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revision 1.45, Mon May 8 20:37:02 2006 UTC revision 1.117, Thu Apr 2 01:13:32 2009 UTC
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1  #  # -*- perl -*-
2    ########################################################################
3  # Copyright (c) 2003-2006 University of Chicago and Fellowship  # Copyright (c) 2003-2006 University of Chicago and Fellowship
4  # for Interpretations of Genomes. All Rights Reserved.  # for Interpretations of Genomes. All Rights Reserved.
5  #  #
# Line 13  Line 14 
14  # at info@ci.uchicago.edu or the Fellowship for Interpretation of  # at info@ci.uchicago.edu or the Fellowship for Interpretation of
15  # Genomes at veronika@thefig.info or download a copy from  # Genomes at veronika@thefig.info or download a copy from
16  # http://www.theseed.org/LICENSE.TXT.  # http://www.theseed.org/LICENSE.TXT.
17  #  ########################################################################
18    
19  package Tracer;  package Tracer;
20    
     require Exporter;  
     @ISA = ('Exporter');  
     @EXPORT = qw(Trace T TSetup QTrace Confess Cluck Min Max Assert Open OpenDir TICK StandardSetup ScriptSetup ScriptFinish Insure ChDir);  
     @EXPORT_OK = qw(GetFile GetOptions Merge MergeOptions ParseCommand ParseRecord UnEscape Escape);  
21      use strict;      use strict;
22      use Carp qw(longmess croak);      use base qw(Exporter);
23        use vars qw(@EXPORT @EXPORT_OK);
24        @EXPORT = qw(Trace T TSetup QTrace Confess MemTrace Cluck Min Max Assert Open OpenDir TICK StandardSetup EmergencyKey ETracing Constrain Insure ChDir Emergency Warn TraceDump IDHASH);
25        @EXPORT_OK = qw(GetFile GetOptions Merge MergeOptions ParseCommand ParseRecord UnEscape Escape PrintLine PutLine);
26        use Carp qw(longmess croak carp);
27      use CGI;      use CGI;
28        use Cwd;
29      use FIG_Config;      use FIG_Config;
30      use PageBuilder;      use PageBuilder;
31      use Digest::MD5;      use Digest::MD5;
32      use File::Basename;      use File::Basename;
33      use File::Path;      use File::Path;
34        use File::stat;
35        use LWP::UserAgent;
36        use Time::HiRes 'gettimeofday';
37        use URI::Escape;
38        use Time::Local;
39        use POSIX qw(strftime);
40        use Time::Zone;
41        use Fcntl qw(:DEFAULT :flock);
42        use Data::Dumper;
43    
44    
45  =head1 Tracing and Debugging Helpers  =head1 Tracing and Debugging Helpers
46    
47  =head2 Introduction  =head2 Tracing
48    
49  This package provides simple tracing for debugging and reporting purposes. To use it simply call the  This package provides simple tracing for debugging and reporting purposes. To use it simply call the
50  L</TSetup> method to set the options and call L</Trace> to write out trace messages. Each trace  L</TSetup> or L</ETracing> method to set the options and call L</Trace> to write out trace messages.
51  message has a I<trace level> and I<category> associated with it. In addition, the tracing package itself  L</TSetup> and L</ETracing> both establish a I<trace level> and a list of I<categories>. Similarly,
52  has a list of categories and a single trace level set by the B<TSetup> method. Only messages whose trace  each trace message has a I<trace level> and I<category> associated with it. Only messages whose trace
53  level is less than or equal to this package's trace level and whose category is activated will  level is less than or equal to the setup trace level and whose category is activated will
54  be written. Thus, a higher trace level on a message indicates that the message  be written. Thus, a higher trace level on a message indicates that the message
55  is less likely to be seen. A higher trace level passed to B<TSetup> means more trace messages will  is less likely to be seen, while a higher trace level passed to B<TSetup> means more trace messages will
56  appear. To generate a trace message, use the following syntax.  appear.
57    
58    =head3 Putting Trace Messages in Your Code
59    
60  C<< Trace($message) if T(errors => 4); >>  To generate a trace message, use the following syntax.
61    
62        Trace($message) if T(errors => 4);
63    
64  This statement will produce a trace message if the trace level is 4 or more and the C<errors>  This statement will produce a trace message if the trace level is 4 or more and the C<errors>
65  category is active. Note that the special category C<main> is always active, so  category is active. There is a special category C<main> that is always active, so
66    
67  C<< Trace($message) if T(main => 4); >>      Trace($message) if T(main => 4);
68    
69  will trace if the trace level is 4 or more.  will trace if the trace level is 4 or more.
70    
# Line 56  Line 72 
72  following call is made in the B<Sprout> package, it will appear if the C<Sprout> category is  following call is made in the B<Sprout> package, it will appear if the C<Sprout> category is
73  active and the trace level is 2 or more.  active and the trace level is 2 or more.
74    
75  C<< Trace($message) if T(2); >>      Trace($message) if T(2);
76    
77    In scripts, where no package name is available, the category defaults to C<main>.
78    
79    =head3 Custom Tracing
80    
81    Many programs have customized tracing configured using the L</TSetup> method. This is no longer
82    the preferred method, but a knowledge of how custom tracing works can make the more modern
83    L</Emergency Tracing> easier to understand.
84    
85  To set up tracing, you call the L</TSetup> method. The method takes as input a trace level, a list  To set up custom tracing, you call the L</TSetup> method. The method takes as input a trace level,
86  of category names, and a set of options. The trace level and list of category names are  a list of category names, and a destination. The trace level and list of category names are
87  specified as a space-delimited string. Thus  specified as a space-delimited string. Thus
88    
89  C<< TSetup('3 errors Sprout ERDB', 'HTML'); >>      TSetup('3 errors Sprout ERDB', 'TEXT');
90    
91  sets the trace level to 3, activates the C<errors>, C<Sprout>, and C<ERDB> categories, and  sets the trace level to 3, activates the C<errors>, C<Sprout>, and C<ERDB> categories, and
92  specifies that messages should be output as HTML paragraphs.  specifies that messages should be sent to the standard output.
93    
94  To turn on tracing for ALL categories, use an asterisk. The call below sets every category to  To turn on tracing for ALL categories, use an asterisk. The call below sets every category to
95  level 3 and writes the output to the standard error output. This sort of thing might be  level 3 and writes the output to the standard error output. This sort of thing might be
96  useful in a CGI environment.  useful in a CGI environment.
97    
98  C<< TSetup('3 *', 'WARN'); >>      TSetup('3 *', 'WARN');
99    
100  In addition to HTML and file output for trace messages, you can specify that the trace messages  In addition standard error and file output for trace messages, you can specify that the trace messages
101  be queued. The messages can then be retrieved by calling the L</QTrace> method. This approach  be queued. The messages can then be retrieved by calling the L</QTrace> method. This approach
102  is useful if you are building a web page. Instead of having the trace messages interspersed with  is useful if you are building a web page. Instead of having the trace messages interspersed with
103  the page output, they can be gathered together and displayed at the end of the page. This makes  the page output, they can be gathered together and displayed at the end of the page. This makes
104  it easier to debug page formatting problems.  it easier to debug page formatting problems.
105    
106  Finally, you can specify that all trace messages be emitted as warnings.  Finally, you can specify that all trace messages be emitted to a file, or the standard output and
107    a file at the same time. To trace to a file, specify the filename with an output character in front
108    of it.
109    
110        TSetup('4 SQL', ">$fileName");
111    
112    To trace to the standard output and a file at the same time, put a C<+> in front of the angle
113    bracket.
114    
115        TSetup('3 *', "+>$fileName");
116    
117  The flexibility of tracing makes it superior to simple use of directives like C<die> and C<warn>.  The flexibility of tracing makes it superior to simple use of directives like C<die> and C<warn>.
118  Tracer calls can be left in the code with minimal overhead and then turned on only when needed.  Tracer calls can be left in the code with minimal overhead and then turned on only when needed.
119  Thus, debugging information is available and easily retrieved even when the application is  Thus, debugging information is available and easily retrieved even when the application is
120  being used out in the field.  being used out in the field.
121    
122    =head3 Trace Levels
123    
124  There is no hard and fast rule on how to use trace levels. The following is therefore only  There is no hard and fast rule on how to use trace levels. The following is therefore only
125  a suggestion.  a suggestion.
126    
# Line 116  Line 151 
151    
152  =back  =back
153    
154    The format of trace messages is important because some utilities analyze trace files.
155    There are three fields-- the time stamp, the category name, and the text.
156    The time stamp is between square brackets and the category name between angle brackets.
157    After the category name there is a colon (C<:>) followed by the message text.
158    If the square brackets or angle brackets are missing, then the trace management
159    utilities assume that they are encountering a set of pre-formatted lines.
160    
161    Note, however, that this formatting is done automatically by the tracing functions. You
162    only need to know about it if you want to parse a trace file.
163    
164    =head3 Emergency Tracing
165    
166    Sometimes, you need a way for tracing to happen automatically without putting parameters
167    in a form or on the command line. Emergency tracing does this. You invoke emergency tracing
168    from the debug form, which is accessed from the [[DebugConsole]]. Emergency tracing requires
169    that you specify a tracing key. For command-line tools, the key is
170    taken from the C<TRACING> environment variable. For web services, the key is taken from
171    a cookie. Either way, the key tells the tracing facility who you are, so that you control
172    the tracing in your environment without stepping on other users.
173    
174    The key can be anything you want. If you don't have a key, the C<SetPassword> page will
175    generate one for you.
176    
177    You can activate and de-activate emergency tracing from the debugging control panel, as
178    well as display the trace file itself.
179    
180    To enable emergency tracing in your code, call
181    
182        ETracing($cgi)
183    
184    from a web script and
185    
186        ETracing()
187    
188    from a command-line script.
189    
190    The web script will look for the tracing key in the cookies, and the command-line
191    script will look for it in the C<TRACING> environment variable. If you are
192    using the L</StandardSetup> method or a [[WebApplication]], emergency tracing
193    will be configured automatically.
194    
195  =cut  =cut
196    
197  # Declare the configuration variables.  # Declare the configuration variables.
198    
199  my $Destination = "NONE";   # Description of where to send the trace output.  my $Destination = "WARN";   # Description of where to send the trace output.
200  my $TeeFlag = 0;            # TRUE if output is going to a file and to the  my $TeeFlag = 0;            # TRUE if output is going to a file and to the
201                              # standard output                              # standard output
202  my %Categories = ( main => 1 );  my %Categories = ( main => 1 );
203                              # hash of active category names                              # hash of active category names
204    my @LevelNames = qw(error warn notice info detail);
205  my $TraceLevel = 0;         # trace level; a higher trace level produces more  my $TraceLevel = 0;         # trace level; a higher trace level produces more
206                              # messages                              # messages
207  my @Queue = ();             # queued list of trace messages.  my @Queue = ();             # queued list of trace messages.
208  my $LastCategory = "main";  # name of the last category interrogated  my $LastCategory = "main";  # name of the last category interrogated
209    my $LastLevel = 0;          # level of the last test call
210  my $SetupCount = 0;         # number of times TSetup called  my $SetupCount = 0;         # number of times TSetup called
211  my $AllTrace = 0;           # TRUE if we are tracing all categories.  my $AllTrace = 0;           # TRUE if we are tracing all categories.
212    my $SavedCGI;               # CGI object passed to ETracing
213    my $CommandLine;            # Command line passed to StandardSetup
214    umask 2;                    # Fix the damn umask so everything is group-writable.
215    
216    =head2 Tracing Methods
217    
218    =head3 Setups
219    
220        my $count = Tracer::Setups();
221    
222    Return the number of times L</TSetup> has been called.
223    
224    This method allows for the creation of conditional tracing setups where, for example, we
225    may want to set up tracing if nobody else has done it before us.
226    
227    =cut
228    
229  =head2 Public Methods  sub Setups {
230        return $SetupCount;
231    }
232    
233  =head3 TSetup  =head3 TSetup
234    
235  C<< TSetup($categoryList, $target); >>      TSetup($categoryList, $target);
236    
237  This method is used to specify the trace options. The options are stored as package data  This method is used to specify the trace options. The options are stored as package data
238  and interrogated by the L</Trace> and L</T> methods.  and interrogated by the L</Trace> and L</T> methods.
# Line 186  Line 282 
282          }          }
283      }      }
284      # Now we need to process the destination information. The most important special      # Now we need to process the destination information. The most important special
285      # cases are the single ">", which requires we clear the file first, and the      # case is when we're writing to a file. This is indicated by ">" (overwrite) and
286      # "+" prefix which indicates a double echo.      # ">>" (append). A leading "+" for either indicates that we are also writing to
287        # the standard output (tee mode).
288      if ($target =~ m/^\+?>>?/) {      if ($target =~ m/^\+?>>?/) {
289          if ($target =~ m/^\+/) {          if ($target =~ m/^\+/) {
290              $TeeFlag = 1;              $TeeFlag = 1;
291              $target = substr($target, 1);              $target = substr($target, 1);
292          }          }
293          if ($target =~ m/^>[^>]/) {          if ($target =~ m/^>[^>]/) {
294                # We need to initialize the file (which clears it).
295              open TRACEFILE, $target;              open TRACEFILE, $target;
296              print TRACEFILE Now() . " Tracing initialized.\n";              print TRACEFILE "[" . Now() . "] [notice] [Tracer] Tracing initialized.\n";
297              close TRACEFILE;              close TRACEFILE;
298                # Set to append mode now that the file has been cleared.
299              $Destination = ">$target";              $Destination = ">$target";
300          } else {          } else {
301              $Destination = $target;              $Destination = $target;
# Line 208  Line 307 
307      $SetupCount++;      $SetupCount++;
308  }  }
309    
310  =head3 StandardSetup  =head3 SetLevel
311    
312  C<< my ($options, @parameters) = StandardSetup(\@categories, \%options, $parmHelp, @ARGV); >>      Tracer::SetLevel($newLevel);
313    
314  This method performs standard command-line parsing and tracing setup. The return  Modify the trace level. A higher trace level will cause more messages to appear.
 values are a hash of the command-line options and a list of the positional  
 parameters. Tracing is automatically set up and the command-line options are  
 validated.  
315    
316  This is a complex method that does a lot of grunt work. The parameters can  =over 4
 be more easily understood, however, once they are examined individually.  
317    
318  The I<categories> parameter is the most obtuse. It is a reference to a list of  =item newLevel
 special-purpose tracing categories. Most tracing categories are PERL package  
 names. So, for example, if you wanted to turn on tracing inside the B<Sprout>,  
 B<ERDB>, and B<SproutLoad> packages, you would specify the categories  
319    
320      ["Sprout", "SproutLoad", "ERDB"]  Proposed new trace level.
321    
322  This would cause trace messages in the specified three packages to appear in  =back
 the output. There are threer special tracing categories that are automatically  
 handled by this method. In other words, if you used L</TSetup> you would need  
 to include these categories manually, but if you use this method they are turned  
 on automatically.  
323    
324  =over 4  =cut
325    
326  =item FIG  sub SetLevel {
327        $TraceLevel = $_[0];
328    }
329    
330  Turns on trace messages inside the B<FIG> package.  =head3 ParseDate
331    
332  =item SQL      my $time = Tracer::ParseDate($dateString);
333    
334  Traces SQL commands and activity.  Convert a date into a PERL time number. This method expects a date-like string
335    and parses it into a number. The string must be vaguely date-like or it will
336    return an undefined value. Our requirement is that a month and day be
337    present and that three pieces of the date string (time of day, month and day,
338    year) be separated by likely delimiters, such as spaces, commas, and such-like.
339    
340  =item Tracer  If a time of day is present, it must be in military time with two digits for
341    everything but the hour.
342    
343  Traces error messages and call stacks.  The year must be exactly four digits.
344    
345  =back  Additional stuff can be in the string. We presume it's time zones or weekdays or something
346    equally innocuous. This means, however, that a sufficiently long sentence with date-like
347    parts in it may be interpreted as a date. Hopefully this will not be a problem.
348    
349  C<SQL> is only turned on if the C<-sql> option is specified in the command line.  It should be guaranteed that this method will parse the output of the L</Now> function.
 The trace level is specified using the C<-trace> command-line option. For example,  
 the following command line for C<TransactFeatures> turns on SQL tracing and runs  
 all tracing at level 3.  
350    
351      TransactFeatures -trace=3 -sql register ../xacts IDs.tbl  The parameters are as follows.
352    
353  Standard tracing is output to the standard output and echoed to the file  =over 4
 C<trace>I<$$>C<.log> in the FIG temporary directory, where I<$$> is the  
 process ID. You can also specify the C<user> parameter to put a user ID  
 instead of a process ID in the trace file name. So, for example  
354    
355  The default trace level is 2. To get all messages, specify a trace level of 4.  =item dateString
 For a genome-by-genome update, use 3.  
356    
357      TransactFeatures -trace=3 -sql -user=Bruce register ../xacts IDs.tbl  The date string to convert.
358    
359  would send the trace output to C<traceBruce.log> in the temporary directory.  =item RETURN
360    
361  The I<options> parameter is a reference to a hash containing the command-line  Returns a PERL time, that is, a number of seconds since the epoch, or C<undef> if
362  options, their default values, and an explanation of what they mean. Command-line  the date string is invalid. A valid date string must contain a month and day.
 options may be in the form of switches or keywords. In the case of a switch, the  
 option value is 1 if it is specified and 0 if it is not specified. In the case  
 of a keyword, the value is separated from the option name by an equal sign. You  
 can see this last in the command-line example above.  
363    
364  You can specify a different default trace level by setting C<$options->{trace}>  =back
 prior to calling this method.  
365    
366  An example at this point would help. Consider, for example, the command-line utility  =cut
 C<TransactFeatures>. It accepts a list of positional parameters plus the options  
 C<safe>, C<noAlias>, C<start>, and C<tblFiles>. To start up this command, we execute  
 the following code.  
367    
368      my ($options, @parameters) = Tracer::StandardSetup(["DocUtils"],  # Universal month conversion table.
369                          { safe => [0, "use database transactions"],  use constant MONTHS => {    Jan =>  0, January   =>  0, '01' =>  0,  '1' =>  0,
370                            noAlias => [0, "do not expect aliases in CHANGE transactions"],                              Feb =>  1, February  =>  1, '02' =>  1,  '2' =>  1,
371                            start => [' ', "start with this genome"],                              Mar =>  2, March     =>  2, '03' =>  2,  '3' =>  2,
372                            tblFiles => [0, "output TBL files containing the corrected IDs"] },                              Apr =>  3, April     =>  3, '04' =>  3,  '4' =>  3,
373                          "command transactionDirectory IDfile",                              May =>  4, May       =>  4, '05' =>  4,  '5' =>  4,
374                        @ARGV);                              Jun =>  5, June      =>  5, '06' =>  5,  '6' =>  5,
375                                Jul =>  6, July      =>  6, '07' =>  6,  '7' =>  6,
376                                Aug =>  7, August    =>  7, '08' =>  7,  '8' =>  7,
377                                Sep =>  8, September =>  8, '09' =>  8,  '9' =>  8,
378                                Oct =>  9, October  =>   9, '10' =>  9,
379                                Nov => 10, November =>  10, '11' => 10,
380                                Dec => 11, December =>  11, '12' => 11
381                            };
382    
383    sub ParseDate {
384        # Get the parameters.
385        my ($dateString) = @_;
386        # Declare the return variable.
387        my $retVal;
388        # Find the month and day of month. There are two ways that can happen. We check for the
389        # numeric style first. That way, if the user's done something like "Sun 12/22", then we
390        # won't be fooled into thinking the month is Sunday.
391        if ($dateString =~ m#\b(\d{1,2})/(\d{1,2})\b# || $dateString =~ m#\b(\w+)\s(\d{1,2})\b#) {
392            my ($mon, $mday) = (MONTHS->{$1}, $2);
393            # Insist that the month and day are valid.
394            if (defined($mon) && $2 >= 1 && $2 <= 31) {
395                # Find the time.
396                my ($hour, $min, $sec) = (0, 0, 0);
397                if ($dateString =~ /\b(\d{1,2}):(\d{2}):(\d{2})\b/) {
398                    ($hour, $min, $sec) = ($1, $2, $3);
399                }
400                # Find the year.
401                my $year;
402                if ($dateString =~ /\b(\d{4})\b/) {
403                    $year = $1;
404                } else {
405                    # Get the default year, which is this one. Note we must convert it to
406                    # the four-digit value expected by "timelocal".
407                    (undef, undef, undef, undef, undef, $year) = localtime();
408                    $year += 1900;
409                }
410                $retVal = timelocal($sec, $min, $hour, $mday, $mon, $year);
411            }
412        }
413        # Return the result.
414        return $retVal;
415    }
416    
417  The call to C<ParseCommand> specifies the default values for the options and  =head3 LogErrors
 stores the actual options in a hash that is returned as C<$options>. The  
 positional parameters are returned in C<@parameters>.  
418    
419  The following is a sample command line for C<TransactFeatures>.      Tracer::LogErrors($fileName);
420    
421      TransactFeatures -trace=2 -noAlias register ../xacts IDs.tbl  Route the standard error output to a log file.
422    
423  In this case, C<register>, C<../xacts>, and C<IDs.tbl> are the positional  =over 4
 parameters, and would find themselves in I<@parameters> after executing the  
 above code fragment. The tracing would be set to level 2, and the categories  
 would be C<FIG>, C<Tracer>, and <DocUtils>. C<FIG> and C<Tracer> are standard,  
 and C<DocUtils> was included because it came in within the first parameter  
 to this method. The I<$options> hash would be  
424    
425      { trace => 2, sql => 0, safe => 0,  =item fileName
       noAlias => 1, start => ' ', tblFiles => 0 }  
426    
427  Use of C<StandardSetup> in this way provides a simple way of performing  Name of the file to receive the error output.
 standard tracing setup and command-line parsing. Note that the caller is  
 not even aware of the command-line switches C<-trace> and C<-sql>, which  
 are used by this method to control the tracing. If additional tracing features  
 need to be added in the future, they can be processed by this method without  
 upsetting the command-line utilities.  
428    
429  If the C<background> option is specified on the command line, then the  =back
 standard and error outputs will be directed to files in the temporary  
 directory, using the same suffix as the trace file. So, if the command  
 line specified  
430    
431      -user=Bruce -background  =cut
432    
433  then the trace output would go to C<traceBruce.log>, the standard output to  sub LogErrors {
434  C<outBruce.log>, and the error output to C<errBruce.log>. This is designed to      # Get the file name.
435  simplify starting a command in the background.      my ($fileName) = @_;
436        # Open the file as the standard error output.
437        open STDERR, '>', $fileName;
438    }
439    
440  Finally, if the special option C<-h> is specified, the option names will  =head3 Trace
 be traced at level 0 and the program will exit without processing.  
 This provides a limited help capability. For example, if the user enters  
441    
442      TransactFeatures -h      Trace($message);
443    
444  he would see the following output.  Write a trace message to the target location specified in L</TSetup>. If there has not been
445    any prior call to B<TSetup>.
446    
447      TransactFeatures [options] command transactionDirectory IDfile  =over 4
         -trace    tracing level (default 2)  
         -sql      trace SQL commands  
         -safe     use database transactions  
         -noAlias  do not expect aliases in CHANGE transactions  
         -start    start with this genome  
         -tblFiles output TBL files containing the corrected IDs  
448    
449  The caller has the option of modifying the tracing scheme by placing a value  =item message
 for C<trace> in the incoming options hash. The default value can be overridden,  
 or the tracing to the standard output can be turned off by suffixing a minus  
 sign to the trace level. So, for example,  
450    
451      { trace => [0, "tracing level (default 0)"],  Message to write.
        ...  
452    
453  would set the default trace level to 0 instead of 2, while  =back
454    
455      { trace => ["2-", "tracing level (default 2)"],  =cut
        ...  
456    
457  would leave the default at 2, but trace only to the log file, not to the  sub Trace {
458  standard output.      # Get the parameters.
459        my ($message) = @_;
460        # Strip off any line terminators at the end of the message. We will add
461        # new-line stuff ourselves.
462        my $stripped = Strip($message);
463        # Compute the caller information.
464        my ($callPackage, $callFile, $callLine) = caller();
465        my $callFileTitle = basename($callFile);
466        # Check the caller.
467        my $callerInfo = ($callFileTitle ne "Tracer.pm" ? " [$callFileTitle $callLine]" : "");
468        # Get the timestamp.
469        my $timeStamp = Now();
470        # Build the prefix.
471        my $level = $LevelNames[$LastLevel] || "($LastLevel)";
472        my $prefix = "[$timeStamp] [$level] [$LastCategory]$callerInfo";
473        # Format the message.
474        my $formatted = "$prefix $stripped";
475        # Process according to the destination.
476        if ($Destination eq "TEXT") {
477            # Write the message to the standard output.
478            print "$formatted\n";
479        } elsif ($Destination eq "ERROR") {
480            # Write the message to the error output. Here, we want our prefix fields.
481            print STDERR "$formatted\n";
482        } elsif ($Destination eq "WARN") {
483            # Emit the message to the standard error output. It is presumed that the
484            # error logger will add its own prefix fields, the notable exception being
485            # the caller info.
486            print STDERR "$callerInfo$stripped\n";
487        } elsif ($Destination eq "QUEUE") {
488            # Push the message into the queue.
489            push @Queue, "$formatted";
490        } elsif ($Destination eq "HTML") {
491            # Convert the message to HTML.
492            my $escapedMessage = CGI::escapeHTML($stripped);
493            # The stuff after the first line feed should be pre-formatted.
494            my @lines = split /\s*\n/, $escapedMessage;
495            # Get the normal portion.
496            my $line1 = shift @lines;
497            print "<p>$timeStamp $LastCategory $LastLevel: $line1</p>\n";
498            if (@lines) {
499                print "<pre>" . join("\n", @lines, "<pre>");
500            }
501        } elsif ($Destination =~ m/^>>/) {
502            # Write the trace message to an output file.
503            open(TRACING, $Destination) || die "Tracing open for \"$Destination\" failed: $!";
504            # Lock the file.
505            flock TRACING, LOCK_EX;
506            print TRACING "$formatted\n";
507            close TRACING;
508            # If the Tee flag is on, echo it to the standard output.
509            if ($TeeFlag) {
510                print "$formatted\n";
511            }
512        }
513    }
514    
515  The parameters to this method are as follows.  =head3 MemTrace
516    
517        MemTrace($message);
518    
519    Output a trace message that includes memory size information.
520    
521  =over 4  =over 4
522    
523  =item categories  =item message
524    
525  Reference to a list of tracing category names. These should be names of  Message to display. The message will be followed by a sentence about the memory size.
 packages whose internal workings will need to be debugged to get the  
 command working.  
526    
527  =item options  =back
528    
529  Reference to a hash containing the legal options for the current command mapped  =cut
 to their default values and descriptions. The user can override the defaults  
 by specifying the options as command-line switches prefixed by a hyphen.  
 Tracing-related options may be added to this hash. If the C<-h> option is  
 specified on the command line, the option descriptions will be used to  
 explain the options. To turn off tracing to the standard output, add a  
 minus sign to the value for C<trace> (see above).  
530    
531  =item parmHelp  sub MemTrace {
532        # Get the parameters.
533        my ($message) = @_;
534        my $memory = GetMemorySize();
535        Trace("$message $memory in use.");
536    }
537    
 A string that vaguely describes the positional parameters. This is used  
 if the user specifies the C<-h> option.  
538    
539  =item argv  =head3 TraceDump
540    
541  List of command line parameters, including the option switches, which must      TraceDump($title, $object);
 precede the positional parameters and be prefixed by a hyphen.  
542    
543  =item RETURN  Dump an object to the trace log. This method simply calls the C<Dumper>
544    function, but routes the output to the trace log instead of returning it
545    as a string. The output is arranged so that it comes out monospaced when
546    it appears in an HTML trace dump.
547    
548  Returns a list. The first element of the list is the reference to a hash that  =over 4
549  maps the command-line option switches to their values. These will either be the  
550  default values or overrides specified on the command line. The remaining  =item title
551  elements of the list are the position parameters, in order.  
552    Title to give to the object being dumped.
553    
554    =item object
555    
556    Reference to a list, hash, or object to dump.
557    
558  =back  =back
559    
560  =cut  =cut
561    
562  sub StandardSetup {  sub TraceDump {
563      # Get the parameters.      # Get the parameters.
564      my ($categories, $options, $parmHelp, @argv) = @_;      my ($title, $object) = @_;
565      # Add the tracing options.      # Trace the object.
566      if (! exists $options->{trace}) {      Trace("Object dump for $title:\n" . Dumper($object));
         $options->{trace} = [2, "tracing level"];  
567      }      }
568      $options->{sql} = [0, "turn on SQL tracing"];  
569      $options->{h} = [0, "display command-line options"];  =head3 T
570      $options->{user} = [$$, "trace log file name suffix"];  
571      $options->{background} = [0, "spool standard and error output"];      my $switch = T($category, $traceLevel);
572      # Create a parsing hash from the options hash. The parsing hash  
573      # contains the default values rather than the default value      or
574      # and the description. While we're at it, we'll memorize the  
575      # length of the longest option name.      my $switch = T($traceLevel);
576      my $longestName = 0;  
577      my %parseOptions = ();  Return TRUE if the trace level is at or above a specified value and the specified category
578      for my $key (keys %{$options}) {  is active, else FALSE. If no category is specified, the caller's package name is used.
579          if (length $key > $longestName) {  
580    =over 4
581    
582    =item category
583    
584    Category to which the message belongs. If not specified, the caller's package name is
585    used.
586    
587    =item traceLevel
588    
589    Relevant tracing level.
590    
591    =item RETURN
592    
593    TRUE if a message at the specified trace level would appear in the trace, else FALSE.
594    
595    =back
596    
597    =cut
598    
599    sub T {
600        # Declare the return variable.
601        my $retVal = 0;
602        # Only proceed if tracing is turned on.
603        if ($Destination ne "NONE") {
604            # Get the parameters.
605            my ($category, $traceLevel) = @_;
606            if (!defined $traceLevel) {
607                # Here we have no category, so we need to get the calling package.
608                # The calling package is normally the first parameter. If it is
609                # omitted, the first parameter will be the tracelevel. So, the
610                # first thing we do is shift the so-called category into the
611                # $traceLevel variable where it belongs.
612                $traceLevel = $category;
613                my ($package, $fileName, $line) = caller;
614                # If there is no calling package, we default to "main".
615                if (!$package) {
616                    $category = "main";
617                } else {
618                    my @cats = split /::/, $package;
619                    $category = $cats[$#cats];
620                }
621            }
622            # Save the category name and level.
623            $LastCategory = $category;
624            $LastLevel = $traceLevel;
625            # Convert it to lower case before we hash it.
626            $category = lc $category;
627            # Validate the trace level.
628            if (ref $traceLevel) {
629                Confess("Bad trace level.");
630            } elsif (ref $TraceLevel) {
631                Confess("Bad trace config.");
632            }
633            # Make the check. Note that level 0 shows even if the category is turned off.
634            $retVal = ($traceLevel <= $TraceLevel && ($traceLevel == 0 || $AllTrace || exists $Categories{$category}));
635        }
636        # Return the computed result.
637        return $retVal;
638    }
639    
640    =head3 QTrace
641    
642        my $data = QTrace($format);
643    
644    Return the queued trace data in the specified format.
645    
646    =over 4
647    
648    =item format
649    
650    C<html> to format the data as an HTML list, C<text> to format it as straight text.
651    
652    =back
653    
654    =cut
655    
656    sub QTrace {
657        # Get the parameter.
658        my ($format) = @_;
659        # Create the return variable.
660        my $retVal = "";
661        # Only proceed if there is an actual queue.
662        if (@Queue) {
663            # Process according to the format.
664            if ($format =~ m/^HTML$/i) {
665                # Convert the queue into an HTML list.
666                $retVal = "<ul>\n";
667                for my $line (@Queue) {
668                    my $escapedLine = CGI::escapeHTML($line);
669                    $retVal .= "<li>$escapedLine</li>\n";
670                }
671                $retVal .= "</ul>\n";
672            } elsif ($format =~ m/^TEXT$/i) {
673                # Convert the queue into a list of text lines.
674                $retVal = join("\n", @Queue) . "\n";
675            }
676            # Clear the queue.
677            @Queue = ();
678        }
679        # Return the formatted list.
680        return $retVal;
681    }
682    
683    =head3 Confess
684    
685        Confess($message);
686    
687    Trace the call stack and abort the program with the specified message. When used with
688    the OR operator and the L</Assert> method, B<Confess> can function as a debugging assert.
689    So, for example
690    
691        Assert($recNum >= 0) || Confess("Invalid record number $recNum.");
692    
693    Will abort the program with a stack trace if the value of C<$recNum> is negative.
694    
695    =over 4
696    
697    =item message
698    
699    Message to include in the trace.
700    
701    =back
702    
703    =cut
704    
705    sub Confess {
706        # Get the parameters.
707        my ($message) = @_;
708        # Set up the category and level.
709        $LastCategory = "(confess)";
710        $LastLevel = 0;
711        # Trace the call stack.
712        Cluck($message);
713        # Abort the program.
714        croak(">>> $message");
715    }
716    
717    =head3 SaveCGI
718    
719        Tracer::SaveCGI($cgi);
720    
721    This method saves the CGI object but does not activate emergency tracing.
722    It is used to allow L</Warn> to work in situations where emergency
723    tracing is contra-indicated (e.g. the wiki).
724    
725    =over 4
726    
727    =item cgi
728    
729    Active CGI query object.
730    
731    =back
732    
733    =cut
734    
735    sub SaveCGI {
736        $SavedCGI = $_[0];
737    }
738    
739    =head3 Warn
740    
741        Warn($message, @options);
742    
743    This method traces an important message. If an RSS feed is configured
744    (via I<FIG_Config::error_feed>) and the tracing destination is C<WARN>,
745    then the message will be echoed to the feed. In general, a tracing
746    destination of C<WARN> indicates that the caller is running as a web
747    service in a production environment; however, this is not a requirement.
748    
749    To force warnings into the RSS feed even when the tracing destination
750    is not C<WARN>, simply specify the C<Feed> tracing module. This can be
751    configured automatically when L</StandardSetup> is used.
752    
753    The L</Cluck> method calls this one for its final message. Since
754    L</Confess> calls L</Cluck>, this means that any error which is caught
755    and confessed will put something in the feed. This insures that someone
756    will be alerted relatively quickly when a failure occurs.
757    
758    =over 4
759    
760    =item message
761    
762    Message to be traced.
763    
764    =item options
765    
766    A list containing zero or more options.
767    
768    =back
769    
770    The permissible options are as follows.
771    
772    =over 4
773    
774    =item noStack
775    
776    If specified, then the stack trace is not included in the output.
777    
778    =back
779    
780    =cut
781    
782    sub Warn {
783        # Get the parameters.
784        my $message = shift @_;
785        my %options = map { $_ => 1 } @_;
786        # Save $@;
787        my $savedError = $@;
788        # Trace the message.
789        Trace($message);
790        # This will contain the lock handle. If it's defined, it means we need to unlock.
791        my $lock;
792        # Check for feed forcing.
793        my $forceFeed = exists $Categories{feed};
794        # An error here would be disastrous. Note that if debug mode is specified,
795        # we do this stuff even in a test environment.
796        eval {
797            # Do we need to put this in the RSS feed?
798            if ($FIG_Config::error_feed && ($Destination eq 'WARN' || $forceFeed)) {
799                # Probably. We need to check first, however, to see if it's from an
800                # ignored IP. For non-CGI situations, we default the IP to the self-referent.
801                my $key = "127.0.0.1";
802                if (defined $SavedCGI) {
803                    # Get the IP address.
804                    $key = $ENV{HTTP_X_FORWARDED_FOR} || $ENV{REMOTE_ADDR};
805                }
806                # Is the IP address in the ignore list?
807                my $found = scalar(grep { $_ eq $key } @FIG_Config::error_ignore_ips);
808                if (! $found) {
809                    # No. We're good. We now need to compute the date, the link, and the title.
810                    # First, the date, in a very specific format.
811                    my $date = strftime("%a, %02e %b %H:%M:%S %Y ", localtime) .
812                        (tz_local_offset() / 30);
813                    # Environment data goes in here. We start with the date.
814                    my $environment = "$date.  ";
815                    # If we need to recap the message (because it's too long to be a title), we'll
816                    # put it in here.
817                    my $recap;
818                    # Copy the message and remove excess space.
819                    my $title = $message;
820                    $title =~ s/\s+/ /gs;
821                    # If it's too long, we have to split it up.
822                    if (length $title > 60) {
823                        # Put the full message in the environment string.
824                        $recap = $title;
825                        # Excerpt it as the title.
826                        $title = substr($title, 0, 50) . "...";
827                    }
828                    # If we have a CGI object, then this is a web error. Otherwise, it's
829                    # command-line.
830                    if (defined $SavedCGI) {
831                        # We're in a web service. The environment is the user's IP, and the link
832                        # is the URL that got us here.
833                        $environment .= "Event Reported at IP address $key process $$.";
834                        my $url = $SavedCGI->self_url();
835                        # We need the user agent string and (if available) the referrer.
836                        # The referrer will be the link.
837                        $environment .= " User Agent $ENV{HTTP_USER_AGENT}";
838                        if ($ENV{HTTP_REFERER}) {
839                            my $link = $ENV{HTTP_REFERER};
840                            $environment .= " referred from <a href=\"$link\">$link</a>.";
841                        } else {
842                            $environment .= " referrer unknown.";
843                        }
844                        # Close off the sentence with the original link.
845                        $environment .= " URL of event is <a href=\"$url\">$url</a>.";
846                    } else {
847                        # No CGI object, so we're a command-line tool. Use the tracing
848                        # key and the PID as the user identifier, and add the command.
849                        my $key = EmergencyKey();
850                        $environment .= "Event Reported by $key process $$.";
851                        if ($CommandLine) {
852                            # We're in a StandardSetup script, so we have the real command line.
853                            $environment .= "\n<pre>" . CGI::escapeHTML($CommandLine) . "</pre>\n";
854                        } elsif ($ENV{_}) {
855                            # We're in a BASH script, so the command has been stored in the _ variable.
856                            $environment .= "  Command = " . CGI::escapeHTML($ENV{_}) . "\n";
857                        }
858                    }
859                    # Build a GUID. We use the current time, the title, and the process ID,
860                    # then digest the result.
861                    my $guid = Digest::MD5::md5_base64(gettimeofday(), $title, $$);
862                    # Finally, the description. This is a stack trace plus various environmental stuff.
863                    # The trace is optional.
864                    my $stackTrace;
865                    if ($options{noStack}) {
866                        $stackTrace = "";
867                    } else {
868                        my @trace = LongMess();
869                        # Only proceed if we got something back.
870                        if (scalar(@trace) > 0) {
871                            $trace[0] =~ s/Tracer::Warn.+?called/Event occurred/;
872                            $stackTrace = "Stack trace:<pre>" . join("\n", @trace, "</pre>");
873                        }
874                    }
875                    # We got the stack trace. Now it's time to put it all together.
876                    # We have a goofy thing here in that we need to HTML-escape some sections of the description
877                    # twice. They will be escaped once here, and then once when written by XML::Simple. They are
878                    # unescaped once when processed by the RSS reader, and stuff in the description is treated as
879                    # HTML. So, anything escaped here is treated as a literal when viewed in the RSS reader, but
880                    # our <br>s and <pre>s are used to format the description.
881                    $recap = (defined $recap ? "<em>" . CGI::escapeHTML($recap) . "</em><br /><br />" : "");
882                    my $description = "$recap$environment  $stackTrace";
883                    # Okay, we have all the pieces. Create a hash of the new event.
884                    my $newItem = { title => $title,
885                                    description => $description,
886                                    category => $LastCategory,
887                                    pubDate => $date,
888                                    guid => $guid,
889                                  };
890                    # We need XML capability for this.
891                    require XML::Simple;
892                    # The RSS document goes in here.
893                    my $rss;
894                    # Get the name of the RSS file. It's in the FIG temporary directory.
895                    my $fileName = "$FIG_Config::temp/$FIG_Config::error_feed";
896                    # Open the config file and lock it.
897                    $lock = Open(undef, "<$FIG_Config::fig_disk/config/FIG_Config.pm");
898                    flock $lock, LOCK_EX;
899                    # Does it exist?
900                    if (-s $fileName) {
901                        # Slurp it in.
902                        $rss = XML::Simple::XMLin($fileName, ForceArray => ['item']);
903                    } else {
904                        my $size = -s $fileName;
905                        # Create an empty channel.
906                        $rss = {
907                            channel => {
908                                title => 'NMPDR Warning Feed',
909                                link => "$FIG_Config::temp_url/$FIG_Config::error_feed",
910                                description => "Important messages regarding the status of the NMPDR.",
911                                generator => "NMPDR Trace Facility",
912                                docs => "http://blogs.law.harvard.edu/tech/rss",
913                                item => []
914                            },
915                        };
916                    }
917                    # Get the channel object.
918                    my $channel = $rss->{channel};
919                    # Update the last-build date.
920                    $channel->{lastBuildDate} = $date;
921                    # Get the item array.
922                    my $items = $channel->{item};
923                    # Insure it has only 100 entries.
924                    while (scalar @{$items} > 100) {
925                        pop @{$items};
926                    }
927                    # Add our new item at the front.
928                    unshift @{$items}, $newItem;
929                    # Create the XML. Note we do not include the root or the declaration. XML Simple can't handle
930                    # the requirements for those.
931                    my $xml = XML::Simple::XMLout($channel, NoAttr => 1, RootName => 'channel', XmlDecl => '');
932                    # Here we put in the root and declaration. The problem is that the root has to have the version attribute
933                    # in it. So, we suppress the root and do it by hand, and that requires suppressing the declaration, too.
934                    $xml = "<?xml version=\"1.0\" encoding=\"utf-8\"?>\n<rss version=\"2.0\">$xml\n</rss>";
935                    # We don't use Open here because we can't afford an error.
936                    if (open XMLOUT, ">$fileName") {
937                        print XMLOUT $xml;
938                        close XMLOUT;
939                    }
940                }
941            }
942        };
943        if ($@) {
944            # If the feed failed, we need to know why. The error will be traced, but this method will not be involved
945            # (which is a good thing).
946            my $error = $@;
947            Trace("Feed Error: $error") if T(Feed => 0);
948        }
949        # Be sure to unlock.
950        if ($lock) {
951            flock $lock, LOCK_UN;
952            undef $lock;
953        }
954        # Restore the error message.
955        $@ = $savedError;
956    }
957    
958    
959    
960    
961    =head3 Assert
962    
963        Assert($condition1, $condition2, ... $conditionN);
964    
965    Return TRUE if all the conditions are true. This method can be used in conjunction with
966    the OR operator and the L</Confess> method as a debugging assert.
967    So, for example
968    
969        Assert($recNum >= 0) || Confess("Invalid record number $recNum.");
970    
971    Will abort the program with a stack trace if the value of C<$recNum> is negative.
972    
973    =cut
974    sub Assert {
975        my $retVal = 1;
976        LOOP: for my $condition (@_) {
977            if (! $condition) {
978                $retVal = 0;
979                last LOOP;
980            }
981        }
982        return $retVal;
983    }
984    
985    =head3 Cluck
986    
987        Cluck($message);
988    
989    Trace the call stack. Note that for best results, you should qualify the call with a
990    trace condition. For example,
991    
992        Cluck("Starting record parse.") if T(3);
993    
994    will only trace the stack if the trace level for the package is 3 or more.
995    
996    =over 4
997    
998    =item message
999    
1000    Message to include in the trace.
1001    
1002    =back
1003    
1004    =cut
1005    
1006    sub Cluck {
1007        # Get the parameters.
1008        my ($message) = @_;
1009        # Trace what's happening.
1010        Trace("Stack trace for event: $message");
1011        # Get the stack trace.
1012        my @trace = LongMess();
1013        # Convert the trace to a series of messages.
1014        for my $line (@trace) {
1015            # Replace the tab at the beginning with spaces.
1016            $line =~ s/^\t/    /;
1017            # Trace the line.
1018            Trace($line);
1019        }
1020        # Issue a warning. This displays the event message and inserts it into the RSS error feed.
1021        Warn($message);
1022    }
1023    
1024    =head3 LongMess
1025    
1026        my @lines = Tracer::LongMess();
1027    
1028    Return a stack trace with all tracing methods removed. The return will be in the form of a list
1029    of message strings.
1030    
1031    =cut
1032    
1033    sub LongMess {
1034        # Declare the return variable.
1035        my @retVal = ();
1036        my $confession = longmess("");
1037        for my $line (split /\s*\n/, $confession) {
1038            unless ($line =~ /Tracer\.pm/) {
1039                # Here we have a line worth keeping. Push it onto the result list.
1040                push @retVal, $line;
1041            }
1042        }
1043        # Return the result.
1044        return @retVal;
1045    }
1046    
1047    =head3 ETracing
1048    
1049        ETracing($parameter);
1050    
1051    Set up emergency tracing. Emergency tracing is tracing that is turned
1052    on automatically for any program that calls this method. The emergency
1053    tracing parameters are stored in a a file identified by a tracing key.
1054    If this method is called with a CGI object, then the tracing key is
1055    taken from a cookie. If it is called with no parameters, then the tracing
1056    key is taken from an environment variable. If it is called with a string,
1057    the tracing key is that string.
1058    
1059    =over 4
1060    
1061    =item parameter
1062    
1063    A parameter from which the tracing key is computed. If it is a scalar,
1064    that scalar is used as the tracing key. If it is a CGI object, the
1065    tracing key is taken from the C<IP> cookie. If it is omitted, the
1066    tracing key is taken from the C<TRACING> environment variable. If it
1067    is a CGI object and emergency tracing is not on, the C<Trace> and
1068    C<TF> parameters will be used to determine the type of tracing.
1069    
1070    =back
1071    
1072    =cut
1073    
1074    sub ETracing {
1075        # Get the parameter.
1076        my ($parameter) = @_;
1077        # Check for CGI mode.
1078        if (defined $parameter && ref $parameter eq 'CGI') {
1079            $SavedCGI = $parameter;
1080        } else {
1081            $SavedCGI = undef;
1082        }
1083        # Default to no tracing except errors.
1084        my ($tracing, $dest) = ("0", "WARN");
1085        # Check for emergency tracing.
1086        my $tkey = EmergencyKey($parameter);
1087        my $emergencyFile = EmergencyFileName($tkey);
1088        if (-e $emergencyFile) {
1089            # We have the file. Read in the data.
1090            my @tracing = GetFile($emergencyFile);
1091            # Pull off the time limit.
1092            my $expire = shift @tracing;
1093            # Convert it to seconds.
1094            $expire *= 3600;
1095            # Check the file data.
1096            my $stat = stat($emergencyFile);
1097            my ($now) = gettimeofday;
1098            if ($now - $stat->mtime > $expire) {
1099                # Delete the expired file.
1100                unlink $emergencyFile;
1101            } else {
1102                # Emergency tracing is on. Pull off the destination and
1103                # the trace level;
1104                $dest = shift @tracing;
1105                my $level = shift @tracing;
1106                # Convert the destination to a real tracing destination.
1107                # temp directory.
1108                $dest = EmergencyTracingDest($tkey, $dest);
1109                # Insure Tracer is specified.
1110                my %moduleHash = map { $_ => 1 } @tracing;
1111                $moduleHash{Tracer} = 1;
1112                # Set the trace parameter.
1113                $tracing = join(" ", $level, sort keys %moduleHash);
1114            }
1115        } elsif (defined $SavedCGI) {
1116            # There's no emergency tracing, but we have a CGI object, so check
1117            # for tracing from the form parameters.
1118            if ($SavedCGI->param('Trace')) {
1119                # Here the user has requested tracing via a form.
1120                $dest = ($SavedCGI->param('TF') ? ">$FIG_Config::temp/Trace$$.log" : "QUEUE");
1121                $tracing = $SavedCGI->param('Trace') . " Tracer";
1122            }
1123        }
1124        # Setup the tracing we've determined from all the stuff above.
1125        TSetup($tracing, $dest);
1126        # Check to see if we're a web script.
1127        if (defined $SavedCGI) {
1128            # Yes we are. Trace the form and environment data.
1129            TraceParms($SavedCGI);
1130            # Check for RAW mode. In raw mode, we print a fake header so that we see everything
1131            # emitted by the script in its raw form.
1132            if (T(Raw => 3)) {
1133                print CGI::header(-type => 'text/plain', -tracing => 'Raw');
1134            }
1135        }
1136    }
1137    
1138    =head3 EmergencyFileName
1139    
1140        my $fileName = Tracer::EmergencyFileName($tkey);
1141    
1142    Return the emergency tracing file name. This is the file that specifies
1143    the tracing information.
1144    
1145    =over 4
1146    
1147    =item tkey
1148    
1149    Tracing key for the current program.
1150    
1151    =item RETURN
1152    
1153    Returns the name of the file to contain the emergency tracing information.
1154    
1155    =back
1156    
1157    =cut
1158    
1159    sub EmergencyFileName {
1160        # Get the parameters.
1161        my ($tkey) = @_;
1162        # Compute the emergency tracing file name.
1163        return "$FIG_Config::temp/Emergency$tkey.txt";
1164    }
1165    
1166    =head3 EmergencyFileTarget
1167    
1168        my $fileName = Tracer::EmergencyFileTarget($tkey);
1169    
1170    Return the emergency tracing target file name. This is the file that receives
1171    the tracing output for file-based tracing.
1172    
1173    =over 4
1174    
1175    =item tkey
1176    
1177    Tracing key for the current program.
1178    
1179    =item RETURN
1180    
1181    Returns the name of the file to contain the trace output.
1182    
1183    =back
1184    
1185    =cut
1186    
1187    sub EmergencyFileTarget {
1188        # Get the parameters.
1189        my ($tkey) = @_;
1190        # Compute the emergency tracing file name.
1191        return "$FIG_Config::temp/trace$tkey.log";
1192    }
1193    
1194    =head3 EmergencyTracingDest
1195    
1196        my $dest = Tracer::EmergencyTracingDest($tkey, $myDest);
1197    
1198    This method converts an emergency tracing destination to a real
1199    tracing destination. The main difference is that if the
1200    destination is C<FILE> or C<APPEND>, we convert it to file
1201    output. If the destination is C<DUAL>, we convert it to file
1202    and standard output.
1203    
1204    =over 4
1205    
1206    =item tkey
1207    
1208    Tracing key for this environment.
1209    
1210    =item myDest
1211    
1212    Destination from the emergency tracing file.
1213    
1214    =item RETURN
1215    
1216    Returns a destination that can be passed into L</TSetup>.
1217    
1218    =back
1219    
1220    =cut
1221    
1222    sub EmergencyTracingDest {
1223        # Get the parameters.
1224        my ($tkey, $myDest) = @_;
1225        # Declare the return variable.
1226        my $retVal = $myDest;
1227        # Process according to the destination value.
1228        if ($myDest eq 'FILE') {
1229            $retVal = ">" . EmergencyFileTarget($tkey);
1230        } elsif ($myDest eq 'APPEND') {
1231            $retVal = ">>" . EmergencyFileTarget($tkey);
1232        } elsif ($myDest eq 'DUAL') {
1233            $retVal = "+>" . EmergencyFileTarget($tkey);
1234        } elsif ($myDest eq 'WARN') {
1235            $retVal = "WARN";
1236        }
1237        # Return the result.
1238        return $retVal;
1239    }
1240    
1241    =head3 Emergency
1242    
1243        Emergency($key, $hours, $dest, $level, @modules);
1244    
1245    Turn on emergency tracing. This method is normally invoked over the web from
1246    a debugging console, but it can also be called by the C<trace.pl> script.
1247    The caller specifies the duration of the emergency in hours, the desired tracing
1248    destination, the trace level, and a list of the trace modules to activate.
1249    For the length of the duration, when a program in an environment with the
1250    specified tracing key active invokes a Sprout CGI script, tracing will be
1251    turned on automatically. See L</TSetup> for more about tracing setup and
1252    L</ETracing> for more about emergency tracing.
1253    
1254    =over 4
1255    
1256    =item tkey
1257    
1258    The tracing key. This is used to identify the control file and the trace file.
1259    
1260    =item hours
1261    
1262    Number of hours to keep emergency tracing alive.
1263    
1264    =item dest
1265    
1266    Tracing destination. If no path information is specified for a file
1267    destination, it is put in the FIG temporary directory.
1268    
1269    =item level
1270    
1271    Tracing level. A higher level means more trace messages.
1272    
1273    =item modules
1274    
1275    A list of the tracing modules to activate.
1276    
1277    =back
1278    
1279    =cut
1280    
1281    sub Emergency {
1282        # Get the parameters.
1283        my ($tkey, $hours, $dest, $level, @modules) = @_;
1284        # Create the emergency file.
1285        my $specFile = EmergencyFileName($tkey);
1286        my $outHandle = Open(undef, ">$specFile");
1287        print $outHandle join("\n", $hours, $dest, $level, @modules, "");
1288    }
1289    
1290    =head3 EmergencyKey
1291    
1292        my $tkey = EmergencyKey($parameter);
1293    
1294    Return the Key to be used for emergency tracing. This could be an IP address,
1295     a session ID, or a user name, depending on the environment.
1296    
1297    =over 4
1298    
1299    =item parameter
1300    
1301    Parameter defining the method for finding the tracing key. If it is a scalar,
1302    then it is presumed to be the tracing key itself. If it is a CGI object, then
1303    the tracing key is taken from the C<IP> cookie. Otherwise, the tracing key is
1304    taken from the C<TRACING> environment variable.
1305    
1306    =item RETURN
1307    
1308    Returns the key to be used for labels in emergency tracing.
1309    
1310    =back
1311    
1312    =cut
1313    
1314    sub EmergencyKey {
1315        # Get the parameters.
1316        my ($parameter) = @_;
1317        # Declare the return variable.
1318        my $retVal;
1319        # Determine the parameter type.
1320        if (! defined $parameter || defined($ENV{TRACING})) {
1321            # Here we're supposed to check the environment. If that fails, we
1322            # get the effective login ID.
1323            $retVal = $ENV{TRACING} || scalar getpwuid($<);
1324        } else {
1325            my $ptype = ref $parameter;
1326            if ($ptype eq 'CGI') {
1327                # Here we were invoked from a web page. Look for a cookie.
1328                $retVal = $parameter->cookie('IP');
1329            } elsif (! $ptype) {
1330                # Here the key was passed in.
1331                $retVal = $parameter;
1332            }
1333        }
1334        # If no luck finding a key, use the PID.
1335        if (! defined $retVal) {
1336            $retVal = $$;
1337        }
1338        # Return the result.
1339        return $retVal;
1340    }
1341    
1342    
1343    =head3 TraceParms
1344    
1345        Tracer::TraceParms($cgi);
1346    
1347    Trace the CGI parameters at trace level CGI => 3 and the environment variables
1348    at level CGI => 4. A self-referencing URL is traced at level CGI => 2.
1349    
1350    =over 4
1351    
1352    =item cgi
1353    
1354    CGI query object containing the parameters to trace.
1355    
1356    =back
1357    
1358    =cut
1359    
1360    sub TraceParms {
1361        # Get the parameters.
1362        my ($cgi) = @_;
1363        if (T(CGI => 2)) {
1364            # Here we trace the GET-style URL for the script, but only if it's
1365            # relatively small.
1366            my $url = $cgi->url(-relative => 1, -query => 1);
1367            my $len = length($url);
1368            if ($len < 500) {
1369                Trace("[URL] $url");
1370            } elsif ($len > 2048) {
1371                Trace("[URL] URL is too long to use with GET ($len characters).");
1372            } else {
1373                Trace("[URL] URL length is $len characters.");
1374            }
1375        }
1376        if (T(CGI => 3)) {
1377            # Here we want to trace the parameter data.
1378            my @names = $cgi->param;
1379            for my $parmName (sort @names) {
1380                # Note we skip the Trace parameters, which are for our use only.
1381                if ($parmName ne 'Trace' && $parmName ne 'TF') {
1382                    my @values = $cgi->param($parmName);
1383                    Trace("[CGI] $parmName = " . join(", ", @values));
1384                }
1385            }
1386            # Display the request method.
1387            my $method = $cgi->request_method();
1388            Trace("Method: $method");
1389        }
1390        if (T(CGI => 4)) {
1391            # Here we want the environment data too.
1392            for my $envName (sort keys %ENV) {
1393                Trace("[ENV] $envName = $ENV{$envName}");
1394            }
1395        }
1396    }
1397    
1398    =head3 TraceImages
1399    
1400        Tracer::TraceImages($htmlString);
1401    
1402    Trace information about all of an html document's images. The tracing
1403    will be for type "IMG" at level 3. The image's source string
1404    will be displayed. This is generally either the URL of the image or
1405    raw data for the image itself. If the source is too long, only the first 300
1406    characters will be shown at trace level 3. The entire source will be shown,
1407    however, at trace level 4. This method is not very smart, and might catch
1408    Javascript code, but it is still useful when debugging the arcane
1409    behavior of images in multiple browser environments.
1410    
1411    =over 4
1412    
1413    =item htmlString
1414    
1415    HTML text for an outgoing web page.
1416    
1417    =back
1418    
1419    =cut
1420    
1421    sub TraceImages {
1422        # Only proceed if we're at the proper trace level.
1423        if (T(IMG => 3)) {
1424            # For performance reasons we're manipulating $_[0] instead of retrieving the string
1425            # into a variable called "$htmlString". This is because we expect html strings to be
1426            # long, and don't want to copy them any more than we have to.
1427            Trace(length($_[0]) . " characters in web page.");
1428            # Loop through the HTML, culling image tags.
1429            while ($_[0] =~ /<img\s+[^>]+?src="([^"]+)"/sgi) {
1430                # Extract the source string and determine whether or not it's too long.
1431                my $srcString = $1;
1432                my $pos = pos($_[0]) - length($srcString);
1433                my $excess = length($srcString) - 300;
1434                # We'll put the display string in here.
1435                my $srcDisplay = $srcString;
1436                # If it's a data string, split it at the comma.
1437                $srcDisplay =~ s/^(data[^,]+,)/$1\n/;
1438                # If there's no excess or we're at trace level 4, we're done. At level 3 with
1439                # a long string, however, we only show the first 300 characters.
1440                if ($excess > 0 && ! T(IMG => 4)) {
1441                    $srcDisplay = substr($srcDisplay,0,300) . "\nplus $excess characters.";
1442                }
1443                # Output the trace message.
1444                Trace("Image tag at position $pos:\n$srcDisplay");
1445            }
1446        }
1447    }
1448    
1449    =head2 Command-Line Utility Methods
1450    
1451    =head3 SendSMS
1452    
1453        my $msgID = Tracer::SendSMS($phoneNumber, $msg);
1454    
1455    Send a text message to a phone number using Clickatell. The FIG_Config file must contain the
1456    user name, password, and API ID for the relevant account in the hash reference variable
1457    I<$FIG_Config::phone>, using the keys C<user>, C<password>, and C<api_id>. For
1458    example, if the user name is C<BruceTheHumanPet>, the password is C<silly>, and the API ID
1459    is C<2561022>, then the FIG_Config file must contain
1460    
1461        $phone =  { user => 'BruceTheHumanPet',
1462                    password => 'silly',
1463                    api_id => '2561022' };
1464    
1465    The original purpose of this method was to insure Bruce would be notified immediately when the
1466    Sprout Load terminates. Care should be taken if you do not wish Bruce to be notified immediately
1467    when you call this method.
1468    
1469    The message ID will be returned if successful, and C<undef> if an error occurs.
1470    
1471    =over 4
1472    
1473    =item phoneNumber
1474    
1475    Phone number to receive the message, in international format. A United States phone number
1476    would be prefixed by "1". A British phone number would be prefixed by "44".
1477    
1478    =item msg
1479    
1480    Message to send to the specified phone.
1481    
1482    =item RETURN
1483    
1484    Returns the message ID if successful, and C<undef> if the message could not be sent.
1485    
1486    =back
1487    
1488    =cut
1489    
1490    sub SendSMS {
1491        # Get the parameters.
1492        my ($phoneNumber, $msg) = @_;
1493        # Declare the return variable. If we do not change it, C<undef> will be returned.
1494        my $retVal;
1495        # Only proceed if we have phone support.
1496        if (! defined $FIG_Config::phone) {
1497            Trace("Phone support not present in FIG_Config.") if T(1);
1498        } else {
1499            # Get the phone data.
1500            my $parms = $FIG_Config::phone;
1501            # Get the Clickatell URL.
1502            my $url = "http://api.clickatell.com/http/";
1503            # Create the user agent.
1504            my $ua = LWP::UserAgent->new;
1505            # Request a Clickatell session.
1506            my $resp = $ua->post("$url/sendmsg", { user => $parms->{user},
1507                                         password => $parms->{password},
1508                                         api_id => $parms->{api_id},
1509                                         to => $phoneNumber,
1510                                         text => $msg});
1511            # Check for an error.
1512            if (! $resp->is_success) {
1513                Trace("Alert failed.") if T(1);
1514            } else {
1515                # Get the message ID.
1516                my $rstring = $resp->content;
1517                if ($rstring =~ /^ID:\s+(.*)$/) {
1518                    $retVal = $1;
1519                } else {
1520                    Trace("Phone attempt failed with $rstring") if T(1);
1521                }
1522            }
1523        }
1524        # Return the result.
1525        return $retVal;
1526    }
1527    
1528    =head3 StandardSetup
1529    
1530        my ($options, @parameters) = StandardSetup(\@categories, \%options, $parmHelp, @ARGV);
1531    
1532    This method performs standard command-line parsing and tracing setup. The return
1533    values are a hash of the command-line options and a list of the positional
1534    parameters. Tracing is automatically set up and the command-line options are
1535    validated.
1536    
1537    This is a complex method that does a lot of grunt work. The parameters can
1538    be more easily understood, however, once they are examined individually.
1539    
1540    The I<categories> parameter is the most obtuse. It is a reference to a list of
1541    special-purpose tracing categories. Most tracing categories are PERL package
1542    names. So, for example, if you wanted to turn on tracing inside the B<Sprout>,
1543    B<ERDB>, and B<SproutLoad> packages, you would specify the categories
1544    
1545        ["Sprout", "SproutLoad", "ERDB"]
1546    
1547    This would cause trace messages in the specified three packages to appear in
1548    the output. There are two special tracing categories that are automatically
1549    handled by this method. In other words, if you used L</TSetup> you would need
1550    to include these categories manually, but if you use this method they are turned
1551    on automatically.
1552    
1553    =over 4
1554    
1555    =item SQL
1556    
1557    Traces SQL commands and activity.
1558    
1559    =item Tracer
1560    
1561    Traces error messages and call stacks.
1562    
1563    =back
1564    
1565    C<SQL> is only turned on if the C<-sql> option is specified in the command line.
1566    The trace level is specified using the C<-trace> command-line option. For example,
1567    the following command line for C<TransactFeatures> turns on SQL tracing and runs
1568    all tracing at level 3.
1569    
1570        TransactFeatures -trace=3 -sql register ../xacts IDs.tbl
1571    
1572    Standard tracing is output to the standard output and echoed to the file
1573    C<trace>I<$$>C<.log> in the FIG temporary directory, where I<$$> is the
1574    process ID. You can also specify the C<user> parameter to put a user ID
1575    instead of a process ID in the trace file name. So, for example
1576    
1577    The default trace level is 2. To get all messages, specify a trace level of 4.
1578    For a genome-by-genome update, use 3.
1579    
1580        TransactFeatures -trace=3 -sql -user=Bruce register ../xacts IDs.tbl
1581    
1582    would send the trace output to C<traceBruce.log> in the temporary directory.
1583    
1584    The I<options> parameter is a reference to a hash containing the command-line
1585    options, their default values, and an explanation of what they mean. Command-line
1586    options may be in the form of switches or keywords. In the case of a switch, the
1587    option value is 1 if it is specified and 0 if it is not specified. In the case
1588    of a keyword, the value is separated from the option name by an equal sign. You
1589    can see this last in the command-line example above.
1590    
1591    You can specify a different default trace level by setting C<$options->{trace}>
1592    prior to calling this method.
1593    
1594    An example at this point would help. Consider, for example, the command-line utility
1595    C<TransactFeatures>. It accepts a list of positional parameters plus the options
1596    C<safe>, C<noAlias>, C<start>, and C<tblFiles>. To start up this command, we execute
1597    the following code.
1598    
1599        my ($options, @parameters) = Tracer::StandardSetup(["DocUtils"],
1600                            { safe => [0, "use database transactions"],
1601                              noAlias => [0, "do not expect aliases in CHANGE transactions"],
1602                              start => [' ', "start with this genome"],
1603                              tblFiles => [0, "output TBL files containing the corrected IDs"] },
1604                            "<command> <transactionDirectory> <IDfile>",
1605                          @ARGV);
1606    
1607    
1608    The call to C<ParseCommand> specifies the default values for the options and
1609    stores the actual options in a hash that is returned as C<$options>. The
1610    positional parameters are returned in C<@parameters>.
1611    
1612    The following is a sample command line for C<TransactFeatures>.
1613    
1614        TransactFeatures -trace=2 -noAlias register ../xacts IDs.tbl
1615    
1616    Single and double hyphens are equivalent. So, you could also code the
1617    above command as
1618    
1619        TransactFeatures --trace=2 --noAlias register ../xacts IDs.tbl
1620    
1621    In this case, C<register>, C<../xacts>, and C<IDs.tbl> are the positional
1622    parameters, and would find themselves in I<@parameters> after executing the
1623    above code fragment. The tracing would be set to level 2, and the categories
1624    would be C<Tracer>, and <DocUtils>. C<Tracer> is standard,
1625    and C<DocUtils> was included because it came in within the first parameter
1626    to this method. The I<$options> hash would be
1627    
1628        { trace => 2, sql => 0, safe => 0,
1629          noAlias => 1, start => ' ', tblFiles => 0 }
1630    
1631    Use of C<StandardSetup> in this way provides a simple way of performing
1632    standard tracing setup and command-line parsing. Note that the caller is
1633    not even aware of the command-line switches C<-trace> and C<-sql>, which
1634    are used by this method to control the tracing. If additional tracing features
1635    need to be added in the future, they can be processed by this method without
1636    upsetting the command-line utilities.
1637    
1638    If the C<background> option is specified on the command line, then the
1639    standard and error outputs will be directed to files in the temporary
1640    directory, using the same suffix as the trace file. So, if the command
1641    line specified
1642    
1643        -user=Bruce -background
1644    
1645    then the trace output would go to C<traceBruce.log>, the standard output to
1646    C<outBruce.log>, and the error output to C<errBruce.log>. This is designed to
1647    simplify starting a command in the background.
1648    
1649    The user name is also used as the tracing key for L</Emergency Tracing>.
1650    Specifying a value of C<E> for the trace level causes emergency tracing to
1651    be used instead of custom tracing. If the user name is not specified,
1652    the tracing key is taken from the C<Tracing> environment variable. If there
1653    is no value for that variable, the tracing key will be computed from the active
1654    login ID.
1655    
1656    Since the default situation in StandardSetup is to trace to the standard
1657    output, errors that occur in command-line scripts will not generate
1658    RSS events. To force the events, use the C<warn> option.
1659    
1660        TransactFeatures -background -warn register ../xacts IDs.tbl
1661    
1662    Finally, if the special option C<-help> is specified, the option
1663    names will be traced at level 0 and the program will exit without processing.
1664    This provides a limited help capability. For example, if the user enters
1665    
1666        TransactFeatures -help
1667    
1668    he would see the following output.
1669    
1670        TransactFeatures [options] <command> <transactionDirectory> <IDfile>
1671            -trace    tracing level (default E)
1672            -sql      trace SQL commands
1673            -safe     use database transactions
1674            -noAlias  do not expect aliases in CHANGE transactions
1675            -start    start with this genome
1676            -tblFiles output TBL files containing the corrected IDs
1677            -forked   do not erase the trace file before tracing
1678    
1679    The caller has the option of modifying the tracing scheme by placing a value
1680    for C<trace> in the incoming options hash. The default value can be overridden,
1681    or the tracing to the standard output can be turned off by suffixing a minus
1682    sign to the trace level. So, for example,
1683    
1684        { trace => [0, "tracing level (default 0)"],
1685           ...
1686    
1687    would set the default trace level to 0 instead of E, while
1688    
1689        { trace => ["2-", "tracing level (default 2)"],
1690           ...
1691    
1692    would set the default to 2, but trace only to the log file, not to the
1693    standard output.
1694    
1695    The parameters to this method are as follows.
1696    
1697    =over 4
1698    
1699    =item categories
1700    
1701    Reference to a list of tracing category names. These should be names of
1702    packages whose internal workings will need to be debugged to get the
1703    command working.
1704    
1705    =item options
1706    
1707    Reference to a hash containing the legal options for the current command mapped
1708    to their default values and descriptions. The user can override the defaults
1709    by specifying the options as command-line switches prefixed by a hyphen.
1710    Tracing-related options may be added to this hash. If the C<-h> option is
1711    specified on the command line, the option descriptions will be used to
1712    explain the options. To turn off tracing to the standard output, add a
1713    minus sign to the value for C<trace> (see above).
1714    
1715    =item parmHelp
1716    
1717    A string that vaguely describes the positional parameters. This is used
1718    if the user specifies the C<-h> option.
1719    
1720    =item argv
1721    
1722    List of command line parameters, including the option switches, which must
1723    precede the positional parameters and be prefixed by a hyphen.
1724    
1725    =item RETURN
1726    
1727    Returns a list. The first element of the list is the reference to a hash that
1728    maps the command-line option switches to their values. These will either be the
1729    default values or overrides specified on the command line. The remaining
1730    elements of the list are the position parameters, in order.
1731    
1732    =back
1733    
1734    =cut
1735    
1736    sub StandardSetup {
1737        # Get the parameters.
1738        my ($categories, $options, $parmHelp, @argv) = @_;
1739        # Get the default tracing key.
1740        my $tkey = EmergencyKey();
1741        # Save the command line.
1742        $CommandLine = join(" ", $0, map { $_ =~ /\s/ ? "\"$_\"" : $_ } @argv);
1743        # Add the tracing options.
1744        if (! exists $options->{trace}) {
1745            $options->{trace} = ['2', "tracing level (E for emergency tracing)"];
1746        }
1747        if (! exists $options->{forked}) {
1748            $options->{forked} = [0, "keep old trace file"];
1749        }
1750        $options->{sql} = [0, "turn on SQL tracing"];
1751        $options->{help} = [0, "display command-line options"];
1752        $options->{user} = [$tkey, "tracing key"];
1753        $options->{background} = [0, "spool standard and error output"];
1754        $options->{warn} = [0, "send errors to RSS feed"];
1755        $options->{moreTracing} = ["", "comma-delimited list of additional trace modules for debugging"];
1756        # Create a parsing hash from the options hash. The parsing hash
1757        # contains the default values rather than the default value
1758        # and the description. While we're at it, we'll memorize the
1759        # length of the longest option name.
1760        my $longestName = 0;
1761        my %parseOptions = ();
1762        for my $key (keys %{$options}) {
1763            if (length $key > $longestName) {
1764              $longestName = length $key;              $longestName = length $key;
1765          }          }
1766          $parseOptions{$key} = $options->{$key}->[0];          $parseOptions{$key} = $options->{$key}->[0];
1767        }
1768        # Parse the command line.
1769        my ($retOptions, @retParameters) = ParseCommand(\%parseOptions, @argv);
1770        # Get the logfile suffix.
1771        my $suffix = $retOptions->{user};
1772        # We'll put the trace file name in here. We need it later if background
1773        # mode is on.
1774        my $traceFileName;
1775        # Now we want to set up tracing. First, we need to know if the user
1776        # wants emergency tracing.
1777        if ($retOptions->{trace} eq 'E') {
1778            ETracing($retOptions->{user});
1779        } else {
1780            # Here the tracing is controlled from the command line.
1781            my @cats = @{$categories};
1782            if ($retOptions->{sql}) {
1783                push @cats, "SQL";
1784            }
1785            if ($retOptions->{warn}) {
1786                push @cats, "Feed";
1787            }
1788            # Add the default categories.
1789            push @cats, "Tracer";
1790            # Check for more tracing groups.
1791            if ($retOptions->{moreTracing}) {
1792                push @cats, split /,/, $retOptions->{moreTracing};
1793            }
1794            # Next, we create the category string by joining the categories.
1795            my $cats = join(" ", @cats);
1796            # Check to determine whether or not the caller wants to turn off tracing
1797            # to the standard output.
1798            my $traceLevel = $retOptions->{trace};
1799            my $textOKFlag = 1;
1800            if ($traceLevel =~ /^(.)-/) {
1801                $traceLevel = $1;
1802                $textOKFlag = 0;
1803            }
1804            # Now we set up the trace mode.
1805            my $traceMode;
1806            # Verify that we can open a file in the FIG temporary directory.
1807            my $traceFileName = "$FIG_Config::temp/trace$suffix.log";
1808            my $traceFileSpec = ($retOptions->{forked} ? ">>$traceFileName" : ">$traceFileName");
1809            if (open TESTTRACE, "$traceFileSpec") {
1810                # Here we can trace to a file.
1811                $traceMode = ">>$traceFileName";
1812                if ($textOKFlag) {
1813                    # Echo to standard output if the text-OK flag is set.
1814                    $traceMode = "+$traceMode";
1815                }
1816                # Close the test file.
1817                close TESTTRACE;
1818            } else {
1819                # Here we can't trace to a file. Complain about this.
1820                warn "Could not open trace file $traceFileName: $!\n";
1821                # We trace to the standard output if it's
1822                # okay, and the error log otherwise.
1823                if ($textOKFlag) {
1824                    $traceMode = "TEXT";
1825                } else {
1826                    $traceMode = "WARN";
1827                }
1828            }
1829            # Now set up the tracing.
1830            TSetup("$traceLevel $cats", $traceMode);
1831        }
1832        # Check for background mode.
1833        if ($retOptions->{background}) {
1834            my $outFileName = "$FIG_Config::temp/out$suffix$$.log";
1835            my $errFileName = "$FIG_Config::temp/err$suffix$$.log";
1836            # Spool the output.
1837            open STDOUT, ">$outFileName";
1838            # If we have a trace file, trace the errors to the log. Otherwise,
1839            # spool the errors.
1840            if (defined $traceFileName) {
1841                open STDERR, "| Tracer $traceFileName";
1842            } else {
1843                open STDERR, ">$errFileName";
1844            }
1845            # Check for phone support. If we have phone support and a phone number,
1846            # we want to turn it on.
1847            if ($ENV{PHONE} && defined($FIG_Config::phone)) {
1848                $retOptions->{phone} = $ENV{PHONE};
1849            }
1850        }
1851        # Check for the "help" option. If it is specified, dump the command-line
1852        # options and exit the program.
1853        if ($retOptions->{help}) {
1854            $0 =~ m#[/\\](\w+)(\.pl)?$#i;
1855            print "$1 [options] $parmHelp\n";
1856            for my $key (sort keys %{$options}) {
1857                my $name = Pad($key, $longestName, 0, ' ');
1858                my $desc = $options->{$key}->[1];
1859                if ($options->{$key}->[0]) {
1860                    $desc .= " (default " . $options->{$key}->[0] . ")";
1861                }
1862                print "  $name $desc\n";
1863            }
1864            exit(0);
1865        }
1866        # Trace the options, if applicable.
1867        if (T(3)) {
1868            my @parms = grep { $retOptions->{$_} } keys %{$retOptions};
1869            Trace("Selected options: " . join(", ", sort @parms) . ".");
1870        }
1871        # Return the parsed parameters.
1872        return ($retOptions, @retParameters);
1873    }
1874    
1875    =head3 ReadOptions
1876    
1877        my %options = Tracer::ReadOptions($fileName);
1878    
1879    Read a set of options from a file. Each option is encoded in a line of text that has the
1880    format
1881    
1882    I<optionName>C<=>I<optionValue>C<; >I<comment>
1883    
1884    The option name must consist entirely of letters, digits, and the punctuation characters
1885    C<.> and C<_>, and is case sensitive. Blank lines and lines in which the first nonblank
1886    character is a semi-colon will be ignored. The return hash will map each option name to
1887    the corresponding option value.
1888    
1889    =over 4
1890    
1891    =item fileName
1892    
1893    Name of the file containing the option data.
1894    
1895    =item RETURN
1896    
1897    Returns a hash mapping the option names specified in the file to their corresponding option
1898    value.
1899    
1900    =back
1901    
1902    =cut
1903    
1904    sub ReadOptions {
1905        # Get the parameters.
1906        my ($fileName) = @_;
1907        # Open the file.
1908        (open CONFIGFILE, "<$fileName") || Confess("Could not open option file $fileName.");
1909        # Count the number of records read.
1910        my ($records, $comments) = 0;
1911        # Create the return hash.
1912        my %retVal = ();
1913        # Loop through the file, accumulating key-value pairs.
1914        while (my $line = <CONFIGFILE>) {
1915            # Denote we've read a line.
1916            $records++;
1917            # Determine the line type.
1918            if ($line =~ /^\s*[\n\r]/) {
1919                # A blank line is a comment.
1920                $comments++;
1921            } elsif ($line =~ /^\s*([A-Za-z0-9_\.]+)=([^;]*);/) {
1922                # Here we have an option assignment.
1923                retVal{$1} = $2;
1924            } elsif ($line =~ /^\s*;/) {
1925                # Here we have a text comment.
1926                $comments++;
1927            } else {
1928                # Here we have an invalid line.
1929                Trace("Invalid option statement in record $records.") if T(0);
1930            }
1931        }
1932        # Return the hash created.
1933        return %retVal;
1934    }
1935    
1936    =head3 GetOptions
1937    
1938        Tracer::GetOptions(\%defaults, \%options);
1939    
1940    Merge a specified set of options into a table of defaults. This method takes two hash references
1941    as input and uses the data from the second to update the first. If the second does not exist,
1942    there will be no effect. An error will be thrown if one of the entries in the second hash does not
1943    exist in the first.
1944    
1945    Consider the following example.
1946    
1947        my $optionTable = GetOptions({ dbType => 'mySQL', trace => 0 }, $options);
1948    
1949    In this example, the variable B<$options> is expected to contain at most two options-- B<dbType> and
1950    B<trace>. The default database type is C<mySQL> and the default trace level is C<0>. If the value of
1951    B<$options> is C<< {dbType => 'Oracle'} >>, then the database type will be changed to C<Oracle> and
1952    the trace level will remain at 0. If B<$options> is undefined, then the database type and trace level
1953    will remain C<mySQL> and C<0>. If, on the other hand, B<$options> is defined as
1954    
1955        {databaseType => 'Oracle'}
1956    
1957    an error will occur because the B<databaseType> option does not exist.
1958    
1959    =over 4
1960    
1961    =item defaults
1962    
1963    Table of default option values.
1964    
1965    =item options
1966    
1967    Table of overrides, if any.
1968    
1969    =item RETURN
1970    
1971    Returns a reference to the default table passed in as the first parameter.
1972    
1973    =back
1974    
1975    =cut
1976    
1977    sub GetOptions {
1978        # Get the parameters.
1979        my ($defaults, $options) = @_;
1980        # Check for overrides.
1981        if ($options) {
1982            # Loop through the overrides.
1983            while (my ($option, $setting) = each %{$options}) {
1984                # Insure this override exists.
1985                if (!exists $defaults->{$option}) {
1986                    croak "Unrecognized option $option encountered.";
1987                } else {
1988                    # Apply the override.
1989                    $defaults->{$option} = $setting;
1990                }
1991            }
1992        }
1993        # Return the merged table.
1994        return $defaults;
1995    }
1996    
1997    =head3 MergeOptions
1998    
1999        Tracer::MergeOptions(\%table, \%defaults);
2000    
2001    Merge default values into a hash table. This method looks at the key-value pairs in the
2002    second (default) hash, and if a matching key is not found in the first hash, the default
2003    pair is copied in. The process is similar to L</GetOptions>, but there is no error-
2004    checking and no return value.
2005    
2006    =over 4
2007    
2008    =item table
2009    
2010    Hash table to be updated with the default values.
2011    
2012    =item defaults
2013    
2014    Default values to be merged into the first hash table if they are not already present.
2015    
2016    =back
2017    
2018    =cut
2019    
2020    sub MergeOptions {
2021        # Get the parameters.
2022        my ($table, $defaults) = @_;
2023        # Loop through the defaults.
2024        while (my ($key, $value) = each %{$defaults}) {
2025            if (!exists $table->{$key}) {
2026                $table->{$key} = $value;
2027            }
2028        }
2029    }
2030    
2031    =head3 UnparseOptions
2032    
2033        my $optionString = Tracer::UnparseOptions(\%options);
2034    
2035    Convert an option hash into a command-line string. This will not
2036    necessarily be the same text that came in, but it will nonetheless
2037    produce the same ultimate result when parsed by L</StandardSetup>.
2038    
2039    =over 4
2040    
2041    =item options
2042    
2043    Reference to a hash of options to convert into an option string.
2044    
2045    =item RETURN
2046    
2047    Returns a string that will parse to the same set of options when
2048    parsed by L</StandardSetup>.
2049    
2050    =back
2051    
2052    =cut
2053    
2054    sub UnparseOptions {
2055        # Get the parameters.
2056        my ($options) = @_;
2057        # The option segments will be put in here.
2058        my @retVal = ();
2059        # Loop through the options.
2060        for my $key (keys %$options) {
2061            # Get the option value.
2062            my $value = $options->{$key};
2063            # Only use it if it's nonempty.
2064            if (defined $value && $value ne "") {
2065                my $segment = "--$key=$value";
2066                # Quote it if necessary.
2067                if ($segment =~ /[ |<>*]/) {
2068                    $segment = '"' . $segment . '"';
2069                }
2070                # Add it to the return list.
2071                push @retVal, $segment;
2072            }
2073        }
2074        # Return the result.
2075        return join(" ", @retVal);
2076    }
2077    
2078    =head3 ParseCommand
2079    
2080        my ($options, @arguments) = Tracer::ParseCommand(\%optionTable, @inputList);
2081    
2082    Parse a command line consisting of a list of parameters. The initial parameters may be option
2083    specifiers of the form C<->I<option> or C<->I<option>C<=>I<value>. The options are stripped
2084    off and merged into a table of default options. The remainder of the command line is
2085    returned as a list of positional arguments. For example, consider the following invocation.
2086    
2087        my ($options, @arguments) = ParseCommand({ errors => 0, logFile => 'trace.log'}, @words);
2088    
2089    In this case, the list @words will be treated as a command line and there are two options available,
2090    B<errors> and B<logFile>. If @words has the following format
2091    
2092        -logFile=error.log apple orange rutabaga
2093    
2094    then at the end of the invocation, C<$options> will be
2095    
2096        { errors => 0, logFile => 'error.log' }
2097    
2098    and C<@arguments> will contain
2099    
2100        apple orange rutabaga
2101    
2102    The parser allows for some escape sequences. See L</UnEscape> for a description. There is no
2103    support for quote characters. Options can be specified with single or double hyphens.
2104    
2105    =over 4
2106    
2107    =item optionTable
2108    
2109    Table of default options.
2110    
2111    =item inputList
2112    
2113    List of words on the command line.
2114    
2115    =item RETURN
2116    
2117    Returns a reference to the option table and a list of the positional arguments.
2118    
2119    =back
2120    
2121    =cut
2122    
2123    sub ParseCommand {
2124        # Get the parameters.
2125        my ($optionTable, @inputList) = @_;
2126        # Process any options in the input list.
2127        my %overrides = ();
2128        while ((@inputList > 0) && ($inputList[0] =~ /^--?/)) {
2129            # Get the current option.
2130            my $arg = shift @inputList;
2131            # Pull out the option name.
2132            $arg =~ /^--?([^=]*)/g;
2133            my $name = $1;
2134            # Check for an option value.
2135            if ($arg =~ /\G=(.*)$/g) {
2136                # Here we have a value for the option.
2137                $overrides{$name} = UnEscape($1);
2138            } else {
2139                # Here there is no value, so we use 1.
2140                $overrides{$name} = 1;
2141      }      }
     # Parse the command line.  
     my ($retOptions, @retParameters) = ParseCommand(\%parseOptions, @argv);  
     # Get the logfile suffix.  
     my $suffix = $retOptions->{user};  
     # Check for background mode.  
     if ($retOptions->{background}) {  
         my $outFileName = "$FIG_Config::temp/out$suffix.log";  
         my $errFileName = "$FIG_Config::temp/err$suffix.log";  
         open STDOUT, ">$outFileName";  
         open STDERR, ">$errFileName";  
2142      }      }
2143      # Now we want to set up tracing. First, we need to know if SQL is to      # Merge the options into the defaults.
2144      # be traced.      GetOptions($optionTable, \%overrides);
2145      my @cats = @{$categories};      # Translate the remaining parameters.
2146      if ($retOptions->{sql}) {      my @retVal = ();
2147          push @cats, "SQL";      for my $inputParm (@inputList) {
2148            push @retVal, UnEscape($inputParm);
2149      }      }
2150      # Add the default categories.      # Return the results.
2151      push @cats, "Tracer", "FIG";      return ($optionTable, @retVal);
     # Next, we create the category string by joining the categories.  
     my $cats = join(" ", @cats);  
     # Check to determine whether or not the caller wants to turn off tracing  
     # to the standard output.  
     my $traceLevel = $retOptions->{trace};  
     my $textOKFlag = 1;  
     if ($traceLevel =~ /^(.)-/) {  
         $traceLevel = $1;  
         $textOKFlag = 0;  
2152      }      }
2153      # Now we set up the trace mode.  
2154      my $traceMode;  
2155      # Verify that we can open a file in the FIG temporary directory.  =head2 File Utility Methods
2156      my $traceFileName = "$FIG_Config::temp/trace$suffix.log";  
2157      if (open TESTTRACE, ">$traceFileName") {  =head3 GetFile
2158          # Here we can trace to a file.  
2159          $traceMode = ">$traceFileName";      my @fileContents = Tracer::GetFile($fileName);
2160          if ($textOKFlag) {  
2161              # Echo to standard output if the text-OK flag is set.      or
2162              $traceMode = "+$traceMode";  
2163        my $fileContents = Tracer::GetFile($fileName);
2164    
2165    Return the entire contents of a file. In list context, line-ends are removed and
2166    each line is a list element. In scalar context, line-ends are replaced by C<\n>.
2167    
2168    =over 4
2169    
2170    =item fileName
2171    
2172    Name of the file to read.
2173    
2174    =item RETURN
2175    
2176    In a list context, returns the entire file as a list with the line terminators removed.
2177    In a scalar context, returns the entire file as a string. If an error occurs opening
2178    the file, an empty list will be returned.
2179    
2180    =back
2181    
2182    =cut
2183    
2184    sub GetFile {
2185        # Get the parameters.
2186        my ($fileName) = @_;
2187        # Declare the return variable.
2188        my @retVal = ();
2189        # Open the file for input.
2190        my $handle = Open(undef, "<$fileName");
2191        # Read the whole file into the return variable, stripping off any terminator
2192        # characters.
2193        my $lineCount = 0;
2194        while (my $line = <$handle>) {
2195            $lineCount++;
2196            $line = Strip($line);
2197            push @retVal, $line;
2198          }          }
2199          # Close the test file.      # Close it.
2200          close TESTTRACE;      close $handle;
2201      } else {      my $actualLines = @retVal;
2202          # Here we can't trace to a file. We trace to the standard output if it's      Trace("$actualLines lines read from file $fileName.") if T(File => 2);
2203          # okay, and the error log otherwise.      # Return the file's contents in the desired format.
2204          if ($textOKFlag) {      if (wantarray) {
2205              $traceMode = "TEXT";          return @retVal;
2206          } else {          } else {
2207              $traceMode = "WARN";          return join "\n", @retVal;
2208          }          }
2209      }      }
2210      # Now set up the tracing.  
2211      TSetup("$traceLevel $cats", $traceMode);  =head3 PutFile
2212      # Check for the "h" option. If it is specified, dump the command-line  
2213      # options and exit the program.      Tracer::PutFile($fileName, \@lines);
2214      if ($retOptions->{h}) {  
2215          $0 =~ m#[/\\](\w+)(\.pl)?$#i;  Write out a file from a list of lines of text.
2216          Trace("$1 [options] $parmHelp") if T(0);  
2217          for my $key (sort keys %{$options}) {  =over 4
2218              my $name = Pad($key, $longestName, 0, ' ');  
2219              my $desc = $options->{$key}->[1];  =item fileName
2220              if ($options->{$key}->[0]) {  
2221                  $desc .= " (default " . $options->{$key}->[0] . ")";  Name of the output file.
2222    
2223    =item lines
2224    
2225    Reference to a list of text lines. The lines will be written to the file in order, with trailing
2226    new-line characters. Alternatively, may be a string, in which case the string will be written without
2227    modification.
2228    
2229    =back
2230    
2231    =cut
2232    
2233    sub PutFile {
2234        # Get the parameters.
2235        my ($fileName, $lines) = @_;
2236        # Open the output file.
2237        my $handle = Open(undef, ">$fileName");
2238        # Count the lines written.
2239        if (ref $lines ne 'ARRAY') {
2240            # Here we have a scalar, so we write it raw.
2241            print $handle $lines;
2242            Trace("Scalar put to file $fileName.") if T(File => 3);
2243        } else {
2244            # Write the lines one at a time.
2245            my $count = 0;
2246            for my $line (@{$lines}) {
2247                print $handle "$line\n";
2248                $count++;
2249              }              }
2250              Trace("  $name $desc") if T(0);          Trace("$count lines put to file $fileName.") if T(File => 3);
2251          }          }
2252          exit(0);      # Close the output file.
2253        close $handle;
2254      }      }
2255      # Return the parsed parameters.  
2256      return ($retOptions, @retParameters);  =head3 ParseRecord
2257    
2258        my @fields = Tracer::ParseRecord($line);
2259    
2260    Parse a tab-delimited data line. The data line is split into field values. Embedded tab
2261    and new-line characters in the data line must be represented as C<\t> and C<\n>, respectively.
2262    These will automatically be converted.
2263    
2264    =over 4
2265    
2266    =item line
2267    
2268    Line of data containing the tab-delimited fields.
2269    
2270    =item RETURN
2271    
2272    Returns a list of the fields found in the data line.
2273    
2274    =back
2275    
2276    =cut
2277    
2278    sub ParseRecord {
2279        # Get the parameter.
2280        my ($line) = @_;
2281        # Remove the trailing new-line, if any.
2282        chomp $line;
2283        # Split the line read into pieces using the tab character.
2284        my @retVal = split /\t/, $line;
2285        # Trim and fix the escapes in each piece.
2286        for my $value (@retVal) {
2287            # Trim leading whitespace.
2288            $value =~ s/^\s+//;
2289            # Trim trailing whitespace.
2290            $value =~ s/\s+$//;
2291            # Delete the carriage returns.
2292            $value =~ s/\r//g;
2293            # Convert the escapes into their real values.
2294            $value =~ s/\\t/"\t"/ge;
2295            $value =~ s/\\n/"\n"/ge;
2296        }
2297        # Return the result.
2298        return @retVal;
2299  }  }
2300    
2301  =head3 Setups  =head3 Merge
2302    
2303  C<< my $count = Tracer::Setups(); >>      my @mergedList = Tracer::Merge(@inputList);
2304    
2305  Return the number of times L</TSetup> has been called.  Sort a list of strings and remove duplicates.
2306    
2307  This method allows for the creation of conditional tracing setups where, for example, we  =over 4
2308  may want to set up tracing if nobody else has done it before us.  
2309    =item inputList
2310    
2311    List of scalars to sort and merge.
2312    
2313    =item RETURN
2314    
2315    Returns a list containing the same elements sorted in ascending order with duplicates
2316    removed.
2317    
2318    =back
2319    
2320  =cut  =cut
2321    
2322  sub Setups {  sub Merge {
2323      return $SetupCount;      # Get the input list in sort order.
2324        my @inputList = sort @_;
2325        # Only proceed if the list has at least two elements.
2326        if (@inputList > 1) {
2327            # Now we want to move through the list splicing out duplicates.
2328            my $i = 0;
2329            while ($i < @inputList) {
2330                # Get the current entry.
2331                my $thisEntry = $inputList[$i];
2332                # Find out how many elements duplicate the current entry.
2333                my $j = $i + 1;
2334                my $dup1 = $i + 1;
2335                while ($j < @inputList && $inputList[$j] eq $thisEntry) { $j++; };
2336                # If the number is nonzero, splice out the duplicates found.
2337                if ($j > $dup1) {
2338                    splice @inputList, $dup1, $j - $dup1;
2339                }
2340                # Now the element at position $dup1 is different from the element before it
2341                # at position $i. We push $i forward one position and start again.
2342                $i++;
2343            }
2344        }
2345        # Return the merged list.
2346        return @inputList;
2347  }  }
2348    
2349  =head3 Open  =head3 Open
2350    
2351  C<< my $handle = Open($fileHandle, $fileSpec, $message); >>      my $handle = Open($fileHandle, $fileSpec, $message);
2352    
2353  Open a file.  Open a file.
2354    
# Line 605  Line 2440 
2440    
2441  =head3 FindNamePart  =head3 FindNamePart
2442    
2443  C<< my ($fileName, $start, $len) = Tracer::FindNamePart($fileSpec); >>      my ($fileName, $start, $len) = Tracer::FindNamePart($fileSpec);
2444    
2445  Extract the portion of a file specification that contains the file name.  Extract the portion of a file specification that contains the file name.
2446    
# Line 656  Line 2491 
2491    
2492  =head3 OpenDir  =head3 OpenDir
2493    
2494  C<< my @files = OpenDir($dirName, $filtered, $flag); >>      my @files = OpenDir($dirName, $filtered, $flag);
2495    
2496  Open a directory and return all the file names. This function essentially performs  Open a directory and return all the file names. This function essentially performs
2497  the functions of an C<opendir> and C<readdir>. If the I<$filtered> parameter is  the functions of an C<opendir> and C<readdir>. If the I<$filtered> parameter is
# Line 712  Line 2547 
2547          } else {          } else {
2548              @retVal = readdir $dirHandle;              @retVal = readdir $dirHandle;
2549          }          }
2550            closedir $dirHandle;
2551      } elsif (! $flag) {      } elsif (! $flag) {
2552          # Here the directory would not open and it's considered an error.          # Here the directory would not open and it's considered an error.
2553          Confess("Could not open directory $dirName.");          Confess("Could not open directory $dirName.");
# Line 720  Line 2556 
2556      return @retVal;      return @retVal;
2557  }  }
2558    
 =head3 SetLevel  
2559    
2560  C<< Tracer::SetLevel($newLevel); >>  =head3 Insure
2561    
2562  Modify the trace level. A higher trace level will cause more messages to appear.      Insure($dirName, $chmod);
2563    
2564    Insure a directory is present.
2565    
2566    =over 4
2567    
2568    =item dirName
2569    
2570    Name of the directory to check. If it does not exist, it will be created.
2571    
2572    =item chmod (optional)
2573    
2574    Security privileges to be given to the directory if it is created.
2575    
2576    =back
2577    
2578    =cut
2579    
2580    sub Insure {
2581        my ($dirName, $chmod) = @_;
2582        if (! -d $dirName) {
2583            Trace("Creating $dirName directory.") if T(2);
2584            eval {
2585                mkpath $dirName;
2586                # If we have permissions specified, set them here.
2587                if (defined($chmod)) {
2588                    chmod $chmod, $dirName;
2589                }
2590            };
2591            if ($@) {
2592                Confess("Error creating $dirName: $@");
2593            }
2594        }
2595    }
2596    
2597    =head3 ChDir
2598    
2599        ChDir($dirName);
2600    
2601    Change to the specified directory.
2602    
2603  =over 4  =over 4
2604    
2605  =item newLevel  =item dirName
2606    
2607  Proposed new trace level.  Name of the directory to which we want to change.
2608    
2609  =back  =back
2610    
2611  =cut  =cut
2612    
2613  sub SetLevel {  sub ChDir {
2614      $TraceLevel = $_[0];      my ($dirName) = @_;
2615        if (! -d $dirName) {
2616            Confess("Cannot change to directory $dirName: no such directory.");
2617        } else {
2618            Trace("Changing to directory $dirName.") if T(File => 4);
2619            my $okFlag = chdir $dirName;
2620            if (! $okFlag) {
2621                Confess("Error switching to directory $dirName.");
2622            }
2623        }
2624  }  }
2625    
2626  =head3 Now  =head3 SetPermissions
2627    
2628  C<< my $string = Tracer::Now(); >>      Tracer::SetPermissions($dirName, $group, $mask, %otherMasks);
2629    
2630  Return a displayable time stamp containing the local time.  Set the permissions for a directory and all the files and folders inside it.
2631    In addition, the group ownership will be changed to the specified value.
2632    
2633  =cut  This method is more vulnerable than most to permission and compatability
2634    problems, so it does internal error recovery.
2635    
2636  sub Now {  =over 4
     my ($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 $retVal;  
 }  
2637    
2638  # Pad a number to 2 digits.  =item dirName
 sub _p2 {  
     my ($value) = @_;  
     $value = "0$value" if ($value < 10);  
     return $value;  
 }  
2639    
2640  =head3 LogErrors  Name of the directory to process.
2641    
2642  C<< Tracer::LogErrors($fileName); >>  =item group
2643    
2644  Route the standard error output to a log file.  Name of the group to be assigned.
2645    
2646  =over 4  =item mask
2647    
2648  =item fileName  Permission mask. Bits that are C<1> in this mask will be ORed into the
2649    permission bits of any file or directory that does not already have them
2650    set to 1.
2651    
2652  Name of the file to receive the error output.  =item otherMasks
2653    
2654    Map of search patterns to permission masks. If a directory name matches
2655    one of the patterns, that directory and all its members and subdirectories
2656    will be assigned the new pattern. For example, the following would
2657    assign 0664 to most files, but would use 0777 for directories named C<tmp>.
2658    
2659        Tracer::SetPermissions($dirName, 'fig', 01664, '^tmp$' => 01777);
2660    
2661    The list is ordered, so the following would use 0777 for C<tmp1> and
2662    0666 for C<tmp>, C<tmp2>, or C<tmp3>.
2663    
2664        Tracer::SetPermissions($dirName, 'fig', 01664, '^tmp1' => 0777,
2665                                                       '^tmp' => 0666);
2666    
2667    Note that the pattern matches are all case-insensitive, and only directory
2668    names are matched, not file names.
2669    
2670  =back  =back
2671    
2672  =cut  =cut
2673    
2674  sub LogErrors {  sub SetPermissions {
2675      # Get the file name.      # Get the parameters.
2676      my ($fileName) = @_;      my ($dirName, $group, $mask, @otherMasks) = @_;
2677      # Open the file as the standard error output.      # Set up for error recovery.
2678      open STDERR, '>', $fileName;      eval {
2679            # Switch to the specified directory.
2680            ChDir($dirName);
2681            # Get the group ID.
2682            my $gid = getgrnam($group);
2683            # Get the mask for tracing.
2684            my $traceMask = sprintf("%04o", $mask) . "($mask)";
2685            Trace("Fixing permissions for directory $dirName using group $group($gid) and mask $traceMask.") if T(File => 2);
2686            my $fixCount = 0;
2687            my $lookCount = 0;
2688            # @dirs will be a stack of directories to be processed.
2689            my @dirs = (getcwd());
2690            while (scalar(@dirs) > 0) {
2691                # Get the current directory.
2692                my $dir = pop @dirs;
2693                # Check for a match to one of the specified directory names. To do
2694                # that, we need to pull the individual part of the name off of the
2695                # whole path.
2696                my $simpleName = $dir;
2697                if ($dir =~ m!/([^/]+)$!) {
2698                    $simpleName = $1;
2699                }
2700                Trace("Simple directory name for $dir is $simpleName.") if T(File => 4);
2701                # Search for a match.
2702                my $match = 0;
2703                my $i;
2704                for ($i = 0; $i < $#otherMasks && ! $match; $i += 2) {
2705                    my $pattern = $otherMasks[$i];
2706                    if ($simpleName =~ /$pattern/i) {
2707                        $match = 1;
2708                    }
2709                }
2710                # Find out if we have a match. Note we use $i-1 because the loop added 2
2711                # before terminating due to the match.
2712                if ($match && $otherMasks[$i-1] != $mask) {
2713                    # This directory matches one of the incoming patterns, and it's
2714                    # a different mask, so we process it recursively with that mask.
2715                    SetPermissions($dir, $group, $otherMasks[$i-1], @otherMasks);
2716                } else {
2717                    # Here we can process normally. Get all of the non-hidden members.
2718                    my @submems = OpenDir($dir, 1);
2719                    for my $submem (@submems) {
2720                        # Get the full name.
2721                        my $thisMem = "$dir/$submem";
2722                        Trace("Checking member $thisMem.") if T(4);
2723                        $lookCount++;
2724                        if ($lookCount % 1000 == 0) {
2725                            Trace("$lookCount members examined. Current is $thisMem. Mask is $traceMask") if T(File => 3);
2726                        }
2727                        # Fix the group.
2728                        chown -1, $gid, $thisMem;
2729                        # Insure this member is not a symlink.
2730                        if (! -l $thisMem) {
2731                            # Get its info.
2732                            my $fileInfo = stat $thisMem;
2733                            # Only proceed if we got the info. Otherwise, it's a hard link
2734                            # and we want to skip it anyway.
2735                            if ($fileInfo) {
2736                                my $fileMode = $fileInfo->mode;
2737                                if (($fileMode & $mask) != $mask) {
2738                                    # Fix this member.
2739                                    $fileMode |= $mask;
2740                                    chmod $fileMode, $thisMem;
2741                                    $fixCount++;
2742                                }
2743                                # If it's a subdirectory, stack it.
2744                                if (-d $thisMem) {
2745                                    push @dirs, $thisMem;
2746                                }
2747                            }
2748                        }
2749                    }
2750                }
2751            }
2752            Trace("$lookCount files and directories processed, $fixCount fixed.") if T(File => 2);
2753        };
2754        # Check for an error.
2755        if ($@) {
2756            Confess("SetPermissions error: $@");
2757        }
2758  }  }
2759    
2760  =head3 ReadOptions  =head3 GetLine
   
 C<< my %options = Tracer::ReadOptions($fileName); >>  
   
 Read a set of options from a file. Each option is encoded in a line of text that has the  
 format  
2761    
2762  I<optionName>C<=>I<optionValue>C<; >I<comment>      my @data = Tracer::GetLine($handle);
2763    
2764  The option name must consist entirely of letters, digits, and the punctuation characters  Read a line of data from a tab-delimited file.
 C<.> and C<_>, and is case sensitive. Blank lines and lines in which the first nonblank  
 character is a semi-colon will be ignored. The return hash will map each option name to  
 the corresponding option value.  
2765    
2766  =over 4  =over 4
2767    
2768  =item fileName  =item handle
2769    
2770  Name of the file containing the option data.  Open file handle from which to read.
2771    
2772  =item RETURN  =item RETURN
2773    
2774  Returns a hash mapping the option names specified in the file to their corresponding option  Returns a list of the fields in the record read. The fields are presumed to be
2775  value.  tab-delimited. If we are at the end of the file, then an empty list will be
2776    returned. If an empty line is read, a single list item consisting of a null
2777    string will be returned.
2778    
2779  =back  =back
2780    
2781  =cut  =cut
2782    
2783  sub ReadOptions {  sub GetLine {
2784      # Get the parameters.      # Get the parameters.
2785      my ($fileName) = @_;      my ($handle) = @_;
2786      # Open the file.      # Declare the return variable.
2787      (open CONFIGFILE, "<$fileName") || Confess("Could not open option file $fileName.");      my @retVal = ();
2788      # Count the number of records read.      Trace("File position is " . tell($handle) . ". EOF flag is " . eof($handle) . ".") if T(File => 4);
2789      my ($records, $comments) = 0;      # Read from the file.
2790      # Create the return hash.      my $line = <$handle>;
2791      my %retVal = ();      # Only proceed if we found something.
2792      # Loop through the file, accumulating key-value pairs.      if (defined $line) {
2793      while (my $line = <CONFIGFILE>) {          # Remove the new-line. We are a bit over-cautious here because the file may be coming in via an
2794          # Denote we've read a line.          # upload control and have a nonstandard EOL combination.
2795          $records++;          $line =~ s/(\r|\n)+$//;
2796          # Determine the line type.          # Here we do some fancy tracing to help in debugging complicated EOL marks.
2797          if ($line =~ /^\s*[\n\r]/) {          if (T(File => 4)) {
2798              # A blank line is a comment.              my $escapedLine = $line;
2799              $comments++;              $escapedLine =~ s/\n/\\n/g;
2800          } elsif ($line =~ /^\s*([A-Za-z0-9_\.]+)=([^;]*);/) {              $escapedLine =~ s/\r/\\r/g;
2801              # Here we have an option assignment.              $escapedLine =~ s/\t/\\t/g;
2802              retVal{$1} = $2;              Trace("Line read: -->$escapedLine<--");
2803          } elsif ($line =~ /^\s*;/) {          }
2804              # Here we have a text comment.          # If the line is empty, return a single empty string; otherwise, parse
2805              $comments++;          # it into fields.
2806            if ($line eq "") {
2807                push @retVal, "";
2808          } else {          } else {
2809              # Here we have an invalid line.              push @retVal, split /\t/,$line;
             Trace("Invalid option statement in record $records.") if T(0);  
2810          }          }
2811        } else {
2812            # Trace the reason the read failed.
2813            Trace("End of file: $!") if T(File => 3);
2814      }      }
2815      # Return the hash created.      # Return the result.
2816      return %retVal;      return @retVal;
2817  }  }
2818    
2819  =head3 GetOptions  =head3 PutLine
   
 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  
2820    
2821  C<< {databaseType => 'Oracle'} >>      Tracer::PutLine($handle, \@fields, $eol);
2822    
2823  an error will occur because the B<databaseType> option does not exist.  Write a line of data to a tab-delimited file. The specified field values will be
2824    output in tab-separated form, with a trailing new-line.
2825    
2826  =over 4  =over 4
2827    
2828  =item defaults  =item handle
2829    
2830  Table of default option values.  Output file handle.
2831    
2832  =item options  =item fields
2833    
2834  Table of overrides, if any.  List of field values.
2835    
2836  =item RETURN  =item eol (optional)
2837    
2838  Returns a reference to the default table passed in as the first parameter.  End-of-line character (default is "\n").
2839    
2840  =back  =back
2841    
2842  =cut  =cut
2843    
2844  sub GetOptions {  sub PutLine {
2845      # Get the parameters.      # Get the parameters.
2846      my ($defaults, $options) = @_;      my ($handle, $fields, $eol) = @_;
2847      # Check for overrides.      # Write the data.
2848      if ($options) {      print $handle join("\t", @{$fields}) . ($eol || "\n");
         # Loop through the overrides.  
         while (my ($option, $setting) = each %{$options}) {  
             # Insure this override exists.  
             if (!exists $defaults->{$option}) {  
                 croak "Unrecognized option $option encountered.";  
             } else {  
                 # Apply the override.  
                 $defaults->{$option} = $setting;  
             }  
         }  
2849      }      }
     # Return the merged table.  
     return $defaults;  
 }  
   
 =head3 MergeOptions  
2850    
 C<< Tracer::MergeOptions(\%table, \%defaults); >>  
2851    
2852  Merge default values into a hash table. This method looks at the key-value pairs in the  =head3 PrintLine
 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.  
2853    
2854  =over 4      Tracer::PrintLine($line);
2855    
2856  =item table  Print a line of text with a trailing new-line.
2857    
2858  Hash table to be updated with the default values.  =over 4
2859    
2860  =item defaults  =item line
2861    
2862  Default values to be merged into the first hash table if they are not already present.  Line of text to print.
2863    
2864  =back  =back
2865    
2866  =cut  =cut
2867    
2868  sub MergeOptions {  sub PrintLine {
2869      # Get the parameters.      # Get the parameters.
2870      my ($table, $defaults) = @_;      my ($line) = @_;
2871      # Loop through the defaults.      # Print the line.
2872      while (my ($key, $value) = each %{$defaults}) {      print "$line\n";
         if (!exists $table->{$key}) {  
             $table->{$key} = $value;  
         }  
2873      }      }
2874    
2875    
2876    =head2 Other Useful Methods
2877    
2878    =head3 IDHASH
2879    
2880        my $hash = SHTargetSearch::IDHASH(@keys);
2881    
2882    This is a dinky little method that converts a list of values to a reference
2883    to hash of values to labels. The values and labels are the same.
2884    
2885    =cut
2886    
2887    sub IDHASH {
2888        my %retVal = map { $_ => $_ } @_;
2889        return \%retVal;
2890  }  }
2891    
2892  =head3 Trace  =head3 Pluralize
2893    
2894  C<< Trace($message); >>      my $plural = Tracer::Pluralize($word);
2895    
2896  Write a trace message to the target location specified in L</TSetup>. If there has not been  This is a very simple pluralization utility. It adds an C<s> at the end
2897  any prior call to B<TSetup>.  of the input word unless it already ends in an C<s>, in which case it
2898    adds C<es>.
2899    
2900  =over 4  =over 4
2901    
2902  =item message  =item word
2903    
2904  Message to write.  Singular word to pluralize.
2905    
2906    =item RETURN
2907    
2908    Returns the probable plural form of the word.
2909    
2910  =back  =back
2911    
2912  =cut  =cut
2913    
2914  sub Trace {  sub Pluralize {
2915      # Get the parameters.      # Get the parameters.
2916      my ($message) = @_;      my ($word) = @_;
2917      # Get the timestamp.      # Declare the return variable.
2918      my $timeStamp = Now();      my $retVal;
2919      # Format the message. Note we strip off any line terminators at the end.      if ($word =~ /s$/) {
2920      my $formatted = "$timeStamp <$LastCategory>: " . Strip($message);          $retVal = $word . 'es';
2921      # Process according to the destination.      } else {
2922      if ($Destination eq "TEXT") {          $retVal = $word . 's';
         # Write the message to the standard output.  
         print "$formatted\n";  
     } elsif ($Destination eq "ERROR") {  
         # Write the message to the error output.  
         print STDERR "$formatted\n";  
     } elsif ($Destination eq "QUEUE") {  
         # Push the message into the queue.  
         push @Queue, "$formatted";  
     } elsif ($Destination eq "HTML") {  
         # Convert the message to HTML and write it to the standard output.  
         my $escapedMessage = CGI::escapeHTML($message);  
         print "<p>$formatted</p>\n";  
     } elsif ($Destination eq "WARN") {  
        # Emit the message as a warning.  
        warn $message;  
     } elsif ($Destination =~ m/^>>/) {  
         # Write the trace message to an output file.  
         (open TRACING, $Destination) || die "Tracing open for \"$Destination\" failed: $!";  
         print TRACING "$formatted\n";  
         close TRACING;  
         # If the Tee flag is on, echo it to the standard output.  
         if ($TeeFlag) {  
             print "$formatted\n";  
         }  
2923      }      }
2924        # Return the result.
2925        return $retVal;
2926  }  }
2927    
2928  =head3 T  =head3 Numeric
   
 C<< my $switch = T($category, $traceLevel); >>  
   
     or  
2929    
2930  C<< my $switch = T($traceLevel); >>      my $okFlag = Tracer::Numeric($string);
2931    
2932  Return TRUE if the trace level is at or above a specified value and the specified category  Return the value of the specified string if it is numeric, or an undefined value
2933  is active, else FALSE. If no category is specified, the caller's package name is used.  if it is not numeric.
2934    
2935  =over 4  =over 4
2936    
2937  =item category  =item string
   
 Category to which the message belongs. If not specified, the caller's package name is  
 used.  
   
 =item traceLevel  
2938    
2939  Relevant tracing level.  String to check.
2940    
2941  =item RETURN  =item RETURN
2942    
2943  TRUE if a message at the specified trace level would appear in the trace, else FALSE.  Returns the numeric value of the string if successful, or C<undef> if the string
2944    is not numeric.
2945    
2946  =back  =back
2947    
2948  =cut  =cut
2949    
2950  sub T {  sub Numeric {
     # Declare the return variable.  
     my $retVal = 0;  
     # Only proceed if tracing is turned on.  
     if ($Destination ne "NONE") {  
2951          # Get the parameters.          # Get the parameters.
2952          my ($category, $traceLevel) = @_;      my ($string) = @_;
2953          if (!defined $traceLevel) {      # We'll put the value in here if we succeed.
2954              # Here we have no category, so we need to get the calling package.      my $retVal;
2955              # The calling package is normally the first parameter. If it is      # Get a working copy of the string.
2956              # omitted, the first parameter will be the tracelevel. So, the      my $copy = $string;
2957              # first thing we do is shift the so-called category into the      # Trim leading and trailing spaces.
2958              # $traceLevel variable where it belongs.      $copy =~ s/^\s+//;
2959              $traceLevel = $category;      $copy =~ s/\s+$//;
2960              my ($package, $fileName, $line) = caller;      # Check the result.
2961              # If there is no calling package, we default to "main".      if ($copy =~ /^[+-]?\d+$/) {
2962              if (!$package) {          $retVal = $copy;
2963                  $category = "main";      } elsif ($copy =~ /^([+-]\d+|\d*)[eE][+-]?\d+$/) {
2964              } else {          $retVal = $copy;
2965                  $category = $package;      } elsif ($copy =~ /^([+-]\d+|\d*)\.\d*([eE][+-]?\d+)?$/) {
2966              }          $retVal = $copy;
         }  
         # Save the category name.  
         $LastCategory = $category;  
         # Convert it to lower case before we hash it.  
         $category = lc $category;  
         # Use the category and tracelevel to compute the result.  
         if (ref $traceLevel) {  
             Confess("Bad trace level.");  
         } elsif (ref $TraceLevel) {  
             Confess("Bad trace config.");  
         }  
         $retVal = ($traceLevel <= $TraceLevel && ($AllTrace || exists $Categories{$category}));  
2967      }      }
2968      # Return the computed result.      # Return the result.
2969      return $retVal;      return $retVal;
2970  }  }
2971    
 =head3 ParseCommand  
2972    
2973  C<< my ($options, @arguments) = Tracer::ParseCommand(\%optionTable, @inputList); >>  =head3 ParseParm
2974    
2975        my $listValue = Tracer::ParseParm($string);
2976    
2977    Convert a parameter into a list reference. If the parameter is undefined,
2978    an undefined value will be returned. Otherwise, it will be parsed as a
2979    comma-separated list of values.
2980    
2981    =over 4
2982    
2983  Parse a command line consisting of a list of parameters. The initial parameters may be option  =item string
 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.  
2984    
2985  C<< my ($options, @arguments) = ParseCommand({ errors => 0, logFile => 'trace.log'}, @words); >>  Incoming string.
2986    
2987  In this case, the list @words will be treated as a command line. There are two options available,  =item RETURN
 B<errors> and B<logFile>. If @words has the following format  
2988    
2989  C<< -logFile=error.log apple orange rutabaga >>  Returns a reference to a list of values, or C<undef> if the incoming value
2990    was undefined.
2991    
2992  then at the end of the invocation, C<$options> will be  =back
2993    
2994  C<< { errors => 0, logFile => 'error.log' } >>  =cut
2995    
2996  and C<@arguments> will contain  sub ParseParm {
2997        # Get the parameters.
2998        my ($string) = @_;
2999        # Declare the return variable.
3000        my $retVal;
3001        # Check for data.
3002        if (defined $string) {
3003            # We have some, so split it into a list.
3004            $retVal = [ split /\s*,\s*/, $string];
3005        }
3006        # Return the result.
3007        return $retVal;
3008    }
3009    
3010  C<< apple orange rutabaga >>  =head3 Now
3011    
3012  The parser allows for some escape sequences. See L</UnEscape> for a description. There is no      my $string = Tracer::Now();
 support for quote characters.  
3013    
3014  =over 4  Return a displayable time stamp containing the local time. Whatever format this
3015    method produces must be parseable by L</ParseDate>.
3016    
3017  =item optionTable  =cut
3018    
3019  Table of default options.  sub Now {
3020        return DisplayTime(time);
3021    }
3022    
3023  =item inputList  =head3 DisplayTime
3024    
3025  List of words on the command line.      my $string = Tracer::DisplayTime($time);
3026    
3027    Convert a time value to a displayable time stamp. Whatever format this
3028    method produces must be parseable by L</ParseDate>.
3029    
3030    =over 4
3031    
3032    =item time
3033    
3034    Time to display, in seconds since the epoch, or C<undef> if the time is unknown.
3035    
3036  =item RETURN  =item RETURN
3037    
3038  Returns a reference to the option table and a list of the positional arguments.  Returns a displayable time, or C<(n/a)> if the incoming time is undefined.
3039    
3040  =back  =back
3041    
3042  =cut  =cut
3043    
3044  sub ParseCommand {  sub DisplayTime {
3045      # Get the parameters.      my ($time) = @_;
3046      my ($optionTable, @inputList) = @_;      my $retVal = "(n/a)";
3047      # Process any options in the input list.      if (defined $time) {
3048      my %overrides = ();          my ($sec,$min,$hour,$mday,$mon,$year,$wday,$yday,$isdst) = localtime($time);
3049      while ((@inputList > 0) && ($inputList[0] =~ /^-/)) {          $retVal = _p2($mon+1) . "/" . _p2($mday) . "/" . ($year + 1900) . " " .
3050          # Get the current option.                    _p2($hour) . ":" . _p2($min) . ":" . _p2($sec);
         my $arg = shift @inputList;  
         # Pull out the option name.  
         $arg =~ /^-([^=]*)/g;  
         my $name = $1;  
         # Check for an option value.  
         if ($arg =~ /\G=(.*)$/g) {  
             # Here we have a value for the option.  
             $overrides{$name} = UnEscape($1);  
         } else {  
             # Here there is no value, so we use 1.  
             $overrides{$name} = 1;  
         }  
3051      }      }
3052      # Merge the options into the defaults.      return $retVal;
     GetOptions($optionTable, \%overrides);  
     # Translate the remaining parameters.  
     my @retVal = ();  
     for my $inputParm (@inputList) {  
         push @retVal, UnEscape($inputParm);  
3053      }      }
3054      # Return the results.  
3055      return ($optionTable, @retVal);  # Pad a number to 2 digits.
3056    sub _p2 {
3057        my ($value) = @_;
3058        $value = "0$value" if ($value < 10);
3059        return $value;
3060  }  }
3061    
3062  =head3 Escape  =head3 Escape
3063    
3064  C<< my $codedString = Tracer::Escape($realString); >>      my $codedString = Tracer::Escape($realString);
3065    
3066  Escape a string for use in a command length. Tabs will be replaced by C<\t>, new-lines  Escape a string for use in a command. Tabs will be replaced by C<\t>, new-lines
3067  replaced by C<\n>, carriage returns will be deleted, and backslashes will be doubled. The  replaced by C<\n>, carriage returns will be deleted, and backslashes will be doubled. The
3068  result is to reverse the effect of L</UnEscape>.  result is to reverse the effect of L</UnEscape>.
3069    
# Line 1195  Line 3116 
3116    
3117  =head3 UnEscape  =head3 UnEscape
3118    
3119  C<< my $realString = Tracer::UnEscape($codedString); >>      my $realString = Tracer::UnEscape($codedString);
3120    
3121  Replace escape sequences with their actual equivalents. C<\t> will be replaced by  Replace escape sequences with their actual equivalents. C<\t> will be replaced by
3122  a tab, C<\n> by a new-line character, and C<\\> by a backslash. C<\r> codes will  a tab, C<\n> by a new-line character, and C<\\> by a backslash. C<\r> codes will
# Line 1236  Line 3157 
3157                  # Get the escape value.                  # Get the escape value.
3158                  my $char = $2;                  my $char = $2;
3159                  # If we have a "\r", we are done.                  # If we have a "\r", we are done.
3160                  if ($char ne 'r') {                  if ($char ne 'r') {
3161                      # Here it's not an 'r', so we convert it.                      # Here it's not an 'r', so we convert it.
3162                      $char =~ tr/\\tn/\\\t\n/;                      $char =~ tr/\\tn/\\\t\n/;
3163                      $retVal .= $char;                      $retVal .= $char;
                 }  
             } else {  
                 # Here there are no more escape sequences. The rest of the string is  
                 # transferred unmodified.  
                 $retVal .= $codedString;  
                 $codedString = "";  
             }  
         }  
     }  
     # Return the result.  
     return $retVal;  
 }  
   
 =head3 ParseRecord  
   
 C<< my @fields = Tracer::ParseRecord($line); >>  
   
 Parse a tab-delimited data line. The data line is split into field values. Embedded tab  
 and new-line characters in the data line must be represented as C<\t> and C<\n>, respectively.  
 These will automatically be converted.  
   
 =over 4  
   
 =item line  
   
 Line of data containing the tab-delimited fields.  
   
 =item RETURN  
   
 Returns a list of the fields found in the data line.  
   
 =back  
   
 =cut  
   
 sub ParseRecord {  
     # Get the parameter.  
     my ($line) = @_;  
     # Remove the trailing new-line, if any.  
     chomp $line;  
     # Split the line read into pieces using the tab character.  
     my @retVal = split /\t/, $line;  
     # Trim and fix the escapes in each piece.  
     for my $value (@retVal) {  
         # Trim leading whitespace.  
         $value =~ s/^\s+//;  
         # Trim trailing whitespace.  
         $value =~ s/\s+$//;  
         # Delete the carriage returns.  
         $value =~ s/\r//g;  
         # Convert the escapes into their real values.  
         $value =~ s/\\t/"\t"/ge;  
         $value =~ s/\\n/"\n"/ge;  
     }  
     # Return the result.  
     return @retVal;  
 }  
   
 =head3 Merge  
   
 C<< my @mergedList = Tracer::Merge(@inputList); >>  
   
 Sort a list of strings and remove duplicates.  
   
 =over 4  
   
 =item inputList  
   
 List of scalars to sort and merge.  
   
 =item RETURN  
   
 Returns a list containing the same elements sorted in ascending order with duplicates  
 removed.  
   
 =back  
   
 =cut  
   
 sub Merge {  
     # Get the input list in sort order.  
     my @inputList = sort @_;  
     # Only proceed if the list has at least two elements.  
     if (@inputList > 1) {  
         # Now we want to move through the list splicing out duplicates.  
         my $i = 0;  
         while ($i < @inputList) {  
             # Get the current entry.  
             my $thisEntry = $inputList[$i];  
             # Find out how many elements duplicate the current entry.  
             my $j = $i + 1;  
             my $dup1 = $i + 1;  
             while ($j < @inputList && $inputList[$j] eq $thisEntry) { $j++; };  
             # If the number is nonzero, splice out the duplicates found.  
             if ($j > $dup1) {  
                 splice @inputList, $dup1, $j - $dup1;  
             }  
             # Now the element at position $dup1 is different from the element before it  
             # at position $i. We push $i forward one position and start again.  
             $i++;  
         }  
     }  
     # Return the merged list.  
     return @inputList;  
 }  
   
 =head3 GetFile  
   
 C<< my @fileContents = Tracer::GetFile($fileName); >>  
   
     or  
   
 C<< my $fileContents = Tracer::GetFile($fileName); >>  
   
 Return the entire contents of a file. In list context, line-ends are removed and  
 each line is a list element. In scalar context, line-ends are replaced by C<\n>.  
   
 =over 4  
   
 =item fileName  
   
 Name of the file to read.  
   
 =item RETURN  
   
 In a list context, returns the entire file as a list with the line terminators removed.  
 In a scalar context, returns the entire file as a string. If an error occurs opening  
 the file, an empty list will be returned.  
   
 =back  
   
 =cut  
   
 sub GetFile {  
     # Get the parameters.  
     my ($fileName) = @_;  
     # Declare the return variable.  
     my @retVal = ();  
     # Open the file for input.  
     my $ok = open INPUTFILE, "<$fileName";  
     if (!$ok) {  
         # If we had an error, trace it. We will automatically return a null value.  
         Trace("Could not open \"$fileName\" for input: $!") if T(0);  
     } else {  
         # Read the whole file into the return variable, stripping off any terminator  
         # characters.  
         my $lineCount = 0;  
         while (my $line = <INPUTFILE>) {  
             $lineCount++;  
             $line = Strip($line);  
             push @retVal, $line;  
         }  
         # Close it.  
         close INPUTFILE;  
         my $actualLines = @retVal;  
     }  
     # Return the file's contents in the desired format.  
     if (wantarray) {  
         return @retVal;  
     } else {  
         return join "\n", @retVal;  
     }  
 }  
   
 =head3 QTrace  
   
 C<< my $data = QTrace($format); >>  
   
 Return the queued trace data in the specified format.  
   
 =over 4  
   
 =item format  
   
 C<html> to format the data as an HTML list, C<text> to format it as straight text.  
   
 =back  
   
 =cut  
   
 sub QTrace {  
     # Get the parameter.  
     my ($format) = @_;  
     # Create the return variable.  
     my $retVal = "";  
     # Only proceed if there is an actual queue.  
     if (@Queue) {  
         # Process according to the format.  
         if ($format =~ m/^HTML$/i) {  
             # Convert the queue into an HTML list.  
             $retVal = "<ul>\n";  
             for my $line (@Queue) {  
                 my $escapedLine = CGI::escapeHTML($line);  
                 $retVal .= "<li>$escapedLine</li>\n";  
3164              }              }
3165              $retVal .= "</ul>\n";              } else {
3166          } elsif ($format =~ m/^TEXT$/i) {                  # Here there are no more escape sequences. The rest of the string is
3167              # Convert the queue into a list of text lines.                  # transferred unmodified.
3168              $retVal = join("\n", @Queue) . "\n";                  $retVal .= $codedString;
3169                    $codedString = "";
3170          }          }
         # Clear the queue.  
         @Queue = ();  
3171      }      }
3172      # Return the formatted list.      }
3173        # Return the result.
3174      return $retVal;      return $retVal;
3175  }  }
3176    
3177  =head3 Confess  =head3 Percent
3178    
3179  C<< Confess($message); >>      my $percent = Tracer::Percent($number, $base);
3180    
3181  Trace the call stack and abort the program with the specified message. When used with  Returns the percent of the base represented by the given number. If the base
3182  the OR operator and the L</Assert> method, B<Confess> can function as a debugging assert.  is zero, returns zero.
 So, for example  
3183    
3184  C<< Assert($recNum >= 0) || Confess("Invalid record number $recNum."); >>  =over 4
3185    
3186  Will abort the program with a stack trace if the value of C<$recNum> is negative.  =item number
3187    
3188  =over 4  Percent numerator.
3189    
3190  =item message  =item base
3191    
3192  Message to include in the trace.  Percent base.
3193    
3194    =item RETURN
3195    
3196    Returns the percentage of the base represented by the numerator.
3197    
3198  =back  =back
3199    
3200  =cut  =cut
3201    
3202  sub Confess {  sub Percent {
3203      # Get the parameters.      # Get the parameters.
3204      my ($message) = @_;      my ($number, $base) = @_;
3205      # Trace the call stack.      # Declare the return variable.
3206      Cluck($message);      my $retVal = 0;
3207      # Abort the program.      # Compute the percent.
3208      croak(">>> $message");      if ($base != 0) {
3209            $retVal = $number * 100 / $base;
3210        }
3211        # Return the result.
3212        return $retVal;
3213  }  }
3214    
3215  =head3 Assert  =head3 In
   
 C<< Assert($condition1, $condition2, ... $conditionN); >>  
   
 Return TRUE if all the conditions are true. This method can be used in conjunction with  
 the OR operator and the L</Confess> method as a debugging assert.  
 So, for example  
3216    
3217  C<< Assert($recNum >= 0) || Confess("Invalid record number $recNum."); >>      my $flag = Tracer::In($value, $min, $max);
3218    
3219  Will abort the program with a stack trace if the value of C<$recNum> is negative.  Return TRUE if the value is between the minimum and the maximum, else FALSE.
3220    
3221  =cut  =cut
 sub Assert {  
     my $retVal = 1;  
     LOOP: for my $condition (@_) {  
         if (! $condition) {  
             $retVal = 0;  
             last LOOP;  
         }  
     }  
     return $retVal;  
 }  
3222    
3223  =head3 Cluck  sub In {
3224        return ($_[0] <= $_[2] && $_[0] >= $_[1]);
3225    }
3226    
 C<< Cluck($message); >>  
3227    
3228  Trace the call stack. Note that for best results, you should qualify the call with a  =head3 Constrain
 trace condition. For example,  
3229    
3230  C<< Cluck("Starting record parse.") if T(3); >>      my $constrained = Constrain($value, $min, $max);
3231    
3232  will only trace the stack if the trace level for the package is 3 or more.  Modify a numeric value to bring it to a point in between a maximum and a minimum.
3233    
3234  =over 4  =over 4
3235    
3236  =item message  =item value
3237    
3238  Message to include in the trace.  Value to constrain.
3239    
3240    =item min (optional)
3241    
3242    Minimum permissible value. If this parameter is undefined, no minimum constraint will be applied.
3243    
3244    =item max (optional)
3245    
3246    Maximum permissible value. If this parameter is undefined, no maximum constraint will be applied.
3247    
3248    =item RETURN
3249    
3250    Returns the incoming value, constrained according to the other parameters.
3251    
3252  =back  =back
3253    
3254  =cut  =cut
3255    
3256  sub Cluck {  sub Constrain {
3257      # Get the parameters.      # Get the parameters.
3258      my ($message) = @_;      my ($value, $min, $max) = @_;
3259      # Trace what's happening.      # Declare the return variable.
3260      Trace("Stack trace for event: $message");      my $retVal = $value;
3261      my $confession = longmess($message);      # Apply the minimum constraint.
3262      # Convert the confession to a series of trace messages. Note we skip any      if (defined $min && $retVal < $min) {
3263      # messages relating to calls into Tracer.          $retVal = $min;
3264      for my $line (split /\s*\n/, $confession) {      }
3265          Trace($line) if ($line !~ /Tracer\.pm/);      # Apply the maximum constraint.
3266        if (defined $max && $retVal > $max) {
3267            $retVal = $max;
3268      }      }
3269        # Return the result.
3270        return $retVal;
3271  }  }
3272    
3273  =head3 Min  =head3 Min
3274    
3275  C<< my $min = Min($value1, $value2, ... $valueN); >>      my $min = Min($value1, $value2, ... $valueN);
3276    
3277  Return the minimum argument. The arguments are treated as numbers.  Return the minimum argument. The arguments are treated as numbers.
3278    
# Line 1571  Line 3305 
3305    
3306  =head3 Max  =head3 Max
3307    
3308  C<< my $max = Max($value1, $value2, ... $valueN); >>      my $max = Max($value1, $value2, ... $valueN);
3309    
3310  Return the maximum argument. The arguments are treated as numbers.  Return the maximum argument. The arguments are treated as numbers.
3311    
# Line 1602  Line 3336 
3336      return $retVal;      return $retVal;
3337  }  }
3338    
3339  =head3 AddToListMap  =head3 Strip
3340    
3341  C<< Tracer::AddToListMap(\%hash, $key, $value); >>      my $string = Tracer::Strip($line);
3342    
3343  Add a key-value pair to a hash of lists. If no value exists for the key, a singleton list  Strip all line terminators off a string. This is necessary when dealing with files
3344  is created for the key. Otherwise, the new value is pushed onto the list.  that may have been transferred back and forth several times among different
3345    operating environments.
3346    
3347  =over 4  =over 4
3348    
3349  =item hash  =item line
3350    
3351    Line of text to be stripped.
3352    
3353    =item RETURN
3354    
3355  Reference to the target hash.  The same line of text with all the line-ending characters chopped from the end.
3356    
3357  =item key  =back
3358    
3359  Key for which the value is to be added.  =cut
3360    
3361  =item value  sub Strip {
3362        # Get a copy of the parameter string.
3363        my ($string) = @_;
3364        my $retVal = (defined $string ? $string : "");
3365        # Strip the line terminator characters.
3366        $retVal =~ s/(\r|\n)+$//g;
3367        # Return the result.
3368        return $retVal;
3369    }
3370    
3371    =head3 Trim
3372    
3373        my $string = Tracer::Trim($line);
3374    
3375    Trim all spaces from the beginning and ending of a string.
3376    
3377    =over 4
3378    
3379    =item line
3380    
3381    Line of text to be trimmed.
3382    
3383    =item RETURN
3384    
3385    The same line of text with all whitespace chopped off either end.
3386    
3387    =back
3388    
3389    =cut
3390    
3391    sub Trim {
3392        # Get a copy of the parameter string.
3393        my ($string) = @_;
3394        my $retVal = (defined $string ? $string : "");
3395        # Strip the front spaces.
3396        $retVal =~ s/^\s+//;
3397        # Strip the back spaces.
3398        $retVal =~ s/\s+$//;
3399        # Return the result.
3400        return $retVal;
3401    }
3402    
3403    =head3 Pad
3404    
3405  Value to add to the key's value list.      my $paddedString = Tracer::Pad($string, $len, $left, $padChar);
3406    
3407    Pad a string to a specified length. The pad character will be a
3408    space, and the padding will be on the right side unless specified
3409    in the third parameter.
3410    
3411    =over 4
3412    
3413    =item string
3414    
3415    String to be padded.
3416    
3417    =item len
3418    
3419    Desired length of the padded string.
3420    
3421    =item left (optional)
3422    
3423    TRUE if the string is to be left-padded; otherwise it will be padded on the right.
3424    
3425    =item padChar (optional)
3426    
3427    Character to use for padding. The default is a space.
3428    
3429    =item RETURN
3430    
3431    Returns a copy of the original string with the pad character added to the
3432    specified end so that it achieves the desired length.
3433    
3434  =back  =back
3435    
3436  =cut  =cut
3437    
3438  sub AddToListMap {  sub Pad {
3439      # Get the parameters.      # Get the parameters.
3440      my ($hash, $key, $value) = @_;      my ($string, $len, $left, $padChar) = @_;
3441      # Process according to whether or not the key already has a value.      # Compute the padding character.
3442      if (! exists $hash->{$key}) {      if (! defined $padChar) {
3443          $hash->{$key} = [$value];          $padChar = " ";
3444        }
3445        # Compute the number of spaces needed.
3446        my $needed = $len - length $string;
3447        # Copy the string into the return variable.
3448        my $retVal = $string;
3449        # Only proceed if padding is needed.
3450        if ($needed > 0) {
3451            # Create the pad string.
3452            my $pad = $padChar x $needed;
3453            # Affix it to the return value.
3454            if ($left) {
3455                $retVal = $pad . $retVal;
3456      } else {      } else {
3457          push @{$hash->{$key}}, $value;              $retVal .= $pad;
3458            }
3459      }      }
3460        # Return the result.
3461        return $retVal;
3462  }  }
3463    
3464  =head3 DebugMode  =head3 EOF
3465    
3466  C<< if (Tracer::DebugMode) { ...code... } >>  This is a constant that is lexically greater than any useful string.
3467    
3468  Return TRUE if debug mode has been turned on, else output an error  =cut
 page and return FALSE.  
3469    
3470  Certain CGI scripts are too dangerous to exist in the production  sub EOF {
3471  environment. This method provides a simple way to prevent them      return "\xFF\xFF\xFF\xFF\xFF";
3472  from working unless they are explicitly turned on by creating a password  }
 cookie via the B<SetPassword> script.  If debugging mode  
 is not turned on, an error web page will be output directing the  
 user to enter in the correct password.  
3473    
3474  =cut  =head3 TICK
3475    
3476  sub DebugMode {      my @results = TICK($commandString);
3477      # Declare the return variable.  
3478      my $retVal = 0;  Perform a back-tick operation on a command. If this is a Windows environment, any leading
3479      # Check the debug configuration.  dot-slash (C<./> will be removed. So, for example, if you were doing
3480      my $password = CGI::cookie("DebugMode");  
3481      my $encrypted = Digest::MD5::md5_hex($password);      `./protein.cgi`
3482      if ($encrypted eq "252dec43280e0c0d6a75ffcec486e61d") {  
3483          $retVal = 1;  from inside a CGI script, it would work fine in Unix, but would issue an error message
3484      } else {  in Windows complaining that C<'.'> is not a valid command. If instead you code
3485          # Here debug mode is off, so we generate an error page.  
3486          my $pageString = PageBuilder::Build("<Html/ErrorPage.html", {}, "Html");      TICK("./protein.cgi")
3487          print $pageString;  
3488    it will work correctly in both environments.
3489    
3490    =over 4
3491    
3492    =item commandString
3493    
3494    The command string to pass to the system.
3495    
3496    =item RETURN
3497    
3498    Returns the standard output from the specified command, as a list.
3499    
3500    =back
3501    
3502    =cut
3503    #: Return Type @;
3504    sub TICK {
3505        # Get the parameters.
3506        my ($commandString) = @_;
3507        # Chop off the dot-slash if this is Windows.
3508        if ($FIG_Config::win_mode) {
3509            $commandString =~ s!^\./!!;
3510        }
3511        # Activate the command and return the result.
3512        return `$commandString`;
3513      }      }
3514      # Return the determination indicator.  
3515    
3516    =head3 CommaFormat
3517    
3518        my $formatted = Tracer::CommaFormat($number);
3519    
3520    Insert commas into a number.
3521    
3522    =over 4
3523    
3524    =item number
3525    
3526    A sequence of digits.
3527    
3528    =item RETURN
3529    
3530    Returns the same digits with commas strategically inserted.
3531    
3532    =back
3533    
3534    =cut
3535    
3536    sub CommaFormat {
3537        # Get the parameters.
3538        my ($number) = @_;
3539        # Pad the length up to a multiple of three.
3540        my $padded = "$number";
3541        $padded = " " . $padded while length($padded) % 3 != 0;
3542        # This is a fancy PERL trick. The parentheses in the SPLIT pattern
3543        # cause the delimiters to be included in the output stream. The
3544        # GREP removes the empty strings in between the delimiters.
3545        my $retVal = join(",", grep { $_ ne '' } split(/(...)/, $padded));
3546        # Clean out the spaces.
3547        $retVal =~ s/ //g;
3548        # Return the result.
3549      return $retVal;      return $retVal;
3550  }  }
3551    
 =head3 Strip  
3552    
3553  C<< my $string = Tracer::Strip($line); >>  =head3 GetMemorySize
3554    
3555  Strip all line terminators off a string. This is necessary when dealing with files      my $string = Tracer::GetMemorySize();
3556  that may have been transferred back and forth several times among different  
3557  operating environments.  Return a memory size string for the current process. The string will be
3558    in comma format, with a size indicator (K, M, G) at the end.
3559    
3560    =cut
3561    
3562    sub GetMemorySize {
3563        # Get the memory size from Unix.
3564        my ($retVal) = `ps h -o vsz $$`;
3565        # Remove the ending new-line.
3566        chomp $retVal;
3567        # Format and return the result.
3568        return CommaFormat($retVal) . "K";
3569    }
3570    
3571    =head3 CompareLists
3572    
3573        my ($inserted, $deleted) = Tracer::CompareLists(\@newList, \@oldList, $keyIndex);
3574    
3575    Compare two lists of tuples, and return a hash analyzing the differences. The lists
3576    are presumed to be sorted alphabetically by the value in the $keyIndex column.
3577    The return value contains a list of items that are only in the new list
3578    (inserted) and only in the old list (deleted).
3579    
3580  =over 4  =over 4
3581    
3582  =item line  =item newList
3583    
3584  Line of text to be stripped.  Reference to a list of new tuples.
3585    
3586    =item oldList
3587    
3588    Reference to a list of old tuples.
3589    
3590    =item keyIndex (optional)
3591    
3592    Index into each tuple of its key field. The default is 0.
3593    
3594  =item RETURN  =item RETURN
3595    
3596  The same line of text with all the line-ending characters chopped from the end.  Returns a 2-tuple consisting of a reference to the list of items that are only in the new
3597    list (inserted) followed by a reference to the list of items that are only in the old
3598    list (deleted).
3599    
3600  =back  =back
3601    
3602  =cut  =cut
3603    
3604  sub Strip {  sub CompareLists {
3605      # Get a copy of the parameter string.      # Get the parameters.
3606      my ($string) = @_;      my ($newList, $oldList, $keyIndex) = @_;
3607      my $retVal = (defined $string ? $string : "");      if (! defined $keyIndex) {
3608      # Strip the line terminator characters.          $keyIndex = 0;
3609      $retVal =~ s/(\r|\n)+$//g;      }
3610        # Declare the return variables.
3611        my ($inserted, $deleted) = ([], []);
3612        # Loop through the two lists simultaneously.
3613        my ($newI, $oldI) = (0, 0);
3614        my ($newN, $oldN) = (scalar @{$newList}, scalar @{$oldList});
3615        while ($newI < $newN || $oldI < $oldN) {
3616            # Get the current object in each list. Note that if one
3617            # of the lists is past the end, we'll get undef.
3618            my $newItem = $newList->[$newI];
3619            my $oldItem = $oldList->[$oldI];
3620            if (! defined($newItem) || defined($oldItem) && $newItem->[$keyIndex] gt $oldItem->[$keyIndex]) {
3621                # The old item is not in the new list, so mark it deleted.
3622                push @{$deleted}, $oldItem;
3623                $oldI++;
3624            } elsif (! defined($oldItem) || $oldItem->[$keyIndex] gt $newItem->[$keyIndex]) {
3625                # The new item is not in the old list, so mark it inserted.
3626                push @{$inserted}, $newItem;
3627                $newI++;
3628            } else {
3629                # The item is in both lists, so push forward.
3630                $oldI++;
3631                $newI++;
3632            }
3633        }
3634      # Return the result.      # Return the result.
3635      return $retVal;      return ($inserted, $deleted);
3636  }  }
3637    
3638  =head3 Pad  =head3 Cmp
3639    
3640  C<< my $paddedString = Tracer::Pad($string, $len, $left, $padChar); >>      my $cmp = Tracer::Cmp($a, $b);
3641    
3642  Pad a string to a specified length. The pad character will be a  This method performs a universal sort comparison. Each value coming in is
3643  space, and the padding will be on the right side unless specified  separated into a leading text part and a trailing number part. The text
3644  in the third parameter.  part is string compared, and if both parts are equal, then the number
3645    parts are compared numerically. A stream of just numbers or a stream of
3646    just strings will sort correctly, and a mixed stream will sort with the
3647    numbers first. Strings with a label and a number will sort in the
3648    expected manner instead of lexically.
3649    
3650  =over 4  =over 4
3651    
3652  =item string  =item a
   
 String to be padded.  
   
 =item len  
   
 Desired length of the padded string.  
   
 =item left (optional)  
3653    
3654  TRUE if the string is to be left-padded; otherwise it will be padded on the right.  First item to compare.
3655    
3656  =item padChar (optional)  =item b
3657    
3658  Character to use for padding. The default is a space.  Second item to compare.
3659    
3660  =item RETURN  =item RETURN
3661    
3662  Returns a copy of the original string with the pad character added to the  Returns a negative number if the first item should sort first (is less), a positive
3663  specified end so that it achieves the desired length.  number if the first item should sort second (is greater), and a zero if the items are
3664    equal.
3665    
3666  =back  =back
3667    
3668  =cut  =cut
3669    
3670  sub Pad {  sub Cmp {
3671      # Get the parameters.      # Get the parameters.
3672      my ($string, $len, $left, $padChar) = @_;      my ($a, $b) = @_;
3673      # Compute the padding character.      # Declare the return value.
3674      if (! defined $padChar) {      my $retVal;
3675          $padChar = " ";      # Check for nulls.
3676      }      if (! defined($a)) {
3677      # Compute the number of spaces needed.          $retVal = (! defined($b) ? 0 : -1);
3678      my $needed = $len - length $string;      } elsif (! defined($b)) {
3679      # Copy the string into the return variable.          $retVal = 1;
     my $retVal = $string;  
     # Only proceed if padding is needed.  
     if ($needed > 0) {  
         # Create the pad string.  
         my $pad = $padChar x $needed;  
         # Affix it to the return value.  
         if ($left) {  
             $retVal = $pad . $retVal;  
3680          } else {          } else {
3681              $retVal .= $pad;          # Here we have two real values. Parse the two strings.
3682            my $aParsed = _Parse($a);
3683            my $bParsed = _Parse($b);
3684            # Compare the string parts insensitively.
3685            $retVal = (lc $aParsed->[0] cmp lc $bParsed->[0]);
3686            # If they're equal, compare them sensitively.
3687            if (! $retVal) {
3688                $retVal = ($aParsed->[0] cmp $bParsed->[0]);
3689            }
3690            # If they're STILL equal, compare the number parts.
3691            if (! $retVal) {
3692                $retVal = $aParsed->[1] <=> $bParsed->[1];
3693          }          }
3694      }      }
3695      # Return the result.      # Return the result.
3696      return $retVal;      return $retVal;
3697  }  }
3698    
3699  =head3 EOF  # This method parses an input string into a string part and a number part.
3700    sub _Parse {
3701  This is a constant that is lexically greater than any useful string.      my ($string) = @_;
3702        my ($alpha, $num);
3703  =cut      if ($string =~ /^(.*?)(\d+(?:\.\d+)?)$/) {
3704            $alpha = $1;
3705  sub EOF {          $num = $2;
3706      return "\xFF\xFF\xFF\xFF\xFF";      } else {
3707            $alpha = $string;
3708            $num = 0;
3709        }
3710        return [$alpha, $num];
3711  }  }
3712    
3713  =head3 TICK  =head3 ListEQ
   
 C<< my @results = TICK($commandString); >>  
   
 Perform a back-tick operation on a command. If this is a Windows environment, any leading  
 dot-slash (C<./> will be removed. So, for example, if you were doing  
3714    
3715      `./protein.cgi`      my $flag = Tracer::ListEQ(\@a, \@b);
3716    
3717  from inside a CGI script, it would work fine in Unix, but would issue an error message  Return TRUE if the specified lists contain the same strings in the same
3718  in Windows complaining that C<'.'> is not a valid command. If instead you code  order, else FALSE.
3719    
3720      TICK("./protein.cgi")  =over 4
3721    
3722  it will work correctly in both environments.  =item a
3723    
3724  =over 4  Reference to the first list.
3725    
3726  =item commandString  =item b
3727    
3728  The command string to pass to the system.  Reference to the second list.
3729    
3730  =item RETURN