1696    maps the command-line option switches to their values. These will either be the
1697    default values or overrides specified on the command line. The remaining
1698    elements of the list are the position parameters, in order.
1699    
1700    =back
1701    
1702    =cut
1703    
1704    sub StandardSetup {
1705        # Get the parameters.
1706        my ($categories, $options, $parmHelp, @argv) = @_;
1707        # Get the default tracing key.
1708        my $tkey = EmergencyKey();
1709        # Add the tracing options.
1710        if (! exists $options->{trace}) {
1711            $options->{trace} = ['2', "tracing level (E for emergency tracing)"];
1712        }
1713        $options->{sql} = [0, "turn on SQL tracing"];
1714        $options->{help} = [0, "display command-line options"];
1715        $options->{user} = [$tkey, "tracing key"];
1716        $options->{background} = [0, "spool standard and error output"];
1717        # Create a parsing hash from the options hash. The parsing hash
1718        # contains the default values rather than the default value
1719        # and the description. While we're at it, we'll memorize the
1720        # length of the longest option name.
1721        my $longestName = 0;
1722        my %parseOptions = ();
1723        for my $key (keys %{$options}) {
1724            if (length $key > $longestName) {
1725                $longestName = length $key;
1726            }
1727            $parseOptions{$key} = $options->{$key}->[0];
1728        }
1729        # Parse the command line.
1730        my ($retOptions, @retParameters) = ParseCommand(\%parseOptions, @argv);
1731        # Get the logfile suffix.
1732        my $suffix = $retOptions->{user};
1733        # Check for background mode.
1734        if ($retOptions->{background}) {
1735            my $outFileName = "$FIG_Config::temp/out$suffix.log";
1736            my $errFileName = "$FIG_Config::temp/err$suffix.log";
1737            open STDOUT, ">$outFileName";
1738            open STDERR, ">$errFileName";
1739            # Check for phone support. If we have phone support and a phone number,
1740            # we want to turn it on.
1741            if ($ENV{PHONE} && defined($FIG_Config::phone)) {
1742                $retOptions->{phone} = $ENV{PHONE};
1743            }
1744        }
1745        # Now we want to set up tracing. First, we need to know if the user
1746        # wants emergency tracing.
1747        if ($retOptions->{trace} eq 'E') {
1748            ETracing($retOptions->{user});
1749        } else {
1750            # Here the tracing is controlled from the command line.
1751            my @cats = @{$categories};
1752            if ($retOptions->{sql}) {
1753                push @cats, "SQL";
1754            }
1755            # Add the default categories.
1756            push @cats, "Tracer";
1757            # Next, we create the category string by joining the categories.
1758            my $cats = join(" ", @cats);
1759            # Check to determine whether or not the caller wants to turn off tracing
1760            # to the standard output.
1761            my $traceLevel = $retOptions->{trace};
1762            my $textOKFlag = 1;
1763            if ($traceLevel =~ /^(.)-/) {
1764                $traceLevel = $1;
1765                $textOKFlag = 0;
1766            }
1767            # Now we set up the trace mode.
1768            my $traceMode;
1769            # Verify that we can open a file in the FIG temporary directory.
1770            my $traceFileName = "$FIG_Config::temp/trace$suffix.log";
1771            if (open TESTTRACE, ">$traceFileName") {
1772                # Here we can trace to a file.
1773                $traceMode = ">$traceFileName";
1774                if ($textOKFlag) {
1775                    # Echo to standard output if the text-OK flag is set.
1776                    $traceMode = "+$traceMode";
1777                }
1778                # Close the test file.
1779                close TESTTRACE;
1780            } else {
1781                # Here we can't trace to a file. Complain about this.
1782                warn "Could not open trace file $traceFileName: $!\n";
1783                # We trace to the standard output if it's
1784                # okay, and the error log otherwise.
1785                if ($textOKFlag) {
1786                    $traceMode = "TEXT";
1787                } else {
1788                    $traceMode = "WARN";
1789                }
1790            }
1791            # Now set up the tracing.
1792            TSetup("$traceLevel $cats", $traceMode);
1793        }
1794        # Check for the "help" option. If it is specified, dump the command-line
1795        # options and exit the program.
1796        if ($retOptions->{help}) {
1797            $0 =~ m#[/\\](\w+)(\.pl)?$#i;
1798            print "$1 [options] $parmHelp\n";
1799            for my $key (sort keys %{$options}) {
1800                my $name = Pad($key, $longestName, 0, ' ');
1801                my $desc = $options->{$key}->[1];
1802                if ($options->{$key}->[0]) {
1803                    $desc .= " (default " . $options->{$key}->[0] . ")";
1804                }
1805                print "  $name $desc\n";
1806            }
1807            exit(0);
1808        }
1809        # Trace the options, if applicable.
1810        if (T(3)) {
1811            my @parms = grep { $retOptions->{$_} } keys %{$retOptions};
1812            Trace("Selected options: " . join(", ", sort @parms) . ".");
1813        }
1814        # Return the parsed parameters.
1815        return ($retOptions, @retParameters);
1816    }
1817    
1818    =head3 ReadOptions
1819    
1820        my %options = Tracer::ReadOptions($fileName);
1821    
1822    Read a set of options from a file. Each option is encoded in a line of text that has the
1823    format
1824    
1825    I<optionName>C<=>I<optionValue>C<; >I<comment>
1826    
1827    The option name must consist entirely of letters, digits, and the punctuation characters
1828    C<.> and C<_>, and is case sensitive. Blank lines and lines in which the first nonblank
1829    character is a semi-colon will be ignored. The return hash will map each option name to
1830    the corresponding option value.
1831    
1832    =over 4
1833    
1834    =item fileName
1835    
1836    Name of the file containing the option data.
1837    
1838    =item RETURN
1839    
1840    Returns a hash mapping the option names specified in the file to their corresponding option
1841    value.
1842    
1843    =back
1844    
1845    =cut
1846    
1847    sub ReadOptions {
1848        # Get the parameters.
1849        my ($fileName) = @_;
1850        # Open the file.
1851        (open CONFIGFILE, "<$fileName") || Confess("Could not open option file $fileName.");
1852        # Count the number of records read.
1853        my ($records, $comments) = 0;
1854        # Create the return hash.
1855        my %retVal = ();
1856        # Loop through the file, accumulating key-value pairs.
1857        while (my $line = <CONFIGFILE>) {
1858            # Denote we've read a line.
1859            $records++;
1860            # Determine the line type.
1861            if ($line =~ /^\s*[\n\r]/) {
1862                # A blank line is a comment.
1863                $comments++;
1864            } elsif ($line =~ /^\s*([A-Za-z0-9_\.]+)=([^;]*);/) {
1865                # Here we have an option assignment.
1866                retVal{$1} = $2;
1867            } elsif ($line =~ /^\s*;/) {
1868                # Here we have a text comment.
1869                $comments++;
1870            } else {
1871                # Here we have an invalid line.
1872                Trace("Invalid option statement in record $records.") if T(0);
1873            }
1874        }
1875        # Return the hash created.
1876        return %retVal;
1877    }
1878    
1879    =head3 GetOptions
1880    
1881        Tracer::GetOptions(\%defaults, \%options);
1882    
1883    Merge a specified set of options into a table of defaults. This method takes two hash references
1884    as input and uses the data from the second to update the first. If the second does not exist,
1885    there will be no effect. An error will be thrown if one of the entries in the second hash does not
1886    exist in the first.
1887    
1888    Consider the following example.
1889    
1890        my $optionTable = GetOptions({ dbType => 'mySQL', trace => 0 }, $options);
1891    
1892    In this example, the variable B<$options> is expected to contain at most two options-- B<dbType> and
1893    B<trace>. The default database type is C<mySQL> and the default trace level is C<0>. If the value of
1894    B<$options> is C<< {dbType => 'Oracle'} >>, then the database type will be changed to C<Oracle> and
1895    the trace level will remain at 0. If B<$options> is undefined, then the database type and trace level
1896    will remain C<mySQL> and C<0>. If, on the other hand, B<$options> is defined as
1897    
1898        {databaseType => 'Oracle'}
1899    
1900    an error will occur because the B<databaseType> option does not exist.
1901    
1902    =over 4
1903    
1904    =item defaults
1905    
1906    Table of default option values.
1907    
1908    =item options
1909    
1910    Table of overrides, if any.
1911    
1912    =item RETURN
1913    
1914    Returns a reference to the default table passed in as the first parameter.
1915    
1916    =back
1917    
1918    =cut
1919    
1920    sub GetOptions {
1921        # Get the parameters.
1922        my ($defaults, $options) = @_;
1923        # Check for overrides.
1924        if ($options) {
1925            # Loop through the overrides.
1926            while (my ($option, $setting) = each %{$options}) {
1927                # Insure this override exists.
1928                if (!exists $defaults->{$option}) {
1929                    croak "Unrecognized option $option encountered.";
1930                } else {
1931                    # Apply the override.
1932                    $defaults->{$option} = $setting;
1933                }
1934            }
1935        }
1936        # Return the merged table.
1937        return $defaults;
1938    }
1939    
1940    =head3 MergeOptions
1941    
1942        Tracer::MergeOptions(\%table, \%defaults);
1943    
1944    Merge default values into a hash table. This method looks at the key-value pairs in the
1945    second (default) hash, and if a matching key is not found in the first hash, the default
1946    pair is copied in. The process is similar to L</GetOptions>, but there is no error-
1947    checking and no return value.
1948    
1949    =over 4
1950    
1951    =item table
1952    
1953    Hash table to be updated with the default values.
1954    
1955    =item defaults
1956    
1957    Default values to be merged into the first hash table if they are not already present.
1958    
1959    =back
1960    
1961    =cut
1962    
1963    sub MergeOptions {
1964        # Get the parameters.
1965        my ($table, $defaults) = @_;
1966        # Loop through the defaults.
1967        while (my ($key, $value) = each %{$defaults}) {
1968            if (!exists $table->{$key}) {
1969                $table->{$key} = $value;
1970            }
1971        }
1972    }
1973    
1974    =head3 ParseCommand
1975    
1976        my ($options, @arguments) = Tracer::ParseCommand(\%optionTable, @inputList);
1977    
1978    Parse a command line consisting of a list of parameters. The initial parameters may be option
1979    specifiers of the form C<->I<option> or C<->I<option>C<=>I<value>. The options are stripped
1980    off and merged into a table of default options. The remainder of the command line is
1981    returned as a list of positional arguments. For example, consider the following invocation.
1982    
1983        my ($options, @arguments) = ParseCommand({ errors => 0, logFile => 'trace.log'}, @words);
1984    
1985    In this case, the list @words will be treated as a command line and there are two options available,
1986    B<errors> and B<logFile>. If @words has the following format
1987    
1988        -logFile=error.log apple orange rutabaga
1989    
1990    then at the end of the invocation, C<$options> will be
1991    
1992        { errors => 0, logFile => 'error.log' }
1993    
1994    and C<@arguments> will contain
1995    
1996        apple orange rutabaga
1997    
1998    The parser allows for some escape sequences. See L</UnEscape> for a description. There is no
1999    support for quote characters. Options can be specified with single or double hyphens.
2000    
2001    =over 4
2002    
2003    =item optionTable
2004    
2005    Table of default options.
2006    
2007    =item inputList
2008    
2009    List of words on the command line.
2010    
2011    =item RETURN
2012    
2013    Returns a reference to the option table and a list of the positional arguments.
2014    
2015    =back
2016    
2017    =cut
2018    
2019    sub ParseCommand {
2020        # Get the parameters.
2021        my ($optionTable, @inputList) = @_;
2022        # Process any options in the input list.
2023          my %overrides = ();          my %overrides = ();
2024          while ((@inputList > 0) && ($inputList[0] =~ /^-/)) {      while ((@inputList > 0) && ($inputList[0] =~ /^--?/)) {
2025                  # Get the current option.                  # Get the current option.
2026                  my $arg = shift @inputList;                  my $arg = shift @inputList;
2027                  # Pull out the option name.                  # Pull out the option name.
2028                  $arg =~ /^-([^=]*)/g;          $arg =~ /^--?([^=]*)/g;
2029                  my $name = $1;                  my $name = $1;
2030                  # Check for an option value.                  # Check for an option value.
2031                  if ($arg =~ /\G=(.*)$/g) {                  if ($arg =~ /\G=(.*)$/g) {
2032                          # Here we have a value for the option.                          # Here we have a value for the option.
2033                          $overrides{$name} = UnEscape($1);                          $overrides{$name} = UnEscape($1);
2034                  } else {                  } else {
2035                          # Here there is no value, so we use 1.              # Here there is no value, so we use 1.
2036                          $overrides{$name} = 1;              $overrides{$name} = 1;
2037            }
2038        }
2039        # Merge the options into the defaults.
2040        GetOptions($optionTable, \%overrides);
2041        # Translate the remaining parameters.
2042        my @retVal = ();
2043        for my $inputParm (@inputList) {
2044            push @retVal, UnEscape($inputParm);
2045        }
2046        # Return the results.
2047        return ($optionTable, @retVal);
2048    }
2049    
2050    
2051    =head2 File Utility Methods
2052    
2053    =head3 GetFile
2054    
2055        my @fileContents = Tracer::GetFile($fileName);
2056    
2057        or
2058    
2059        my $fileContents = Tracer::GetFile($fileName);
2060    
2061    Return the entire contents of a file. In list context, line-ends are removed and
2062    each line is a list element. In scalar context, line-ends are replaced by C<\n>.
2063    
2064    =over 4
2065    
2066    =item fileName
2067    
2068    Name of the file to read.
2069    
2070    =item RETURN
2071    
2072    In a list context, returns the entire file as a list with the line terminators removed.
2073    In a scalar context, returns the entire file as a string. If an error occurs opening
2074    the file, an empty list will be returned.
2075    
2076    =back
2077    
2078    =cut
2079    
2080    sub GetFile {
2081        # Get the parameters.
2082        my ($fileName) = @_;
2083        # Declare the return variable.
2084        my @retVal = ();
2085        # Open the file for input.
2086        my $handle = Open(undef, "<$fileName");
2087        # Read the whole file into the return variable, stripping off any terminator
2088        # characters.
2089        my $lineCount = 0;
2090        while (my $line = <$handle>) {
2091            $lineCount++;
2092            $line = Strip($line);
2093            push @retVal, $line;
2094        }
2095        # Close it.
2096        close $handle;
2097        my $actualLines = @retVal;
2098        Trace("$actualLines lines read from file $fileName.") if T(File => 2);
2099        # Return the file's contents in the desired format.
2100        if (wantarray) {
2101            return @retVal;
2102        } else {
2103            return join "\n", @retVal;
2104        }
2105    }
2106    
2107    =head3 PutFile
2108    
2109        Tracer::PutFile($fileName, \@lines);
2110    
2111    Write out a file from a list of lines of text.
2112    
2113    =over 4
2114    
2115    =item fileName
2116    
2117    Name of the output file.
2118    
2119    =item lines
2120    
2121    Reference to a list of text lines. The lines will be written to the file in order, with trailing
2122    new-line characters. Alternatively, may be a string, in which case the string will be written without
2123    modification.
2124    
2125    =back
2126    
2127    =cut
2128    
2129    sub PutFile {
2130        # Get the parameters.
2131        my ($fileName, $lines) = @_;
2132        # Open the output file.
2133        my $handle = Open(undef, ">$fileName");
2134        # Count the lines written.
2135        if (ref $lines ne 'ARRAY') {
2136            # Here we have a scalar, so we write it raw.
2137            print $handle $lines;
2138            Trace("Scalar put to file $fileName.") if T(File => 3);
2139        } else {
2140            # Write the lines one at a time.
2141            my $count = 0;
2142            for my $line (@{$lines}) {
2143                print $handle "$line\n";
2144                $count++;
2145            }
2146            Trace("$count lines put to file $fileName.") if T(File => 3);
2147        }
2148        # Close the output file.
2149        close $handle;
2150    }
2151    
2152    =head3 ParseRecord
2153    
2154        my @fields = Tracer::ParseRecord($line);
2155    
2156    Parse a tab-delimited data line. The data line is split into field values. Embedded tab
2157    and new-line characters in the data line must be represented as C<\t> and C<\n>, respectively.
2158    These will automatically be converted.
2159    
2160    =over 4
2161    
2162    =item line
2163    
2164    Line of data containing the tab-delimited fields.
2165    
2166    =item RETURN
2167    
2168    Returns a list of the fields found in the data line.
2169    
2170    =back
2171    
2172    =cut
2173    
2174    sub ParseRecord {
2175        # Get the parameter.
2176        my ($line) = @_;
2177        # Remove the trailing new-line, if any.
2178        chomp $line;
2179        # Split the line read into pieces using the tab character.
2180        my @retVal = split /\t/, $line;
2181        # Trim and fix the escapes in each piece.
2182        for my $value (@retVal) {
2183            # Trim leading whitespace.
2184            $value =~ s/^\s+//;
2185            # Trim trailing whitespace.
2186            $value =~ s/\s+$//;
2187            # Delete the carriage returns.
2188            $value =~ s/\r//g;
2189            # Convert the escapes into their real values.
2190            $value =~ s/\\t/"\t"/ge;
2191            $value =~ s/\\n/"\n"/ge;
2192        }
2193        # Return the result.
2194        return @retVal;
2195    }
2196    
2197    =head3 Merge
2198    
2199        my @mergedList = Tracer::Merge(@inputList);
2200    
2201    Sort a list of strings and remove duplicates.
2202    
2203    =over 4
2204    
2205    =item inputList
2206    
2207    List of scalars to sort and merge.
2208    
2209    =item RETURN
2210    
2211    Returns a list containing the same elements sorted in ascending order with duplicates
2212    removed.
2213    
2214    =back
2215    
2216    =cut
2217    
2218    sub Merge {
2219        # Get the input list in sort order.
2220        my @inputList = sort @_;
2221        # Only proceed if the list has at least two elements.
2222        if (@inputList > 1) {
2223            # Now we want to move through the list splicing out duplicates.
2224            my $i = 0;
2225            while ($i < @inputList) {
2226                # Get the current entry.
2227                my $thisEntry = $inputList[$i];
2228                # Find out how many elements duplicate the current entry.
2229                my $j = $i + 1;
2230                my $dup1 = $i + 1;
2231                while ($j < @inputList && $inputList[$j] eq $thisEntry) { $j++; };
2232                # If the number is nonzero, splice out the duplicates found.
2233                if ($j > $dup1) {
2234                    splice @inputList, $dup1, $j - $dup1;
2235                }
2236                # Now the element at position $dup1 is different from the element before it
2237                # at position $i. We push $i forward one position and start again.
2238                $i++;
2239            }
2240        }
2241        # Return the merged list.
2242        return @inputList;
2243    }
2244    
2245    =head3 Open
2246    
2247        my $handle = Open($fileHandle, $fileSpec, $message);
2248    
2249    Open a file.
2250    
2251    The I<$fileSpec> is essentially the second argument of the PERL C<open>
2252    function. The mode is specified using Unix-like shell information. So, for
2253    example,
2254    
2255        Open(\*LOGFILE, '>>/usr/spool/news/twitlog', "Could not open twit log.");
2256    
2257    would open for output appended to the specified file, and
2258    
2259        Open(\*DATASTREAM, "| sort -u >$outputFile", "Could not open $outputFile.");
2260    
2261    would open a pipe that sorts the records written and removes duplicates. Note
2262    the use of file handle syntax in the Open call. To use anonymous file handles,
2263    code as follows.
2264    
2265        my $logFile = Open(undef, '>>/usr/spool/news/twitlog', "Could not open twit log.");
2266    
2267    The I<$message> parameter is used if the open fails. If it is set to C<0>, then
2268    the open returns TRUE if successful and FALSE if an error occurred. Otherwise, a
2269    failed open will throw an exception and the third parameter will be used to construct
2270    an error message. If the parameter is omitted, a standard message is constructed
2271    using the file spec.
2272    
2273        Could not open "/usr/spool/news/twitlog"
2274    
2275    Note that the mode characters are automatically cleaned from the file name.
2276    The actual error message from the file system will be captured and appended to the
2277    message in any case.
2278    
2279        Could not open "/usr/spool/news/twitlog": file not found.
2280    
2281    In some versions of PERL the only error message we get is a number, which
2282    corresponds to the C++ C<errno> value.
2283    
2284        Could not open "/usr/spool/news/twitlog": 6.
2285    
2286    =over 4
2287    
2288    =item fileHandle
2289    
2290    File handle. If this parameter is C<undef>, a file handle will be generated
2291    and returned as the value of this method.
2292    
2293    =item fileSpec
2294    
2295    File name and mode, as per the PERL C<open> function.
2296    
2297    =item message (optional)
2298    
2299    Error message to use if the open fails. If omitted, a standard error message
2300    will be generated. In either case, the error information from the file system
2301    is appended to the message. To specify a conditional open that does not throw
2302    an error if it fails, use C<0>.
2303    
2304    =item RETURN
2305    
2306    Returns the name of the file handle assigned to the file, or C<undef> if the
2307    open failed.
2308    
2309    =back
2310    
2311    =cut
2312    
2313    sub Open {
2314        # Get the parameters.
2315        my ($fileHandle, $fileSpec, $message) = @_;
2316        # Attempt to open the file.
2317        my $rv = open $fileHandle, $fileSpec;
2318        # If the open failed, generate an error message.
2319        if (! $rv) {
2320            # Save the system error message.
2321            my $sysMessage = $!;
2322            # See if we need a default message.
2323            if (!$message) {
2324                # Clean any obvious mode characters and leading spaces from the
2325                # filename.
2326                my ($fileName) = FindNamePart($fileSpec);
2327                $message = "Could not open \"$fileName\"";
2328            }
2329            # Terminate with an error using the supplied message and the
2330            # error message from the file system.
2331            Confess("$message: $!");
2332        }
2333        # Return the file handle.
2334        return $fileHandle;
2335    }
2336    
2337    =head3 FindNamePart
2338    
2339        my ($fileName, $start, $len) = Tracer::FindNamePart($fileSpec);
2340    
2341    Extract the portion of a file specification that contains the file name.
2342    
2343    A file specification is the string passed to an C<open> call. It specifies the file
2344    mode and name. In a truly complex situation, it can specify a pipe sequence. This
2345    method assumes that the file name is whatever follows the first angle bracket
2346    sequence.  So, for example, in the following strings the file name is
2347    C</usr/fig/myfile.txt>.
2348    
2349        >>/usr/fig/myfile.txt
2350        </usr/fig/myfile.txt
2351        | sort -u > /usr/fig/myfile.txt
2352    
2353    If the method cannot find a file name using its normal methods, it will return the
2354    whole incoming string.
2355    
2356    =over 4
2357    
2358    =item fileSpec
2359    
2360    File specification string from which the file name is to be extracted.
2361    
2362    =item RETURN
2363    
2364    Returns a three-element list. The first element contains the file name portion of
2365    the specified string, or the whole string if a file name cannot be found via normal
2366    methods. The second element contains the start position of the file name portion and
2367    the third element contains the length.
2368    
2369    =back
2370    
2371    =cut
2372    #: Return Type $;
2373    sub FindNamePart {
2374        # Get the parameters.
2375        my ($fileSpec) = @_;
2376        # Default to the whole input string.
2377        my ($retVal, $pos, $len) = ($fileSpec, 0, length $fileSpec);
2378        # Parse out the file name if we can.
2379        if ($fileSpec =~ m/(<|>>?)(.+?)(\s*)$/) {
2380            $retVal = $2;
2381            $len = length $retVal;
2382            $pos = (length $fileSpec) - (length $3) - $len;
2383        }
2384        # Return the result.
2385        return ($retVal, $pos, $len);
2386    }
2387    
2388    =head3 OpenDir
2389    
2390        my @files = OpenDir($dirName, $filtered, $flag);
2391    
2392    Open a directory and return all the file names. This function essentially performs
2393    the functions of an C<opendir> and C<readdir>. If the I<$filtered> parameter is
2394    set to TRUE, all filenames beginning with a period (C<.>), dollar sign (C<$>),
2395    or pound sign (C<#>) and all filenames ending with a tilde C<~>) will be
2396    filtered out of the return list. If the directory does not open and I<$flag> is not
2397    set, an exception is thrown. So, for example,
2398    
2399        my @files = OpenDir("/Volumes/fig/contigs", 1);
2400    
2401    is effectively the same as
2402    
2403        opendir(TMP, "/Volumes/fig/contigs") || Confess("Could not open /Volumes/fig/contigs.");
2404        my @files = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir(TMP);
2405    
2406    Similarly, the following code
2407    
2408        my @files = grep { $_ =~ /^\d/ } OpenDir("/Volumes/fig/orgs", 0, 1);
2409    
2410    Returns the names of all files in C</Volumes/fig/orgs> that begin with digits and
2411    automatically returns an empty list if the directory fails to open.
2412    
2413    =over 4
2414    
2415    =item dirName
2416    
2417    Name of the directory to open.
2418    
2419    =item filtered
2420    
2421    TRUE if files whose names begin with a period (C<.>) should be automatically removed
2422    from the list, else FALSE.
2423    
2424    =item flag
2425    
2426    TRUE if a failure to open is okay, else FALSE
2427    
2428    =back
2429    
2430    =cut
2431    #: Return Type @;
2432    sub OpenDir {
2433        # Get the parameters.
2434        my ($dirName, $filtered, $flag) = @_;
2435        # Declare the return variable.
2436        my @retVal = ();
2437        # Open the directory.
2438        if (opendir(my $dirHandle, $dirName)) {
2439            # The directory opened successfully. Get the appropriate list according to the
2440            # strictures of the filter parameter.
2441            if ($filtered) {
2442                @retVal = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir $dirHandle;
2443            } else {
2444                @retVal = readdir $dirHandle;
2445            }
2446        } elsif (! $flag) {
2447            # Here the directory would not open and it's considered an error.
2448            Confess("Could not open directory $dirName.");
2449        }
2450        # Return the result.
2451        return @retVal;
2452    }
2453    
2454    
2455    =head3 Insure
2456    
2457        Insure($dirName, $chmod);
2458    
2459    Insure a directory is present.
2460    
2461    =over 4
2462    
2463    =item dirName
2464    
2465    Name of the directory to check. If it does not exist, it will be created.
2466    
2467    =item chmod (optional)
2468    
2469    Security privileges to be given to the directory if it is created.
2470    
2471    =back
2472    
2473    =cut
2474    
2475    sub Insure {
2476        my ($dirName, $chmod) = @_;
2477        if (! -d $dirName) {
2478            Trace("Creating $dirName directory.") if T(2);
2479            eval {
2480                mkpath $dirName;
2481                # If we have permissions specified, set them here.
2482                if (defined($chmod)) {
2483                    chmod $chmod, $dirName;
2484                }
2485            };
2486            if ($@) {
2487                Confess("Error creating $dirName: $@");
2488            }
2489        }
2490    }
2491    
2492    =head3 ChDir
2493    
2494        ChDir($dirName);
2495    
2496    Change to the specified directory.
2497    
2498    =over 4
2499    
2500    =item dirName
2501    
2502    Name of the directory to which we want to change.
2503    
2504    =back
2505    
2506    =cut
2507    
2508    sub ChDir {
2509        my ($dirName) = @_;
2510        if (! -d $dirName) {
2511            Confess("Cannot change to directory $dirName: no such directory.");
2512        } else {
2513            Trace("Changing to directory $dirName.") if T(File => 4);
2514            my $okFlag = chdir $dirName;
2515            if (! $okFlag) {
2516                Confess("Error switching to directory $dirName.");
2517            }
2518        }
2519    }
2520    
2521    =head3 SetPermissions
2522    
2523        Tracer::SetPermissions($dirName, $group, $mask, %otherMasks);
2524    
2525    Set the permissions for a directory and all the files and folders inside it.
2526    In addition, the group ownership will be changed to the specified value.
2527    
2528    This method is more vulnerable than most to permission and compatability
2529    problems, so it does internal error recovery.
2530    
2531    =over 4
2532    
2533    =item dirName
2534    
2535    Name of the directory to process.
2536    
2537    =item group
2538    
2539    Name of the group to be assigned.
2540    
2541    =item mask
2542    
2543    Permission mask. Bits that are C<1> in this mask will be ORed into the
2544    permission bits of any file or directory that does not already have them
2545    set to 1.
2546    
2547    =item otherMasks
2548    
2549    Map of search patterns to permission masks. If a directory name matches
2550    one of the patterns, that directory and all its members and subdirectories
2551    will be assigned the new pattern. For example, the following would
2552    assign 01664 to most files, but would use 01777 for directories named C<tmp>.
2553    
2554        Tracer::SetPermissions($dirName, 'fig', 01664, '^tmp$' => 01777);
2555    
2556    The list is ordered, so the following would use 0777 for C<tmp1> and
2557    0666 for C<tmp>, C<tmp2>, or C<tmp3>.
2558    
2559        Tracer::SetPermissions($dirName, 'fig', 01664, '^tmp1' => 0777,
2560                                                       '^tmp' => 0666);
2561    
2562    Note that the pattern matches are all case-insensitive, and only directory
2563    names are matched, not file names.
2564    
2565    =back
2566    
2567    =cut
2568    
2569    sub SetPermissions {
2570        # Get the parameters.
2571        my ($dirName, $group, $mask, @otherMasks) = @_;
2572        # Set up for error recovery.
2573        eval {
2574            # Switch to the specified directory.
2575            ChDir($dirName);
2576            # Get the group ID.
2577            my $gid = getgrnam($group);
2578            # Get the mask for tracing.
2579            my $traceMask = sprintf("%04o", $mask) . "($mask)";
2580            Trace("Fixing permissions for directory $dirName using group $group($gid) and mask $traceMask.") if T(File => 2);
2581            my $fixCount = 0;
2582            my $lookCount = 0;
2583            # @dirs will be a stack of directories to be processed.
2584            my @dirs = (getcwd());
2585            while (scalar(@dirs) > 0) {
2586                # Get the current directory.
2587                my $dir = pop @dirs;
2588                # Check for a match to one of the specified directory names. To do
2589                # that, we need to pull the individual part of the name off of the
2590                # whole path.
2591                my $simpleName = $dir;
2592                if ($dir =~ m!/([^/]+)$!) {
2593                    $simpleName = $1;
2594                }
2595                Trace("Simple directory name for $dir is $simpleName.") if T(File => 4);
2596                # Search for a match.
2597                my $match = 0;
2598                my $i;
2599                for ($i = 0; $i < $#otherMasks && ! $match; $i += 2) {
2600                    my $pattern = $otherMasks[$i];
2601                    if ($simpleName =~ /$pattern/i) {
2602                        $match = 1;
2603                    }
2604                }
2605                # Check for a match. Note we use $i-1 because the loop added 2
2606                # before terminating due to the match.
2607                if ($match && $otherMasks[$i-1] != $mask) {
2608                    # This directory matches one of the incoming patterns, and it's
2609                    # a different mask, so we process it recursively with that mask.
2610                    SetPermissions($dir, $group, $otherMasks[$i-1], @otherMasks);
2611                } else {
2612                    # Here we can process normally. Get all of the non-hidden members.
2613                    my @submems = OpenDir($dir, 1);
2614                    for my $submem (@submems) {
2615                        # Get the full name.
2616                        my $thisMem = "$dir/$submem";
2617                        Trace("Checking member $thisMem.") if T(4);
2618                        $lookCount++;
2619                        if ($lookCount % 1000 == 0) {
2620                            Trace("$lookCount members examined. Current is $thisMem. Mask is $traceMask") if T(File => 3);
2621                        }
2622                        # Fix the group.
2623                        chown -1, $gid, $thisMem;
2624                        # Insure this member is not a symlink.
2625                        if (! -l $thisMem) {
2626                            # Get its info.
2627                            my $fileInfo = stat $thisMem;
2628                            # Only proceed if we got the info. Otherwise, it's a hard link
2629                            # and we want to skip it anyway.
2630                            if ($fileInfo) {
2631                                my $fileMode = $fileInfo->mode;
2632                                if (($fileMode & $mask) != $mask) {
2633                                    # Fix this member.
2634                                    $fileMode |= $mask;
2635                                    chmod $fileMode, $thisMem;
2636                                    $fixCount++;
2637                                }
2638                                # If it's a subdirectory, stack it.
2639                                if (-d $thisMem) {
2640                                    push @dirs, $thisMem;
2641                                }
2642                            }
2643                        }
2644                    }
2645                }
2646            }
2647            Trace("$lookCount files and directories processed, $fixCount fixed.") if T(File => 2);
2648        };
2649        # Check for an error.
2650        if ($@) {
2651            Confess("SetPermissions error: $@");
2652                  }                  }
2653          }          }
2654          # Merge the options into the defaults.  
2655          GetOptions($optionTable, \%overrides);  =head3 GetLine
2656          # Translate the remaining parameters.  
2657        my @data = Tracer::GetLine($handle);
2658    
2659    Read a line of data from a tab-delimited file.
2660    
2661    =over 4
2662    
2663    =item handle
2664    
2665    Open file handle from which to read.
2666    
2667    =item RETURN
2668    
2669    Returns a list of the fields in the record read. The fields are presumed to be
2670    tab-delimited. If we are at the end of the file, then an empty list will be
2671    returned. If an empty line is read, a single list item consisting of a null
2672    string will be returned.
2673    
2674    =back
2675    
2676    =cut
2677    
2678    sub GetLine {
2679        # Get the parameters.
2680        my ($handle) = @_;
2681        # Declare the return variable.
2682          my @retVal = ();          my @retVal = ();
2683          for my $inputParm (@inputList) {      Trace("File position is " . tell($handle) . ". EOF flag is " . eof($handle) . ".") if T(File => 4);
2684                  push @retVal, UnEscape($inputParm);      # Read from the file.
2685        my $line = <$handle>;
2686        # Only proceed if we found something.
2687        if (defined $line) {
2688            # Remove the new-line. We are a bit over-cautious here because the file may be coming in via an
2689            # upload control and have a nonstandard EOL combination.
2690            $line =~ s/(\r|\n)+$//;
2691            # Here we do some fancy tracing to help in debugging complicated EOL marks.
2692            if (T(File => 4)) {
2693                my $escapedLine = $line;
2694                $escapedLine =~ s/\n/\\n/g;
2695                $escapedLine =~ s/\r/\\r/g;
2696                $escapedLine =~ s/\t/\\t/g;
2697                Trace("Line read: -->$escapedLine<--");
2698            }
2699            # If the line is empty, return a single empty string; otherwise, parse
2700            # it into fields.
2701            if ($line eq "") {
2702                push @retVal, "";
2703            } else {
2704                push @retVal, split /\t/,$line;
2705          }          }
2706          # Return the results.      } else {
2707          return ($optionTable, @retVal);          # Trace the reason the read failed.
2708            Trace("End of file: $!") if T(File => 3);
2709        }
2710        # Return the result.
2711        return @retVal;
2712    }
2713    
2714    =head3 PutLine
2715    
2716        Tracer::PutLine($handle, \@fields, $eol);
2717    
2718    Write a line of data to a tab-delimited file. The specified field values will be
2719    output in tab-separated form, with a trailing new-line.
2720    
2721    =over 4
2722    
2723    =item handle
2724    
2725    Output file handle.
2726    
2727    =item fields
2728    
2729    List of field values.
2730    
2731    =item eol (optional)
2732    
2733    End-of-line character (default is "\n").
2734    
2735    =back
2736    
2737    =cut
2738    
2739    sub PutLine {
2740        # Get the parameters.
2741        my ($handle, $fields, $eol) = @_;
2742        # Write the data.
2743        print $handle join("\t", @{$fields}) . ($eol || "\n");
2744    }
2745    
2746    
2747    =head3 PrintLine
2748    
2749        Tracer::PrintLine($line);
2750    
2751    Print a line of text with a trailing new-line.
2752    
2753    =over 4
2754    
2755    =item line
2756    
2757    Line of text to print.
2758    
2759    =back
2760    
2761    =cut
2762    
2763    sub PrintLine {
2764        # Get the parameters.
2765        my ($line) = @_;
2766        # Print the line.
2767        print "$line\n";
2768    }
2769    
2770    
2771    =head2 Other Useful Methods
2772    
2773    =head3 ParseParm
2774    
2775        my $listValue = Tracer::ParseParm($string);
2776    
2777    Convert a parameter into a list reference. If the parameter is undefined,
2778    an undefined value will be returned. Otherwise, it will be parsed as a
2779    comma-separated list of values.
2780    
2781    =over 4
2782    
2783    =item string
2784    
2785    Incoming string.
2786    
2787    =item RETURN
2788    
2789    Returns a reference to a list of values, or C<undef> if the incoming value
2790    was undefined.
2791    
2792    =back
2793    
2794    =cut
2795    
2796    sub ParseParm {
2797        # Get the parameters.
2798        my ($string) = @_;
2799        # Declare the return variable.
2800        my $retVal;
2801        # Check for data.
2802        if (defined $string) {
2803            # We have some, so split it into a list.
2804            $retVal = [ split /\s*,\s*/, $string];
2805        }
2806        # Return the result.
2807        return $retVal;
2808    }
2809    
2810    =head3 Now
2811    
2812        my $string = Tracer::Now();
2813    
2814    Return a displayable time stamp containing the local time. Whatever format this
2815    method produces must be parseable by L</ParseDate>.
2816    
2817    =cut
2818    
2819    sub Now {
2820        return DisplayTime(time);
2821    }
2822    
2823    =head3 DisplayTime
2824    
2825        my $string = Tracer::DisplayTime($time);
2826    
2827    Convert a time value to a displayable time stamp. Whatever format this
2828    method produces must be parseable by L</ParseDate>.
2829    
2830    =over 4
2831    
2832    =item time
2833    
2834    Time to display, in seconds since the epoch, or C<undef> if the time is unknown.
2835    
2836    =item RETURN
2837    
2838    Returns a displayable time, or C<(n/a)> if the incoming time is undefined.
2839    
2840    =back
2841    
2842    =cut
2843    
2844    sub DisplayTime {
2845        my ($time) = @_;
2846        my $retVal = "(n/a)";
2847        if (defined $time) {
2848            my ($sec,$min,$hour,$mday,$mon,$year,$wday,$yday,$isdst) = localtime($time);
2849            $retVal = _p2($mon+1) . "/" . _p2($mday) . "/" . ($year + 1900) . " " .
2850                      _p2($hour) . ":" . _p2($min) . ":" . _p2($sec);
2851        }
2852        return $retVal;
2853    }
2854    
2855    # Pad a number to 2 digits.
2856    sub _p2 {
2857        my ($value) = @_;
2858        $value = "0$value" if ($value < 10);
2859        return $value;
2860    }
2861    
2862    =head3 Escape
2863    
2864        my $codedString = Tracer::Escape($realString);
2865    
2866    Escape a string for use in a command. Tabs will be replaced by C<\t>, new-lines
2867    replaced by C<\n>, carriage returns will be deleted, and backslashes will be doubled. The
2868    result is to reverse the effect of L</UnEscape>.
2869    
2870    =over 4
2871    
2872    =item realString
2873    
2874    String to escape.
2875    
2876    =item RETURN
2877    
2878    Escaped equivalent of the real string.
2879    
2880    =back
2881    
2882    =cut
2883    
2884    sub Escape {
2885        # Get the parameter.
2886        my ($realString) = @_;
2887        # Initialize the return variable.
2888        my $retVal = "";
2889        # Loop through the parameter string, looking for sequences to escape.
2890        while (length $realString > 0) {
2891            # Look for the first sequence to escape.
2892            if ($realString =~ /^(.*?)([\n\t\r\\])/) {
2893                # Here we found it. The text preceding the sequence is in $1. The sequence
2894                # itself is in $2. First, move the clear text to the return variable.
2895                $retVal .= $1;
2896                # Strip the processed section off the real string.
2897                $realString = substr $realString, (length $2) + (length $1);
2898                # Get the matched character.
2899                my $char = $2;
2900                # If we have a CR, we are done.
2901                if ($char ne "\r") {
2902                    # It's not a CR, so encode the escape sequence.
2903                    $char =~ tr/\t\n/tn/;
2904                    $retVal .= "\\" . $char;
2905                }
2906            } else {
2907                # Here there are no more escape sequences. The rest of the string is
2908                # transferred unmodified.
2909                $retVal .= $realString;
2910                $realString = "";
2911            }
2912        }
2913        # Return the result.
2914        return $retVal;
2915  }  }
2916    
2917  =head3 UnEscape  =head3 UnEscape
2918    
2919  C<< my $realString = Tracer::UnEscape($codedString); >>      my $realString = Tracer::UnEscape($codedString);
2920    
2921  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
2922  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
2923    be deleted.
2924    
2925  =over 4  =over 4
2926    
# Line 555  Line 2942 
2942          my ($codedString) = @_;          my ($codedString) = @_;
2943          # Initialize the return variable.          # Initialize the return variable.
2944          my $retVal = "";          my $retVal = "";
2945        # Only proceed if the incoming string is nonempty.
2946        if (defined $codedString) {
2947          # 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
2948          # translating because it causes problems with the escaped slash. ("\\b" becomes          # translating because it causes problems with the escaped slash. ("\\t" becomes
2949          # "\ " no matter what we do.)          # "\<tab>" no matter what we do.)
2950          while (length $codedString > 0) {          while (length $codedString > 0) {
2951                  # Look for the first escape sequence.                  # Look for the first escape sequence.
2952                  if ($codedString =~ /^(.*?)\\(\\|b|n|t)/) {              if ($codedString =~ /^(.*?)\\(\\|n|t|r)/) {
2953                          # 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
2954                          # 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.
2955                          $retVal .= $1;                          $retVal .= $1;
2956                          $codedString = substr $codedString, (2 + length $1);                          $codedString = substr $codedString, (2 + length $1);
2957                          # Decode the escape sequence.                  # Get the escape value.
2958                          my $char = $2;                          my $char = $2;
2959                          $char =~ tr/\\btn/\\ \t\n/;                  # If we have a "\r", we are done.
2960                    if ($char ne 'r') {
2961                        # Here it's not an 'r', so we convert it.
2962                        $char =~ tr/\\tn/\\\t\n/;
2963                          $retVal .= $char;                          $retVal .= $char;
2964                    }
2965                  } else {                  } else {
2966                          # 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
2967                          # transferred unmodified.                          # transferred unmodified.
# Line 576  Line 2969 
2969                          $codedString = "";                          $codedString = "";
2970                  }                  }
2971          }          }
2972          # Return the result.      }
2973        # Return the result.
2974        return $retVal;
2975    }
2976    
2977    =head3 Percent
2978    
2979        my $percent = Tracer::Percent($number, $base);
2980    
2981    Returns the percent of the base represented by the given number. If the base
2982    is zero, returns zero.
2983    
2984    =over 4
2985    
2986    =item number
2987    
2988    Percent numerator.
2989    
2990    =item base
2991    
2992    Percent base.
2993    
2994    =item RETURN
2995    
2996    Returns the percentage of the base represented by the numerator.
2997    
2998    =back
2999    
3000    =cut
3001    
3002    sub Percent {
3003        # Get the parameters.
3004        my ($number, $base) = @_;
3005        # Declare the return variable.
3006        my $retVal = 0;
3007        # Compute the percent.
3008        if ($base != 0) {
3009            $retVal = $number * 100 / $base;
3010        }
3011        # Return the result.
3012        return $retVal;
3013    }
3014    
3015    =head3 Constrain
3016    
3017        my $constrained = Constrain($value, $min, $max);
3018    
3019    Modify a numeric value to bring it to a point in between a maximum and a minimum.
3020    
3021    =over 4
3022    
3023    =item value
3024    
3025    Value to constrain.
3026    
3027    =item min (optional)
3028    
3029    Minimum permissible value. If this parameter is undefined, no minimum constraint will be applied.
3030    
3031    =item max (optional)
3032    
3033    Maximum permissible value. If this parameter is undefined, no maximum constraint will be applied.
3034    
3035    =item RETURN
3036    
3037    Returns the incoming value, constrained according to the other parameters.
3038    
3039    =back
3040    
3041    =cut
3042    
3043    sub Constrain {
3044        # Get the parameters.
3045        my ($value, $min, $max) = @_;
3046        # Declare the return variable.
3047        my $retVal = $value;
3048        # Apply the minimum constraint.
3049        if (defined $min && $retVal < $min) {
3050            $retVal = $min;
3051        }
3052        # Apply the maximum constraint.
3053        if (defined $max && $retVal > $max) {
3054            $retVal = $max;
3055        }
3056        # Return the result.
3057        return $retVal;
3058    }
3059    
3060    =head3 Min
3061    
3062        my $min = Min($value1, $value2, ... $valueN);
3063    
3064    Return the minimum argument. The arguments are treated as numbers.
3065    
3066    =over 4
3067    
3068    =item $value1, $value2, ... $valueN
3069    
3070    List of numbers to compare.
3071    
3072    =item RETURN
3073    
3074    Returns the lowest number in the list.
3075    
3076    =back
3077    
3078    =cut
3079    
3080    sub Min {
3081        # Get the parameters. Note that we prime the return value with the first parameter.
3082        my ($retVal, @values) = @_;
3083        # Loop through the remaining parameters, looking for the lowest.
3084        for my $value (@values) {
3085            if ($value < $retVal) {
3086                $retVal = $value;
3087            }
3088        }
3089        # Return the minimum found.
3090        return $retVal;
3091    }
3092    
3093    =head3 Max
3094    
3095        my $max = Max($value1, $value2, ... $valueN);
3096    
3097    Return the maximum argument. The arguments are treated as numbers.
3098    
3099    =over 4
3100    
3101    =item $value1, $value2, ... $valueN
3102    
3103    List of numbers to compare.
3104    
3105    =item RETURN
3106    
3107    Returns the highest number in the list.
3108    
3109    =back
3110    
3111    =cut
3112    
3113    sub Max {
3114        # Get the parameters. Note that we prime the return value with the first parameter.
3115        my ($retVal, @values) = @_;
3116        # Loop through the remaining parameters, looking for the highest.
3117        for my $value (@values) {
3118            if ($value > $retVal) {
3119                $retVal = $value;
3120            }
3121        }
3122        # Return the maximum found.
3123          return $retVal;          return $retVal;
3124  }  }
3125    
 =head3 ParseRecord  
3126    
3127  C<< my @fields = Tracer::ParseRecord($line); >>  =head3 Strip
3128    
3129  Parse a tab-delimited data line. The data line is split into field values. Embedded tab      my $string = Tracer::Strip($line);
3130  and new-line characters in the data line must be represented as C<\t> and C<\n>, respectively.  
3131  These will automatically be converted.  Strip all line terminators off a string. This is necessary when dealing with files
3132    that may have been transferred back and forth several times among different
3133    operating environments.
3134    
3135  =over 4  =over 4
3136    
3137  =item line  =item line
3138    
3139  Line of data containing the tab-delimited fields.  Line of text to be stripped.
3140    
3141  =item RETURN  =item RETURN
3142    
3143  Returns a list of the fields found in the data line.  The same line of text with all the line-ending characters chopped from the end.
3144    
3145  =back  =back
3146    
3147  =cut  =cut
3148    
3149  sub ParseRecord {  sub Strip {
3150          # Get the parameter.      # Get a copy of the parameter string.
3151          my ($line) = @_;      my ($string) = @_;
3152          # Remove the trailing new-line, if any.      my $retVal = (defined $string ? $string : "");
3153          chomp $line;      # Strip the line terminator characters.
3154          # Split the line read into pieces using the tab character.      $retVal =~ s/(\r|\n)+$//g;
         my @retVal = split /\t/, $line;  
         # Trim and fix the escapes in each piece.  
         for my $value (@retVal) {  
                 # Trim leading whitespace.  
                 $value =~ s/^\s+//;  
                 # Trim trailing whitespace.  
                 $value =~ s/\s+$//;  
                 # Delete the carriage returns.  
                 $value =~ s/\r//g;  
                 # Convert the escapes into their real values.  
                 $value =~ s/\\t/"\t"/ge;  
                 $value =~ s/\\n/"\n"/ge;  
         }  
3155          # Return the result.          # Return the result.
3156          return @retVal;      return $retVal;
3157  }  }
3158    
3159  =head3 Merge  =head3 Pad
3160    
3161  C<< my @mergedList = Tracer::Merge(@inputList); >>      my $paddedString = Tracer::Pad($string, $len, $left, $padChar);
3162    
3163  Sort a list of strings and remove duplicates.  Pad a string to a specified length. The pad character will be a
3164    space, and the padding will be on the right side unless specified
3165    in the third parameter.
3166    
3167  =over 4  =over 4
3168    
3169  =item inputList  =item string
3170    
3171  List of scalars to sort and merge.  String to be padded.
3172    
3173    =item len
3174    
3175    Desired length of the padded string.
3176    
3177    =item left (optional)
3178    
3179    TRUE if the string is to be left-padded; otherwise it will be padded on the right.
3180    
3181    =item padChar (optional)
3182    
3183    Character to use for padding. The default is a space.
3184    
3185  =item RETURN  =item RETURN
3186    
3187  Returns a list containing the same elements sorted in ascending order with duplicates  Returns a copy of the original string with the pad character added to the
3188  removed.  specified end so that it achieves the desired length.
3189    
3190  =back  =back
3191    
3192  =cut  =cut
3193    
3194  sub Merge {  sub Pad {
3195          # Get the input list in sort order.      # Get the parameters.
3196          my @inputList = sort @_;      my ($string, $len, $left, $padChar) = @_;
3197          # Only proceed if the list has at least two elements.      # Compute the padding character.
3198          if (@inputList > 1) {      if (! defined $padChar) {
3199                  # Now we want to move through the list splicing out duplicates.          $padChar = " ";
3200                  my $i = 0;      }
3201                  while ($i < @inputList) {      # Compute the number of spaces needed.
3202                          # Get the current entry.      my $needed = $len - length $string;
3203                          my $thisEntry = $inputList[$i];      # Copy the string into the return variable.
3204                          # Find out how many elements duplicate the current entry.      my $retVal = $string;
3205                          my $j = $i + 1;      # Only proceed if padding is needed.
3206                          my $dup1 = $i + 1;      if ($needed > 0) {
3207                          while ($j < @inputList && $inputList[$j] eq $thisEntry) { $j++; };          # Create the pad string.
3208                          # If the number is nonzero, splice out the duplicates found.          my $pad = $padChar x $needed;
3209                          if ($j > $dup1) {          # Affix it to the return value.
3210                                  splice @inputList, $dup1, $j - $dup1;          if ($left) {
3211                $retVal = $pad . $retVal;
3212            } else {
3213                $retVal .= $pad;
3214                          }                          }
                         # 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++;  
3215                  }                  }
3216        # Return the result.
3217        return $retVal;
3218          }          }
3219          # Return the merged list.  
3220          return @inputList;  =head3 EOF
3221    
3222    This is a constant that is lexically greater than any useful string.
3223    
3224    =cut
3225    
3226    sub EOF {
3227        return "\xFF\xFF\xFF\xFF\xFF";
3228  }  }
3229    
3230  =head3 GetFile  =head3 TICK
3231    
3232        my @results = TICK($commandString);
3233    
3234  C<< my @fileContents = Tracer::GetFile($fileName); >>  Perform a back-tick operation on a command. If this is a Windows environment, any leading
3235    dot-slash (C<./> will be removed. So, for example, if you were doing
3236    
3237  Return the entire contents of a file.      `./protein.cgi`
3238    
3239    from inside a CGI script, it would work fine in Unix, but would issue an error message
3240    in Windows complaining that C<'.'> is not a valid command. If instead you code
3241    
3242        TICK("./protein.cgi")
3243    
3244    it will work correctly in both environments.
3245    
3246  =over 4  =over 4
3247    
3248  =item fileName  =item commandString
3249    
3250  Name of the file to read.  The command string to pass to the system.
3251    
3252  =item RETURN  =item RETURN
3253    
3254  In a list context, returns the entire file as a list with the line terminators removed.  Returns the standard output from the specified command, as a list.
 In a scalar context, returns the entire file as a string.  
3255    
3256  =back  =back
3257    
3258  =cut  =cut
3259    #: Return Type @;
3260  sub GetFile {  sub TICK {
3261          # Get the parameters.          # Get the parameters.
3262          my ($fileName) = @_;      my ($commandString) = @_;
3263          # Declare the return variable.      # Chop off the dot-slash if this is Windows.
3264          my @retVal = ();      if ($FIG_Config::win_mode) {
3265          # 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 an terminator  
         # characters.  
         my $lineCount = 0;  
                 while (my $line = <INPUTFILE>) {  
             $lineCount++;  
             $line =~ s/(\r|\n)+$//g;  
                         push @retVal, $line;  
                 }  
                 # Close it.  
                 close INPUTFILE;  
         my $actualLines = @retVal;  
         Trace("$lineCount lines read from $fileName. $actualLines processed.") if T(0);  
         }  
         # Return the file's contents in the desired format.  
     if (wantarray) {  
             return @retVal;  
     } else {  
         return join "\n", @retVal;  
3266      }      }
3267        # Activate the command and return the result.
3268        return `$commandString`;
3269  }  }
3270    
 =head3 QTrace  
3271    
3272  C<< my $data = QTrace($format); >>  =head3 CommaFormat
3273    
3274  Return the queued trace data in the specified format.      my $formatted = Tracer::CommaFormat($number);
3275    
3276    Insert commas into a number.
3277    
3278  =over 4  =over 4
3279    
3280  =item format  =item number
3281    
3282  C<html> to format the data as an HTML list, C<text> to format it as straight text.  A sequence of digits.
3283    
3284    =item RETURN
3285    
3286    Returns the same digits with commas strategically inserted.
3287    
3288  =back  =back
3289    
3290  =cut  =cut
3291    
3292  sub QTrace {  sub CommaFormat {
3293          # Get the parameter.      # Get the parameters.
3294          my ($format) = @_;      my ($number) = @_;
3295          # Create the return variable.      # Pad the length up to a multiple of three.
3296          my $retVal = "";      my $padded = "$number";
3297          # Process according to the format.      $padded = " " . $padded while length($padded) % 3 != 0;
3298          if ($format =~ m/^HTML$/i) {      # This is a fancy PERL trick. The parentheses in the SPLIT pattern
3299                  # Convert the queue into an HTML list.      # cause the delimiters to be included in the output stream. The
3300                  $retVal = "<ul>\n";      # GREP removes the empty strings in between the delimiters.
3301                  for my $line (@Queue) {      my $retVal = join(",", grep { $_ ne '' } split(/(...)/, $padded));
3302                          my $escapedLine = CGI::escapeHTML($line);      # Clean out the spaces.
3303                          $retVal .= "<li>$escapedLine</li>\n";      $retVal =~ s/ //g;
3304                  }      # 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.  
3305          return $retVal;          return $retVal;
3306  }  }
3307    
 =head3 Confess  
   
 C<< Confess($message); >>  
3308    
3309  Trace the call stack and abort the program with the specified message. The stack  =head3 CompareLists
 trace will only appear if the trace level for this package is 1 or more. When used with  
 the OR operator and the L</Assert> method, B<Confess> can function as a debugging assert.  
 So, for example  
3310    
3311  C<< Assert($recNum >= 0) || Confess("Invalid record number $recNum."); >>      my ($inserted, $deleted) = Tracer::CompareLists(\@newList, \@oldList, $keyIndex);
3312    
3313  Will abort the program with a stack trace if the value of C<$recNum> is negative.  Compare two lists of tuples, and return a hash analyzing the differences. The lists
3314    are presumed to be sorted alphabetically by the value in the $keyIndex column.
3315    The return value contains a list of items that are only in the new list
3316    (inserted) and only in the old list (deleted).
3317    
3318  =over 4  =over 4
3319    
3320  =item message  =item newList
   
 Message to include in the trace.  
3321    
3322  =back  Reference to a list of new tuples.
3323    
3324  =cut  =item oldList
3325    
3326  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(">>> $message");  
 }  
3327    
3328  =head3 Assert  =item keyIndex (optional)
3329    
3330  C<< Assert($condition1, $condition2, ... $conditionN); >>  Index into each tuple of its key field. The default is 0.
3331    
3332  Return TRUE if all the conditions are true. This method can be used in conjunction with  =item RETURN
 the OR operator and the L</Confess> method, B<Assert> can function as a debugging assert.  
 So, for example  
3333    
3334  C<< Assert($recNum >= 0) || Confess("Invalid record number $recNum."); >>  Returns a 2-tuple consisting of a reference to the list of items that are only in the new
3335    list (inserted) followed by a reference to the list of items that are only in the old
3336    list (deleted).
3337    
3338  Will abort the program with a stack trace if the value of C<$recNum> is negative.  =back
3339    
3340  =cut  =cut
3341  sub Assert {  
3342      my $retVal = 1;  sub CompareLists {
3343      LOOP: for my $condition (@_) {      # Get the parameters.
3344          if (! $condition) {      my ($newList, $oldList, $keyIndex) = @_;
3345              $retVal = 0;      if (! defined $keyIndex) {
3346              last LOOP;          $keyIndex = 0;
3347        }
3348        # Declare the return variables.
3349        my ($inserted, $deleted) = ([], []);
3350        # Loop through the two lists simultaneously.
3351        my ($newI, $oldI) = (0, 0);
3352        my ($newN, $oldN) = (scalar @{$newList}, scalar @{$oldList});
3353        while ($newI < $newN || $oldI < $oldN) {
3354            # Get the current object in each list. Note that if one
3355            # of the lists is past the end, we'll get undef.
3356            my $newItem = $newList->[$newI];
3357            my $oldItem = $oldList->[$oldI];
3358            if (! defined($newItem) || defined($oldItem) && $newItem->[$keyIndex] gt $oldItem->[$keyIndex]) {
3359                # The old item is not in the new list, so mark it deleted.
3360                push @{$deleted}, $oldItem;
3361                $oldI++;
3362            } elsif (! defined($oldItem) || $oldItem->[$keyIndex] gt $newItem->[$keyIndex]) {
3363                # The new item is not in the old list, so mark it inserted.
3364                push @{$inserted}, $newItem;
3365                $newI++;
3366            } else {
3367                # The item is in both lists, so push forward.
3368                $oldI++;
3369                $newI++;
3370          }          }
3371      }      }
3372      return $retVal;      # Return the result.
3373        return ($inserted, $deleted);
3374  }  }
3375    
3376  =head3 Cluck  =head3 GenerateURL
3377    
3378  C<< Cluck($message); >>      my $queryUrl = Tracer::GenerateURL($page, %parameters);
3379    
3380  Trace the call stack. Note that for best results, you should qualify the call with a  Generate a GET-style URL for the specified page with the specified parameter
3381  trace condition. For example,  names and values. The values will be URL-escaped automatically. So, for
3382    example
3383    
3384  C<< Cluck("Starting record parse.") if T(3); >>      Tracer::GenerateURL("form.cgi", type => 1, string => "\"high pass\" or highway")
3385    
3386  will only trace the stack if the trace level for the package is 3 or more.  would return
3387    
3388        form.cgi?type=1;string=%22high%20pass%22%20or%20highway
3389    
3390  =over 4  =over 4
3391    
3392  =item message  =item page
3393    
3394  Message to include in the trace.  Page URL.
3395    
3396    =item parameters
3397    
3398    Hash mapping parameter names to parameter values.
3399    
3400    =item RETURN
3401    
3402    Returns a GET-style URL that goes to the specified page and passes in the
3403    specified parameters and values.
3404    
3405  =back  =back
3406    
3407  =cut  =cut
3408    
3409  sub Cluck {  sub GenerateURL {
3410          # Get the parameters.          # Get the parameters.
3411          my ($message) = @_;      my ($page, %parameters) = @_;
3412      # Trace what's happening.      # Prime the return variable with the page URL.
3413      Trace("Stack trace for event: $message");      my $retVal = $page;
3414          my $confession = longmess($message);      # Loop through the parameters, creating parameter elements in a list.
3415          # Convert the confession to a series of trace messages. Note we skip any      my @parmList = map { "$_=" . uri_escape($parameters{$_}) } keys %parameters;
3416      # messages relating to calls into Tracer.      # If the list is nonempty, tack it on.
3417          for my $line (split /\s*\n/, $confession) {      if (@parmList) {
3418                  Trace($line) if ($line !~ /Tracer\.pm/);          $retVal .= "?" . join(";", @parmList);
3419          }          }
3420        # Return the result.
3421        return $retVal;
3422  }  }
3423    
3424  =head3 Min  =head3 ApplyURL
3425    
3426  C<< my $min = Min($value1, $value2, ... $valueN); >>      Tracer::ApplyURL($table, $target, $url);
3427    
3428  Return the minimum argument. The arguments are treated as numbers.  Run through a two-dimensional table (or more accurately, a list of lists), converting the
3429    I<$target> column to HTML text having a hyperlink to a URL in the I<$url> column. The
3430    URL column will be deleted by this process and the target column will be HTML-escaped.
3431    
3432    This provides a simple way to process the results of a database query into something
3433    displayable by combining a URL with text.
3434    
3435  =over 4  =over 4
3436    
3437  =item $value1, $value2, ... $valueN  =item table
3438    
3439  List of numbers to compare.  Reference to a list of lists. The elements in the containing list will be updated by
3440    this method.
3441    
3442  =item RETURN  =item target
3443    
3444  Returns the lowest number in the list.  The index of the column to be converted into HTML.
3445    
3446    =item url
3447    
3448    The index of the column containing the URL. Note that the URL must have a recognizable
3449    C<http:> at the beginning.
3450    
3451  =back  =back
3452    
3453  =cut  =cut
3454    
3455  sub Min {  sub ApplyURL {
3456          # Get the parameters. Note that we prime the return value with the first parameter.      # Get the parameters.
3457          my ($retVal, @values) = @_;      my ($table, $target, $url) = @_;
3458          # Loop through the remaining parameters, looking for the lowest.      # Loop through the table.
3459          for my $value (@values) {      for my $row (@{$table}) {
3460                  if ($value < $retVal) {          # Apply the URL to the target cell.
3461                          $retVal = $value;          $row->[$target] = CombineURL($row->[$target], $row->[$url]);
3462                  }          # Delete the URL from the row.
3463            delete $row->[$url];
3464          }          }
         # Return the minimum found.  
         return $retVal;  
3465  }  }
3466    
3467  =head3 Max  =head3 CombineURL
3468    
3469  C<< my $max = Max($value1, $value2, ... $valueN); >>      my $combinedHtml = Tracer::CombineURL($text, $url);
3470    
3471  Return the maximum argument. The arguments are treated as numbers.  This method will convert the specified text into HTML hyperlinked to the specified
3472    URL. The hyperlinking will only take place if the URL looks legitimate: that is, it
3473    is defined and begins with an C<http:> header.
3474    
3475  =over 4  =over 4
3476    
3477  =item $value1, $value2, ... $valueN  =item text
3478    
3479  List of numbers to compare.  Text to return. This will be HTML-escaped automatically.
3480    
3481    =item url
3482    
3483    A URL to be hyperlinked to the text. If it does not look like a URL, then the text
3484    will be returned without any hyperlinking.
3485    
3486  =item RETURN  =item RETURN
3487    
3488  Returns the highest number in the list.  Returns the original text, HTML-escaped, with the URL hyperlinked to it. If the URL
3489    doesn't look right, the HTML-escaped text will be returned without any further
3490    modification.
3491    
3492  =back  =back
3493    
3494  =cut  =cut
3495    
3496  sub Max {  sub CombineURL {
3497          # Get the parameters. Note that we prime the return value with the first parameter.      # Get the parameters.
3498          my ($retVal, @values) = @_;      my ($text, $url) = @_;
3499          # Loop through the remaining parameters, looking for the highest.      # Declare the return variable.
3500          for my $value (@values) {      my $retVal = CGI::escapeHTML($text);
3501                  if ($value > $retVal) {      # Verify the URL.
3502                          $retVal = $value;      if (defined($url) && $url =~ m!http://!i) {
3503                  }          # It's good, so we apply it to the text.
3504            $retVal = "<a href=\"$url\">$retVal</a>";
3505          }          }
3506          # Return the maximum found.      # Return the result.
3507          return $retVal;          return $retVal;
3508  }  }
3509    
3510  =head3 AddToListMap  =head3 Cmp
3511    
3512  C<< Tracer::AddToListMap(\%hash, $key, $value); >>      my $cmp = Tracer::Cmp($a, $b);
3513    
3514  Add a key-value pair to a hash of lists. If no value exists for the key, a singleton list  This method performs a universal sort comparison. Each value coming in is
3515  is created for the key. Otherwise, the new value is pushed onto the list.  separated into a leading text part and a trailing number part. The text
3516    part is string compared, and if both parts are equal, then the number
3517    parts are compared numerically. A stream of just numbers or a stream of
3518    just strings will sort correctly, and a mixed stream will sort with the
3519    numbers first. Strings with a label and a number will sort in the
3520    expected manner instead of lexically.
3521    
3522  =over 4  =over 4
3523    
3524  =item hash  =item a
3525