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revision 1.67, Fri Sep 29 15:00:17 2006 UTC revision 1.98, Thu May 1 07:52:10 2008 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    
21      require Exporter;      require Exporter;
22      @ISA = ('Exporter');      @ISA = ('Exporter');
23      @EXPORT = qw(Trace T TSetup QTrace Confess Cluck Min Max Assert Open OpenDir TICK StandardSetup ScriptSetup ScriptFinish Insure ChDir);      @EXPORT = qw(Trace T TSetup QTrace Confess Cluck Min Max Assert Open OpenDir TICK StandardSetup EmergencyKey ETracing Constrain Insure ChDir Emergency);
24      @EXPORT_OK = qw(GetFile GetOptions Merge MergeOptions ParseCommand ParseRecord UnEscape Escape);      @EXPORT_OK = qw(GetFile GetOptions Merge MergeOptions ParseCommand ParseRecord UnEscape Escape PrintLine PutLine);
25      use strict;      use strict;
26      use Carp qw(longmess croak);      use Carp qw(longmess croak carp);
27      use CGI;      use CGI;
28      use Cwd;      use Cwd;
29      use FIG_Config;      use FIG_Config;
# Line 34  Line 35 
35      use LWP::UserAgent;      use LWP::UserAgent;
36      use Time::HiRes 'gettimeofday';      use Time::HiRes 'gettimeofday';
37      use URI::Escape;      use URI::Escape;
38        use Time::Local;
39    
40  =head1 Tracing and Debugging Helpers  =head1 Tracing and Debugging Helpers
41    
42  =head2 Introduction  =head2 Tracing
43    
44  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
45  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.
46  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,
47  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
48  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
49  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
50  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
51  appear. To generate a trace message, use the following syntax.  appear.
52    
53    =head3 Putting Trace Messages in Your Code
54    
55    To generate a trace message, use the following syntax.
56    
57  C<< Trace($message) if T(errors => 4); >>      Trace($message) if T(errors => 4);
58    
59  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>
60  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
61    
62  C<< Trace($message) if T(main => 4); >>      Trace($message) if T(main => 4);
63    
64  will trace if the trace level is 4 or more.  will trace if the trace level is 4 or more.
65    
# Line 61  Line 67 
67  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
68  active and the trace level is 2 or more.  active and the trace level is 2 or more.
69    
70  C<< Trace($message) if T(2); >>      Trace($message) if T(2);
71    
72  To set up tracing, you call the L</TSetup> method. The method takes as input a trace level, a list  In scripts, where no package name is available, the category defaults to C<main>.
73  of category names, and a set of options. The trace level and list of category names are  
74    =head3 Custom Tracing
75    
76    Many programs have customized tracing configured using the L</TSetup> method. This is no longer
77    the preferred method, but a knowledge of how custom tracing works can make the more modern
78    L</Emergency Tracing> easier to understand.
79    
80    To set up custom tracing, you call the L</TSetup> method. The method takes as input a trace level,
81    a list of category names, and a destination. The trace level and list of category names are
82  specified as a space-delimited string. Thus  specified as a space-delimited string. Thus
83    
84  C<< TSetup('3 errors Sprout ERDB', 'HTML'); >>      TSetup('3 errors Sprout ERDB', 'TEXT');
85    
86  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
87  specifies that messages should be output as HTML paragraphs.  specifies that messages should be sent to the standard output.
88    
89  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
90  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
91  useful in a CGI environment.  useful in a CGI environment.
92    
93  C<< TSetup('3 *', 'WARN'); >>      TSetup('3 *', 'WARN');
94    
95  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
96  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
97  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
98  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
99  it easier to debug page formatting problems.  it easier to debug page formatting problems.
100    
101  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
102    a file at the same time. To trace to a file, specify the filename with an output character in front
103    of it.
104    
105        TSetup('4 SQL', ">$fileName");
106    
107    To trace to the standard output and a file at the same time, put a C<+> in front of the angle
108    bracket.
109    
110        TSetup('3 *', "+>$fileName");
111    
112  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>.
113  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.
114  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
115  being used out in the field.  being used out in the field.
116    
117    =head3 Trace Levels
118    
119  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
120  a suggestion.  a suggestion.
121    
# Line 121  Line 146 
146    
147  =back  =back
148    
149    The format of trace messages is important because some utilities analyze trace files.
150    There are three fields-- the time stamp, the category name, and the text.
151    The time stamp is between square brackets and the category name between angle brackets.
152    After the category name there is a colon (C<:>) followed by the message text.
153    If the square brackets or angle brackets are missing, then the trace management
154    utilities assume that they are encountering a set of pre-formatted lines.
155    
156    Note, however, that this formatting is done automatically by the tracing functions. You
157    only need to know about it if you want to parse a trace file.
158    
159    =head3 Emergency Tracing
160    
161    Sometimes, you need a way for tracing to happen automatically without putting parameters
162    in a form or on the command line. Emergency tracing does this. You invoke emergency tracing
163    from the debug form, which is accessed from the [[DebugConsole]]. Emergency tracing requires
164    that you specify a tracing key. For command-line tools, the key is
165    taken from the C<TRACING> environment variable. For web services, the key is taken from
166    a cookie. Either way, the key tells the tracing facility who you are, so that you control
167    the tracing in your environment without stepping on other users.
168    
169    The key can be anything you want. If you don't have a key, the C<SetPassword> page will
170    generate one for you.
171    
172    You can activate and de-activate emergency tracing from the debugging control panel, as
173    well as display the trace file itself.
174    
175    To enable emergency tracing in your code, call
176    
177        ETracing($cgi)
178    
179    from a web script and
180    
181        ETracing()
182    
183    from a command-line script.
184    
185    The web script will look for the tracing key in the cookies, and the command-line
186    script will look for it in the C<TRACING> environment variable. If you are
187    using the L</StandardSetup> method or a [[WebApplication]], emergency tracing
188    will be configured automatically.
189    
190  =cut  =cut
191    
192  # Declare the configuration variables.  # Declare the configuration variables.
193    
194  my $Destination = "NONE";   # Description of where to send the trace output.  my $Destination = "WARN";   # Description of where to send the trace output.
195  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
196                              # standard output                              # standard output
197  my %Categories = ( main => 1 );  my %Categories = ( main => 1 );
198                              # hash of active category names                              # hash of active category names
199    my @LevelNames = qw(error warn notice info detail);
200  my $TraceLevel = 0;         # trace level; a higher trace level produces more  my $TraceLevel = 0;         # trace level; a higher trace level produces more
201                              # messages                              # messages
202  my @Queue = ();             # queued list of trace messages.  my @Queue = ();             # queued list of trace messages.
203  my $LastCategory = "main";  # name of the last category interrogated  my $LastCategory = "main";  # name of the last category interrogated
204    my $LastLevel = 0;          # level of the last test call
205  my $SetupCount = 0;         # number of times TSetup called  my $SetupCount = 0;         # number of times TSetup called
206  my $AllTrace = 0;           # TRUE if we are tracing all categories.  my $AllTrace = 0;           # TRUE if we are tracing all categories.
207    
208  =head2 Public Methods  =head2 Tracing Methods
209    
210    =head3 Setups
211    
212        my $count = Tracer::Setups();
213    
214    Return the number of times L</TSetup> has been called.
215    
216    This method allows for the creation of conditional tracing setups where, for example, we
217    may want to set up tracing if nobody else has done it before us.
218    
219    =cut
220    
221    sub Setups {
222        return $SetupCount;
223    }
224    
225  =head3 TSetup  =head3 TSetup
226    
227  C<< TSetup($categoryList, $target); >>      TSetup($categoryList, $target);
228    
229  This method is used to specify the trace options. The options are stored as package data  This method is used to specify the trace options. The options are stored as package data
230  and interrogated by the L</Trace> and L</T> methods.  and interrogated by the L</Trace> and L</T> methods.
# Line 191  Line 274 
274          }          }
275      }      }
276      # Now we need to process the destination information. The most important special      # Now we need to process the destination information. The most important special
277      # cases are the single ">", which requires we clear the file first, and the      # case is when we're writing to a file. This is indicated by ">" (overwrite) and
278      # "+" prefix which indicates a double echo.      # ">>" (append). A leading "+" for either indicates that we are also writing to
279        # the standard output (tee mode).
280      if ($target =~ m/^\+?>>?/) {      if ($target =~ m/^\+?>>?/) {
281          if ($target =~ m/^\+/) {          if ($target =~ m/^\+/) {
282              $TeeFlag = 1;              $TeeFlag = 1;
283              $target = substr($target, 1);              $target = substr($target, 1);
284          }          }
285          if ($target =~ m/^>[^>]/) {          if ($target =~ m/^>[^>]/) {
286                # We need to initialize the file (which clears it).
287              open TRACEFILE, $target;              open TRACEFILE, $target;
288              print TRACEFILE Now() . " Tracing initialized.\n";              print TRACEFILE "[" . Now() . "] [notice] [Tracer] Tracing initialized.\n";
289              close TRACEFILE;              close TRACEFILE;
290                # Set to append mode now that the file has been cleared.
291              $Destination = ">$target";              $Destination = ">$target";
292          } else {          } else {
293              $Destination = $target;              $Destination = $target;
# Line 213  Line 299 
299      $SetupCount++;      $SetupCount++;
300  }  }
301    
302  =head3 StandardSetup  =head3 SetLevel
303    
304  C<< my ($options, @parameters) = StandardSetup(\@categories, \%options, $parmHelp, @ARGV); >>      Tracer::SetLevel($newLevel);
305    
306  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.  
307    
308  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.  
309    
310  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  
311    
312      ["Sprout", "SproutLoad", "ERDB"]  Proposed new trace level.
313    
314  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.  
315    
316  =over 4  =cut
317    
318  =item FIG  sub SetLevel {
319        $TraceLevel = $_[0];
320    }
321    
322  Turns on trace messages inside the B<FIG> package.  =head3 ParseDate
323    
324  =item SQL      my $time = Tracer::ParseDate($dateString);
325    
326  Traces SQL commands and activity.  Convert a date into a PERL time number. This method expects a date-like string
327    and parses it into a number. The string must be vaguely date-like or it will
328    return an undefined value. Our requirement is that a month and day be
329    present and that three pieces of the date string (time of day, month and day,
330    year) be separated by likely delimiters, such as spaces, commas, and such-like.
331    
332  =item Tracer  If a time of day is present, it must be in military time with two digits for
333    everything but the hour.
334    
335  Traces error messages and call stacks.  The year must be exactly four digits.
336    
337  =back  Additional stuff can be in the string. We presume it's time zones or weekdays or something
338    equally innocuous. This means, however, that a sufficiently long sentence with date-like
339    parts in it may be interpreted as a date. Hopefully this will not be a problem.
340    
341  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.  
342    
343      TransactFeatures -trace=3 -sql register ../xacts IDs.tbl  The parameters are as follows.
344    
345  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  
346    
347  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.  
348    
349      TransactFeatures -trace=3 -sql -user=Bruce register ../xacts IDs.tbl  The date string to convert.
350    
351  would send the trace output to C<traceBruce.log> in the temporary directory.  =item RETURN
352    
353  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
354  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.  
355    
356  You can specify a different default trace level by setting C<$options->{trace}>  =back
 prior to calling this method.  
357    
358  An example at this point would help. Consider, for example, the command-line utility  =cut
 C<TransactFeatures>. It accepts a list of positional parameters plus the options  
 C<safe>, C<noAlias>, C<start>, and C<tblFiles>. To start up this command, we execute  
 the following code.  
359    
360      my ($options, @parameters) = Tracer::StandardSetup(["DocUtils"],  # Universal month conversion table.
361                          { safe => [0, "use database transactions"],  use constant MONTHS => {    Jan =>  0, January   =>  0, '01' =>  0,  '1' =>  0,
362                            noAlias => [0, "do not expect aliases in CHANGE transactions"],                              Feb =>  1, February  =>  1, '02' =>  1,  '2' =>  1,
363                            start => [' ', "start with this genome"],                              Mar =>  2, March     =>  2, '03' =>  2,  '3' =>  2,
364                            tblFiles => [0, "output TBL files containing the corrected IDs"] },                              Apr =>  3, April     =>  3, '04' =>  3,  '4' =>  3,
365                          "command transactionDirectory IDfile",                              May =>  4, May       =>  4, '05' =>  4,  '5' =>  4,
366                        @ARGV);                              Jun =>  5, June      =>  5, '06' =>  5,  '6' =>  5,
367                                Jul =>  6, July      =>  6, '07' =>  6,  '7' =>  6,
368                                Aug =>  7, August    =>  7, '08' =>  7,  '8' =>  7,
369                                Sep =>  8, September =>  8, '09' =>  8,  '9' =>  8,
370                                Oct =>  9, October  =>   9, '10' =>  9,
371                                Nov => 10, November =>  10, '11' => 10,
372                                Dec => 11, December =>  11, '12' => 11
373                            };
374    
375    sub ParseDate {
376        # Get the parameters.
377        my ($dateString) = @_;
378        # Declare the return variable.
379        my $retVal;
380        # Find the month and day of month. There are two ways that can happen. We check for the
381        # numeric style first. That way, if the user's done something like "Sun 12/22", then we
382        # won't be fooled into thinking the month is Sunday.
383        if ($dateString =~ m#\b(\d{1,2})/(\d{1,2})\b# || $dateString =~ m#\b(\w+)\s(\d{1,2})\b#) {
384            my ($mon, $mday) = (MONTHS->{$1}, $2);
385            # Insist that the month and day are valid.
386            if (defined($mon) && $2 >= 1 && $2 <= 31) {
387                # Find the time.
388                my ($hour, $min, $sec) = (0, 0, 0);
389                if ($dateString =~ /\b(\d{1,2}):(\d{2}):(\d{2})\b/) {
390                    ($hour, $min, $sec) = ($1, $2, $3);
391                }
392                # Find the year.
393                my $year;
394                if ($dateString =~ /\b(\d{4})\b/) {
395                    $year = $1;
396                } else {
397                    # Get the default year, which is this one. Note we must convert it to
398                    # the four-digit value expected by "timelocal".
399                    (undef, undef, undef, undef, undef, $year) = localtime();
400                    $year += 1900;
401                }
402                $retVal = timelocal($sec, $min, $hour, $mday, $mon, $year);
403            }
404        }
405        # Return the result.
406        return $retVal;
407    }
408    
409  The call to C<ParseCommand> specifies the default values for the options and  =head3 LogErrors
 stores the actual options in a hash that is returned as C<$options>. The  
 positional parameters are returned in C<@parameters>.  
410    
411  The following is a sample command line for C<TransactFeatures>.      Tracer::LogErrors($fileName);
412    
413      TransactFeatures -trace=2 -noAlias register ../xacts IDs.tbl  Route the standard error output to a log file.
414    
415  In this case, C<register>, C<../xacts>, and C<IDs.tbl> are the positional  =over 4
 parameters, and would find themselves in I<@parameters> after executing the  
 above code fragment. The tracing would be set to level 2, and the categories  
 would be C<FIG>, C<Tracer>, and <DocUtils>. C<FIG> and C<Tracer> are standard,  
 and C<DocUtils> was included because it came in within the first parameter  
 to this method. The I<$options> hash would be  
416    
417      { trace => 2, sql => 0, safe => 0,  =item fileName
       noAlias => 1, start => ' ', tblFiles => 0 }  
418    
419  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.  
420    
421  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  
422    
423      -user=Bruce -background  =cut
424    
425  then the trace output would go to C<traceBruce.log>, the standard output to  sub LogErrors {
426  C<outBruce.log>, and the error output to C<errBruce.log>. This is designed to      # Get the file name.
427  simplify starting a command in the background.      my ($fileName) = @_;
428        # Open the file as the standard error output.
429        open STDERR, '>', $fileName;
430    }
431    
432  Finally, if the special option C<-h> is specified, the option names will  =head3 Trace
 be traced at level 0 and the program will exit without processing.  
 This provides a limited help capability. For example, if the user enters  
433    
434      TransactFeatures -h      Trace($message);
435    
436  he would see the following output.  Write a trace message to the target location specified in L</TSetup>. If there has not been
437    any prior call to B<TSetup>.
438    
439      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  
440    
441  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,  
442    
443      { trace => [0, "tracing level (default 0)"],  Message to write.
        ...  
444    
445  would set the default trace level to 0 instead of 2, while  =back
446    
447      { trace => ["2-", "tracing level (default 2)"],  =cut
        ...  
448    
449  would leave the default at 2, but trace only to the log file, not to the  sub Trace {
450  standard output.      # Get the parameters.
451        my ($message) = @_;
452        # Strip off any line terminators at the end of the message. We will add
453        # new-line stuff ourselves.
454        my $stripped = Strip($message);
455        # Compute the caller information.
456        my ($callPackage, $callFile, $callLine) = caller();
457        my $callFileTitle = basename($callFile);
458        # Check the caller.
459        my $callerInfo = ($callFileTitle ne "Tracer.pm" ? " [$callFileTitle $callLine]" : "");
460        # Get the timestamp.
461        my $timeStamp = Now();
462        # Build the prefix.
463        my $level = $LevelNames[$LastLevel] || "($LastLevel)";
464        my $prefix = "[$timeStamp] [$level] [$LastCategory]$callerInfo";
465        # Format the message.
466        my $formatted = "$prefix $stripped";
467        # Process according to the destination.
468        if ($Destination eq "TEXT") {
469            # Write the message to the standard output.
470            print "$formatted\n";
471        } elsif ($Destination eq "ERROR") {
472            # Write the message to the error output. Here, we want our prefix fields.
473            print STDERR "$formatted\n";
474        } elsif ($Destination eq "WARN") {
475            # Emit the message to the standard error output. It is presumed that the
476            # error logger will add its own prefix fields, the notable exception being
477            # the caller info.
478            print STDERR "$callerInfo$stripped\n";
479        } elsif ($Destination eq "QUEUE") {
480            # Push the message into the queue.
481            push @Queue, "$formatted";
482        } elsif ($Destination eq "HTML") {
483            # Convert the message to HTML and write it to the standard output.
484            my $escapedMessage = CGI::escapeHTML($stripped);
485            print "<p>$timeStamp $LastCategory $LastLevel: $escapedMessage</p>\n";
486        } elsif ($Destination =~ m/^>>/) {
487            # Write the trace message to an output file.
488            open(TRACING, $Destination) || die "Tracing open for \"$Destination\" failed: $!";
489            print TRACING "$formatted\n";
490            close TRACING;
491            # If the Tee flag is on, echo it to the standard output.
492            if ($TeeFlag) {
493                print "$formatted\n";
494            }
495        }
496    }
497    
498  The parameters to this method are as follows.  =head3 T
499    
500  =over 4      my $switch = T($category, $traceLevel);
501    
502  =item categories      or
503    
504  Reference to a list of tracing category names. These should be names of      my $switch = T($traceLevel);
 packages whose internal workings will need to be debugged to get the  
 command working.  
505    
506  =item options  Return TRUE if the trace level is at or above a specified value and the specified category
507    is active, else FALSE. If no category is specified, the caller's package name is used.
508    
509  Reference to a hash containing the legal options for the current command mapped  =over 4
 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).  
510    
511  =item parmHelp  =item category
512    
513  A string that vaguely describes the positional parameters. This is used  Category to which the message belongs. If not specified, the caller's package name is
514  if the user specifies the C<-h> option.  used.
515    
516  =item argv  =item traceLevel
517    
518  List of command line parameters, including the option switches, which must  Relevant tracing level.
 precede the positional parameters and be prefixed by a hyphen.  
519    
520  =item RETURN  =item RETURN
521    
522  Returns a list. The first element of the list is the reference to a hash that  TRUE if a message at the specified trace level would appear in the trace, else FALSE.
 maps the command-line option switches to their values. These will either be the  
 default values or overrides specified on the command line. The remaining  
 elements of the list are the position parameters, in order.  
523    
524  =back  =back
525    
526  =cut  =cut
527    
528  sub StandardSetup {  sub T {
529        # Declare the return variable.
530        my $retVal = 0;
531        # Only proceed if tracing is turned on.
532        if ($Destination ne "NONE") {
533      # Get the parameters.      # Get the parameters.
534      my ($categories, $options, $parmHelp, @argv) = @_;          my ($category, $traceLevel) = @_;
535      # Add the tracing options.          if (!defined $traceLevel) {
536      if (! exists $options->{trace}) {              # Here we have no category, so we need to get the calling package.
537          $options->{trace} = [2, "tracing level"];              # The calling package is normally the first parameter. If it is
538      }              # omitted, the first parameter will be the tracelevel. So, the
539      $options->{sql} = [0, "turn on SQL tracing"];              # first thing we do is shift the so-called category into the
540      $options->{h} = [0, "display command-line options"];              # $traceLevel variable where it belongs.
541      $options->{user} = [$$, "trace log file name suffix"];              $traceLevel = $category;
542      $options->{background} = [0, "spool standard and error output"];              my ($package, $fileName, $line) = caller;
543      # Create a parsing hash from the options hash. The parsing hash              # If there is no calling package, we default to "main".
544      # contains the default values rather than the default value              if (!$package) {
545      # and the description. While we're at it, we'll memorize the                  $category = "main";
     # length of the longest option name.  
     my $longestName = 0;  
     my %parseOptions = ();  
     for my $key (keys %{$options}) {  
         if (length $key > $longestName) {  
             $longestName = length $key;  
         }  
         $parseOptions{$key} = $options->{$key}->[0];  
     }  
     # 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, ">$errFileName";  
     }  
     # Now we want to set up tracing. First, we need to know if SQL is to  
     # be traced.  
     my @cats = @{$categories};  
     if ($retOptions->{sql}) {  
         push @cats, "SQL";  
     }  
     # Add the default categories.  
     push @cats, "Tracer", "FIG";  
     # 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;  
     }  
     # Now we set up the trace mode.  
     my $traceMode;  
     # Verify that we can open a file in the FIG temporary directory.  
     my $traceFileName = "$FIG_Config::temp/trace$suffix.log";  
     if (open TESTTRACE, ">$traceFileName") {  
         # Here we can trace to a file.  
         $traceMode = ">$traceFileName";  
         if ($textOKFlag) {  
             # Echo to standard output if the text-OK flag is set.  
             $traceMode = "+$traceMode";  
         }  
         # Close the test file.  
         close TESTTRACE;  
     } else {  
         # Here we can't trace to a file. We trace to the standard output if it's  
         # okay, and the error log otherwise.  
         if ($textOKFlag) {  
             $traceMode = "TEXT";  
546          } else {          } else {
547              $traceMode = "WARN";                  my @cats = split /::/, $package;
548          }                  $category = $cats[$#cats];
549      }      }
     # Now set up the tracing.  
     TSetup("$traceLevel $cats", $traceMode);  
     # Check for the "h" option. If it is specified, dump the command-line  
     # options and exit the program.  
     if ($retOptions->{h}) {  
         $0 =~ m#[/\\](\w+)(\.pl)?$#i;  
         Trace("$1 [options] $parmHelp") if T(0);  
         for my $key (sort keys %{$options}) {  
             my $name = Pad($key, $longestName, 0, ' ');  
             my $desc = $options->{$key}->[1];  
             if ($options->{$key}->[0]) {  
                 $desc .= " (default " . $options->{$key}->[0] . ")";  
550              }              }
551              Trace("  $name $desc") if T(0);          # Save the category name and level.
552            $LastCategory = $category;
553            $LastLevel = $traceLevel;
554            # Convert it to lower case before we hash it.
555            $category = lc $category;
556            # Use the category and tracelevel to compute the result.
557            if (ref $traceLevel) {
558                Confess("Bad trace level.");
559            } elsif (ref $TraceLevel) {
560                Confess("Bad trace config.");
561          }          }
562          exit(0);          $retVal = ($traceLevel <= $TraceLevel && ($AllTrace || exists $Categories{$category}));
563      }      }
564      # Return the parsed parameters.      # Return the computed result.
565      return ($retOptions, @retParameters);      return $retVal;
566  }  }
567    
568  =head3 Setups  =head3 QTrace
569    
570  C<< my $count = Tracer::Setups(); >>      my $data = QTrace($format);
571    
572  Return the number of times L</TSetup> has been called.  Return the queued trace data in the specified format.
573    
574  This method allows for the creation of conditional tracing setups where, for example, we  =over 4
575  may want to set up tracing if nobody else has done it before us.  
576    =item format
577    
578    C<html> to format the data as an HTML list, C<text> to format it as straight text.
579    
580    =back
581    
582  =cut  =cut
583    
584  sub Setups {  sub QTrace {
585      return $SetupCount;      # Get the parameter.
586        my ($format) = @_;
587        # Create the return variable.
588        my $retVal = "";
589        # Only proceed if there is an actual queue.
590        if (@Queue) {
591            # Process according to the format.
592            if ($format =~ m/^HTML$/i) {
593                # Convert the queue into an HTML list.
594                $retVal = "<ul>\n";
595                for my $line (@Queue) {
596                    my $escapedLine = CGI::escapeHTML($line);
597                    $retVal .= "<li>$escapedLine</li>\n";
598                }
599                $retVal .= "</ul>\n";
600            } elsif ($format =~ m/^TEXT$/i) {
601                # Convert the queue into a list of text lines.
602                $retVal = join("\n", @Queue) . "\n";
603            }
604            # Clear the queue.
605            @Queue = ();
606        }
607        # Return the formatted list.
608        return $retVal;
609  }  }
610    
611  =head3 Open  =head3 Confess
612    
613  C<< my $handle = Open($fileHandle, $fileSpec, $message); >>      Confess($message);
614    
615  Open a file.  Trace the call stack and abort the program with the specified message. When used with
616    the OR operator and the L</Assert> method, B<Confess> can function as a debugging assert.
617    So, for example
618    
619  The I<$fileSpec> is essentially the second argument of the PERL C<open>      Assert($recNum >= 0) || Confess("Invalid record number $recNum.");
 function. The mode is specified using Unix-like shell information. So, for  
 example,  
620    
621      Open(\*LOGFILE, '>>/usr/spool/news/twitlog', "Could not open twit log.");  Will abort the program with a stack trace if the value of C<$recNum> is negative.
622    
623  would open for output appended to the specified file, and  =over 4
624    
625      Open(\*DATASTREAM, "| sort -u >$outputFile", "Could not open $outputFile.");  =item message
626    
627  would open a pipe that sorts the records written and removes duplicates. Note  Message to include in the trace.
 the use of file handle syntax in the Open call. To use anonymous file handles,  
 code as follows.  
628    
629      my $logFile = Open(undef, '>>/usr/spool/news/twitlog', "Could not open twit log.");  =back
630    
631  The I<$message> parameter is used if the open fails. If it is set to C<0>, then  =cut
 the open returns TRUE if successful and FALSE if an error occurred. Otherwise, a  
 failed open will throw an exception and the third parameter will be used to construct  
 an error message. If the parameter is omitted, a standard message is constructed  
 using the file spec.  
632    
633      Could not open "/usr/spool/news/twitlog"  sub Confess {
634        # Get the parameters.
635        my ($message) = @_;
636        # Set up the category and level.
637        $LastCategory = "(confess)";
638        $LastLevel = 0;
639        if (! defined($FIG_Config::no_tool_hdr)) {
640            # Here we have a tool header. Display its length so that the user can adjust the line numbers.
641            my $toolHeaderFile = "$FIG_Config::fig_disk/dist/releases/current/$FIG_Config::arch/tool_hdr";
642            # Only proceed if the tool header file is actually present.
643            if (-f $toolHeaderFile) {
644                my $fh;
645                if (open $fh, "<$toolHeaderFile") {
646                    my @lines = <$fh>;
647                    Trace("Tool header has " . scalar(@lines) . " lines.");
648                }
649            }
650        }
651        # Trace the call stack.
652        Cluck($message);
653        # Abort the program.
654        croak(">>> $message");
655    }
656    
657  Note that the mode characters are automatically cleaned from the file name.  =head3 Assert
 The actual error message from the file system will be captured and appended to the  
 message in any case.  
658    
659      Could not open "/usr/spool/news/twitlog": file not found.      Assert($condition1, $condition2, ... $conditionN);
660    
661  In some versions of PERL the only error message we get is a number, which  Return TRUE if all the conditions are true. This method can be used in conjunction with
662  corresponds to the C++ C<errno> value.  the OR operator and the L</Confess> method as a debugging assert.
663    So, for example
664    
665      Could not open "/usr/spool/news/twitlog": 6.      Assert($recNum >= 0) || Confess("Invalid record number $recNum.");
666    
667  =over 4  Will abort the program with a stack trace if the value of C<$recNum> is negative.
668    
669  =item fileHandle  =cut
670    sub Assert {
671        my $retVal = 1;
672        LOOP: for my $condition (@_) {
673            if (! $condition) {
674                $retVal = 0;
675                last LOOP;
676            }
677        }
678        return $retVal;
679    }
680    
681  File handle. If this parameter is C<undef>, a file handle will be generated  =head3 Cluck
 and returned as the value of this method.  
682    
683  =item fileSpec      Cluck($message);
684    
685  File name and mode, as per the PERL C<open> function.  Trace the call stack. Note that for best results, you should qualify the call with a
686    trace condition. For example,
687    
688  =item message (optional)      Cluck("Starting record parse.") if T(3);
689    
690  Error message to use if the open fails. If omitted, a standard error message  will only trace the stack if the trace level for the package is 3 or more.
 will be generated. In either case, the error information from the file system  
 is appended to the message. To specify a conditional open that does not throw  
 an error if it fails, use C<0>.  
691    
692  =item RETURN  =over 4
693    
694  Returns the name of the file handle assigned to the file, or C<undef> if the  =item message
695  open failed.  
696    Message to include in the trace.
697    
698  =back  =back
699    
700  =cut  =cut
701    
702  sub Open {  sub Cluck {
703      # Get the parameters.      # Get the parameters.
704      my ($fileHandle, $fileSpec, $message) = @_;      my ($message) = @_;
705      # Attempt to open the file.      # Trace what's happening.
706      my $rv = open $fileHandle, $fileSpec;      Trace("Stack trace for event: $message");
707      # If the open failed, generate an error message.      my $confession = longmess($message);
708      if (! $rv) {      # Convert the confession to a series of trace messages.
709          # Save the system error message.      for my $line (split /\s*\n/, $confession) {
710          my $sysMessage = $!;          # Only proceed if this call trace is for a method outside Tracer itself.
711          # See if we need a default message.          if ($line !~ /Tracer\.pm/) {
712          if (!$message) {              # Replace the leading tab with a series of spaces.
713              # Clean any obvious mode characters and leading spaces from the              $line =~ s/\t/    /;
714              # filename.              # Trace the line.
715              my ($fileName) = FindNamePart($fileSpec);              Trace($line);
             $message = "Could not open \"$fileName\"";  
716          }          }
         # Terminate with an error using the supplied message and the  
         # error message from the file system.  
         Confess("$message: $!");  
717      }      }
     # Return the file handle.  
     return $fileHandle;  
718  }  }
719    
720  =head3 FindNamePart  =head3 ScriptSetup (deprecated)
   
 C<< my ($fileName, $start, $len) = Tracer::FindNamePart($fileSpec); >>  
   
 Extract the portion of a file specification that contains the file name.  
721    
722  A file specification is the string passed to an C<open> call. It specifies the file      my ($cgi, $varHash) = ScriptSetup($noTrace);
 mode and name. In a truly complex situation, it can specify a pipe sequence. This  
 method assumes that the file name is whatever follows the first angle bracket  
 sequence.  So, for example, in the following strings the file name is  
 C</usr/fig/myfile.txt>.  
723    
724      >>/usr/fig/myfile.txt  Perform standard tracing and debugging setup for scripts. The value returned is
725      </usr/fig/myfile.txt  the CGI object followed by a pre-built variable hash. At the end of the script,
726      | sort -u > /usr/fig/myfile.txt  the client should call L</ScriptFinish> to output the web page.
727    
728  If the method cannot find a file name using its normal methods, it will return the  This method calls L</ETracing> to configure tracing, which allows the tracing
729  whole incoming string.  to be configured via the emergency tracing form on the debugging control panel.
730    Tracing will then be turned on automatically for all programs that use the L</ETracing>
731    method, which includes every program that uses this method or L</StandardSetup>.
732    
733  =over 4  =over 4
734    
735  =item fileSpec  =item noTrace (optional)
736    
737  File specification string from which the file name is to be extracted.  If specified, tracing will be suppressed. This is useful if the script wants to set up
738    tracing manually.
739    
740  =item RETURN  =item RETURN
741    
742  Returns a three-element list. The first element contains the file name portion of  Returns a two-element list consisting of a CGI query object and a variable hash for
743  the specified string, or the whole string if a file name cannot be found via normal  the output page.
 methods. The second element contains the start position of the file name portion and  
 the third element contains the length.  
744    
745  =back  =back
746    
747  =cut  =cut
748  #: Return Type $;  
749  sub FindNamePart {  sub ScriptSetup {
750      # Get the parameters.      # Get the parameters.
751      my ($fileSpec) = @_;      my ($noTrace) = @_;
752      # Default to the whole input string.      # Get the CGI query object.
753      my ($retVal, $pos, $len) = ($fileSpec, 0, length $fileSpec);      my $cgi = CGI->new();
754      # Parse out the file name if we can.      # Set up tracing if it's not suppressed.
755      if ($fileSpec =~ m/(<|>>?)(.+?)(\s*)$/) {      ETracing($cgi) unless $noTrace;
756          $retVal = $2;      # Create the variable hash.
757          $len = length $retVal;      my $varHash = { results => '' };
758          $pos = (length $fileSpec) - (length $3) - $len;      # Return the query object and variable hash.
759        return ($cgi, $varHash);
760    }
761    
762    =head3 ETracing
763    
764        ETracing($parameter);
765    
766    Set up emergency tracing. Emergency tracing is tracing that is turned
767    on automatically for any program that calls this method. The emergency
768    tracing parameters are stored in a a file identified by a tracing key.
769    If this method is called with a CGI object, then the tracing key is
770    taken from a cookie. If it is called with no parameters, then the tracing
771    key is taken from an environment variable. If it is called with a string,
772    the tracing key is that string.
773    
774    =over 4
775    
776    =item parameter
777    
778    A parameter from which the tracing key is computed. If it is a scalar,
779    that scalar is used as the tracing key. If it is a CGI object, the
780    tracing key is taken from the C<IP> cookie. If it is omitted, the
781    tracing key is taken from the C<TRACING> environment variable. If it
782    is a CGI object and emergency tracing is not on, the C<Trace> and
783    C<TF> parameters will be used to determine the type of tracing.
784    
785    =back
786    
787    =cut
788    
789    sub ETracing {
790        # Get the parameter.
791        my ($parameter) = @_;
792        # Check for CGI mode.
793        my $cgi = (ref $parameter eq 'CGI' ? $parameter : undef);
794        # Default to no tracing except errors.
795        my ($tracing, $dest) = ("0", "WARN");
796        # Check for emergency tracing.
797        my $tkey = EmergencyKey($parameter);
798        my $emergencyFile = EmergencyFileName($tkey);
799        if (-e $emergencyFile) {
800            # We have the file. Read in the data.
801            my @tracing = GetFile($emergencyFile);
802            # Pull off the time limit.
803            my $expire = shift @tracing;
804            # Convert it to seconds.
805            $expire *= 3600;
806            # Check the file data.
807            my $stat = stat($emergencyFile);
808            my ($now) = gettimeofday;
809            if ($now - $stat->mtime > $expire) {
810                # Delete the expired file.
811                unlink $emergencyFile;
812            } else {
813                # Emergency tracing is on. Pull off the destination and
814                # the trace level;
815                $dest = shift @tracing;
816                my $level = shift @tracing;
817                # Convert the destination to a real tracing destination.
818                # temp directory.
819                $dest = EmergencyTracingDest($tkey, $dest);
820                # Insure Tracer is specified.
821                my %moduleHash = map { $_ => 1 } @tracing;
822                $moduleHash{Tracer} = 1;
823                # Set the trace parameter.
824                $tracing = join(" ", $level, sort keys %moduleHash);
825            }
826        } elsif (defined $cgi) {
827            # There's no emergency tracing, but we have a CGI object, so check
828            # for tracing from the form parameters.
829            if ($cgi->param('Trace')) {
830                # Here the user has requested tracing via a form.
831                $dest = ($cgi->param('TF') ? ">$FIG_Config::temp/Trace$$.log" : "QUEUE");
832                $tracing = $cgi->param('Trace') . " Tracer";
833            }
834        }
835        # Setup the tracing we've determined from all the stuff above.
836        TSetup($tracing, $dest);
837        # Check to see if we're a web script.
838        if (defined $cgi) {
839            # Yes we are. Trace the form and environment data.
840            TraceParms($cgi);
841            # Check for RAW mode. In raw mode, we print a fake header so that we see everything
842            # emitted by the script in its raw form.
843            if (T(Raw => 3)) {
844                print CGI::header(-type => 'text/plain', -tracing => 'Raw');
845            }
846      }      }
     # Return the result.  
     return ($retVal, $pos, $len);  
847  }  }
848    
849  =head3 OpenDir  =head3 EmergencyFileName
850    
851  C<< my @files = OpenDir($dirName, $filtered, $flag); >>      my $fileName = Tracer::EmergencyFileName($tkey);
852    
853  Open a directory and return all the file names. This function essentially performs  Return the emergency tracing file name. This is the file that specifies
854  the functions of an C<opendir> and C<readdir>. If the I<$filtered> parameter is  the tracing information.
 set to TRUE, all filenames beginning with a period (C<.>), dollar sign (C<$>),  
 or pound sign (C<#>) and all filenames ending with a tilde C<~>) will be  
 filtered out of the return list. If the directory does not open and I<$flag> is not  
 set, an exception is thrown. So, for example,  
855    
856      my @files = OpenDir("/Volumes/fig/contigs", 1);  =over 4
857    
858  is effectively the same as  =item tkey
859    
860      opendir(TMP, "/Volumes/fig/contigs") || Confess("Could not open /Volumes/fig/contigs.");  Tracing key for the current program.
     my @files = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir(TMP);  
861    
862  Similarly, the following code  =item RETURN
863    
864      my @files = grep { $_ =~ /^\d/ } OpenDir("/Volumes/fig/orgs", 0, 1);  Returns the name of the file to contain the emergency tracing information.
865    
866  Returns the names of all files in C</Volumes/fig/orgs> that begin with digits and  =back
867  automatically returns an empty list if the directory fails to open.  
868    =cut
869    
870    sub EmergencyFileName {
871        # Get the parameters.
872        my ($tkey) = @_;
873        # Compute the emergency tracing file name.
874        return "$FIG_Config::temp/Emergency$tkey.txt";
875    }
876    
877    =head3 EmergencyFileTarget
878    
879        my $fileName = Tracer::EmergencyFileTarget($tkey);
880    
881    Return the emergency tracing target file name. This is the file that receives
882    the tracing output for file-based tracing.
883    
884  =over 4  =over 4
885    
886  =item dirName  =item tkey
887    
888  Name of the directory to open.  Tracing key for the current program.
889    
890  =item filtered  =item RETURN
891    
892  TRUE if files whose names begin with a period (C<.>) should be automatically removed  Returns the name of the file to contain the trace output.
 from the list, else FALSE.  
893    
894  =item flag  =back
895    
896  TRUE if a failure to open is okay, else FALSE  =cut
897    
898    sub EmergencyFileTarget {
899        # Get the parameters.
900        my ($tkey) = @_;
901        # Compute the emergency tracing file name.
902        return "$FIG_Config::temp/trace$tkey.log";
903    }
904    
905    =head3 EmergencyTracingDest
906    
907        my $dest = Tracer::EmergencyTracingDest($tkey, $myDest);
908    
909    This method converts an emergency tracing destination to a real
910    tracing destination. The main difference is that if the
911    destination is C<FILE> or C<APPEND>, we convert it to file
912    output. If the destination is C<DUAL>, we convert it to file
913    and standard output.
914    
915    =over 4
916    
917    =item tkey
918    
919    Tracing key for this environment.
920    
921    =item myDest
922    
923    Destination from the emergency tracing file.
924    
925    =item RETURN
926    
927    Returns a destination that can be passed into L</TSetup>.
928    
929  =back  =back
930    
931  =cut  =cut
932  #: Return Type @;  
933  sub OpenDir {  sub EmergencyTracingDest {
934      # Get the parameters.      # Get the parameters.
935      my ($dirName, $filtered, $flag) = @_;      my ($tkey, $myDest) = @_;
936      # Declare the return variable.      # Declare the return variable.
937      my @retVal = ();      my $retVal = $myDest;
938      # Open the directory.      # Process according to the destination value.
939      if (opendir(my $dirHandle, $dirName)) {      if ($myDest eq 'FILE') {
940          # The directory opened successfully. Get the appropriate list according to the          $retVal = ">" . EmergencyFileTarget($tkey);
941          # strictures of the filter parameter.      } elsif ($myDest eq 'APPEND') {
942          if ($filtered) {          $retVal = ">>" . EmergencyFileTarget($tkey);
943              @retVal = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir $dirHandle;      } elsif ($myDest eq 'DUAL') {
944          } else {          $retVal = "+>" . EmergencyFileTarget($tkey);
945              @retVal = readdir $dirHandle;      } elsif ($myDest eq 'WARN') {
946          }          $retVal = "WARN";
     } elsif (! $flag) {  
         # Here the directory would not open and it's considered an error.  
         Confess("Could not open directory $dirName.");  
947      }      }
948      # Return the result.      # Return the result.
949      return @retVal;      return $retVal;
950  }  }
951    
952  =head3 SetLevel  =head3 Emergency
953    
954  C<< Tracer::SetLevel($newLevel); >>      Emergency($key, $hours, $dest, $level, @modules);
955    
956  Modify the trace level. A higher trace level will cause more messages to appear.  Turn on emergency tracing. This method is normally invoked over the web from
957    a debugging console, but it can also be called by the C<trace.pl> script.
958    The caller specifies the duration of the emergency in hours, the desired tracing
959    destination, the trace level, and a list of the trace modules to activate.
960    For the length of the duration, when a program in an environment with the
961    specified tracing key active invokes a Sprout CGI script, tracing will be
962    turned on automatically. See L</TSetup> for more about tracing setup and
963    L</ETracing> for more about emergency tracing.
964    
965  =over 4  =over 4
966    
967  =item newLevel  =item tkey
968    
969  Proposed new trace level.  The tracing key. This is used to identify the control file and the trace file.
970    
971    =item hours
972    
973    Number of hours to keep emergency tracing alive.
974    
975    =item dest
976    
977    Tracing destination. If no path information is specified for a file
978    destination, it is put in the FIG temporary directory.
979    
980    =item level
981    
982    Tracing level. A higher level means more trace messages.
983    
984    =item modules
985    
986    A list of the tracing modules to activate.
987    
988  =back  =back
989    
990  =cut  =cut
991    
992  sub SetLevel {  sub Emergency {
993      $TraceLevel = $_[0];      # Get the parameters.
994        my ($tkey, $hours, $dest, $level, @modules) = @_;
995        # Create the emergency file.
996        my $specFile = EmergencyFileName($tkey);
997        my $outHandle = Open(undef, ">$specFile");
998        print $outHandle join("\n", $hours, $dest, $level, @modules, "");
999  }  }
1000    
1001  =head3 Now  =head3 EmergencyKey
1002    
1003        my $tkey = EmergencyKey($parameter);
1004    
1005    Return the Key to be used for emergency tracing. This could be an IP address,
1006     a session ID, or a user name, depending on the environment.
1007    
1008    =over 4
1009    
1010  C<< my $string = Tracer::Now(); >>  =item parameter
1011    
1012  Return a displayable time stamp containing the local time.  Parameter defining the method for finding the tracing key. If it is a scalar,
1013    then it is presumed to be the tracing key itself. If it is a CGI object, then
1014    the tracing key is taken from the C<IP> cookie. Otherwise, the tracing key is
1015    taken from the C<TRACING> environment variable.
1016    
1017    =item RETURN
1018    
1019    Returns the key to be used for labels in emergency tracing.
1020    
1021    =back
1022    
1023  =cut  =cut
1024    
1025  sub Now {  sub EmergencyKey {
1026      my ($sec,$min,$hour,$mday,$mon,$year,$wday,$yday,$isdst) = localtime(time);      # Get the parameters.
1027      my $retVal = _p2($mon+1) . "/" . _p2($mday) . "/" . ($year + 1900) . " " .      my ($parameter) = @_;
1028                   _p2($hour) . ":" . _p2($min) . ":" . _p2($sec);      # Declare the return variable.
1029        my $retVal;
1030        # Determine the parameter type.
1031        if (! defined $parameter) {
1032            # Here we're supposed to check the environment.
1033            $retVal = $ENV{TRACING};
1034        } else {
1035            my $ptype = ref $parameter;
1036            if ($ptype eq 'CGI') {
1037                # Here we were invoked from a web page. Look for a cookie.
1038                $retVal = $parameter->cookie('IP');
1039            } elsif (! $ptype) {
1040                # Here the key was passed in.
1041                $retVal = $parameter;
1042            }
1043        }
1044        # If no luck finding a key, use the PID.
1045        if (! defined $retVal) {
1046            $retVal = $$;
1047        }
1048        # Return the result.
1049      return $retVal;      return $retVal;
1050  }  }
1051    
1052  # Pad a number to 2 digits.  
1053  sub _p2 {  =head3 TraceParms
1054      my ($value) = @_;  
1055      $value = "0$value" if ($value < 10);      Tracer::TraceParms($cgi);
1056      return $value;  
1057    Trace the CGI parameters at trace level CGI => 3 and the environment variables
1058    at level CGI => 4. A self-referencing URL is traced at level CGI => 2.
1059    
1060    =over 4
1061    
1062    =item cgi
1063    
1064    CGI query object containing the parameters to trace.
1065    
1066    =back
1067    
1068    =cut
1069    
1070    sub TraceParms {
1071        # Get the parameters.
1072        my ($cgi) = @_;
1073        if (T(CGI => 2)) {
1074            # Here we trace the GET-style URL for the script.
1075            Trace("[URL] " . $cgi->url(-relative => 1, -query => 1));
1076        }
1077        if (T(CGI => 3)) {
1078            # Here we want to trace the parameter data.
1079            my @names = $cgi->param;
1080            for my $parmName (sort @names) {
1081                # Note we skip the Trace parameters, which are for our use only.
1082                if ($parmName ne 'Trace' && $parmName ne 'TF') {
1083                    my @values = $cgi->param($parmName);
1084                    Trace("[CGI] $parmName = " . join(", ", @values));
1085                }
1086            }
1087            # Display the request method.
1088            my $method = $cgi->request_method();
1089            Trace("Method: $method");
1090        }
1091        if (T(CGI => 4)) {
1092            # Here we want the environment data too.
1093            for my $envName (sort keys %ENV) {
1094                Trace("[ENV] $envName = $ENV{$envName}");
1095            }
1096        }
1097    }
1098    
1099    =head3 TraceImages
1100    
1101        Tracer::TraceImages($htmlString);
1102    
1103    Trace information about all of an html document's images. The tracing
1104    will be for type "IMG" at level 3. The image's source string
1105    will be displayed. This is generally either the URL of the image or
1106    raw data for the image itself. If the source is too long, only the first 300
1107    characters will be shown at trace level 3. The entire source will be shown,
1108    however, at trace level 4. This method is not very smart, and might catch
1109    Javascript code, but it is still useful when debugging the arcane
1110    behavior of images in multiple browser environments.
1111    
1112    =over 4
1113    
1114    =item htmlString
1115    
1116    HTML text for an outgoing web page.
1117    
1118    =back
1119    
1120    =cut
1121    
1122    sub TraceImages {
1123        # Only proceed if we're at the proper trace level.
1124        if (T(IMG => 3)) {
1125            # For performance reasons we're manipulating $_[0] instead of retrieving the string
1126            # into a variable called "$htmlString". This is because we expect html strings to be
1127            # long, and don't want to copy them any more than we have to.
1128            Trace(length($_[0]) . " characters in web page.");
1129            # Loop through the HTML, culling image tags.
1130            while ($_[0] =~ /<img\s+[^>]+?src="([^"]+)"/sgi) {
1131                # Extract the source string and determine whether or not it's too long.
1132                my $srcString = $1;
1133                my $pos = pos($_[0]) - length($srcString);
1134                my $excess = length($srcString) - 300;
1135                # We'll put the display string in here.
1136                my $srcDisplay = $srcString;
1137                # If it's a data string, split it at the comma.
1138                $srcDisplay =~ s/^(data[^,]+,)/$1\n/;
1139                # If there's no excess or we're at trace level 4, we're done. At level 3 with
1140                # a long string, however, we only show the first 300 characters.
1141                if ($excess > 0 && ! T(IMG => 4)) {
1142                    $srcDisplay = substr($srcDisplay,0,300) . "\nplus $excess characters.";
1143                }
1144                # Output the trace message.
1145                Trace("Image tag at position $pos:\n$srcDisplay");
1146            }
1147        }
1148    }
1149    
1150    
1151    =head3 ScriptFinish (deprecated)
1152    
1153        ScriptFinish($webData, $varHash);
1154    
1155    Output a web page at the end of a script. Either the string to be output or the
1156    name of a template file can be specified. If the second parameter is omitted,
1157    it is assumed we have a string to be output; otherwise, it is assumed we have the
1158    name of a template file. The template should have the variable C<DebugData>
1159    specified in any form that invokes a standard script. If debugging mode is turned
1160    on, a form field will be put in that allows the user to enter tracing data.
1161    Trace messages will be placed immediately before the terminal C<BODY> tag in
1162    the output, formatted as a list.
1163    
1164    A typical standard script would loook like the following.
1165    
1166        BEGIN {
1167            # Print the HTML header.
1168            print "CONTENT-TYPE: text/html\n\n";
1169        }
1170        use Tracer;
1171        use CGI;
1172        use FIG;
1173        # ... more uses ...
1174    
1175        my ($cgi, $varHash) = ScriptSetup();
1176        eval {
1177            # ... get data from $cgi, put it in $varHash ...
1178        };
1179        if ($@) {
1180            Trace("Script Error: $@") if T(0);
1181        }
1182        ScriptFinish("Html/MyTemplate.html", $varHash);
1183    
1184    The idea here is that even if the script fails, you'll see trace messages and
1185    useful output.
1186    
1187    =over 4
1188    
1189    =item webData
1190    
1191    A string containing either the full web page to be written to the output or the
1192    name of a template file from which the page is to be constructed. If the name
1193    of a template file is specified, then the second parameter must be present;
1194    otherwise, it must be absent.
1195    
1196    =item varHash (optional)
1197    
1198    If specified, then a reference to a hash mapping variable names for a template
1199    to their values. The template file will be read into memory, and variable markers
1200    will be replaced by data in this hash reference.
1201    
1202    =back
1203    
1204    =cut
1205    
1206    sub ScriptFinish {
1207        # Get the parameters.
1208        my ($webData, $varHash) = @_;
1209        # Check for a template file situation.
1210        my $outputString;
1211        if (defined $varHash) {
1212            # Here we have a template file. We need to determine the template type.
1213            my $template;
1214            if ($FIG_Config::template_url && $webData =~ /\.php$/) {
1215                $template = "$FIG_Config::template_url/$webData";
1216            } else {
1217                $template = "<<$webData";
1218            }
1219            $outputString = PageBuilder::Build($template, $varHash, "Html");
1220        } else {
1221            # Here the user gave us a raw string.
1222            $outputString = $webData;
1223        }
1224        # Check for trace messages.
1225        if ($Destination ne "NONE" && $TraceLevel > 0) {
1226            # We have trace messages, so we want to put them at the end of the body. This
1227            # is either at the end of the whole string or at the beginning of the BODY
1228            # end-tag.
1229            my $pos = length $outputString;
1230            if ($outputString =~ m#</body>#gi) {
1231                $pos = (pos $outputString) - 7;
1232            }
1233            # If the trace messages were queued, we unroll them. Otherwise, we display the
1234            # destination.
1235            my $traceHtml;
1236            if ($Destination eq "QUEUE") {
1237                $traceHtml = QTrace('Html');
1238            } elsif ($Destination =~ /^>>(.+)$/) {
1239                # Here the tracing output it to a file. We code it as a hyperlink so the user
1240                # can copy the file name into the clipboard easily.
1241                my $actualDest = $1;
1242                $traceHtml = "<p>Tracing output to $actualDest.</p>\n";
1243            } else {
1244                # Here we have one of the special destinations.
1245                $traceHtml = "<P>Tracing output type is $Destination.</p>\n";
1246            }
1247            substr $outputString, $pos, 0, $traceHtml;
1248        }
1249        # Write the output string.
1250        print $outputString;
1251    }
1252    
1253    =head2 Command-Line Utility Methods
1254    
1255    =head3 SendSMS
1256    
1257        my $msgID = Tracer::SendSMS($phoneNumber, $msg);
1258    
1259    Send a text message to a phone number using Clickatell. The FIG_Config file must contain the
1260    user name, password, and API ID for the relevant account in the hash reference variable
1261    I<$FIG_Config::phone>, using the keys C<user>, C<password>, and C<api_id>. For
1262    example, if the user name is C<BruceTheHumanPet>, the password is C<silly>, and the API ID
1263    is C<2561022>, then the FIG_Config file must contain
1264    
1265        $phone =  { user => 'BruceTheHumanPet',
1266                    password => 'silly',
1267                    api_id => '2561022' };
1268    
1269    The original purpose of this method was to insure Bruce would be notified immediately when the
1270    Sprout Load terminates. Care should be taken if you do not wish Bruce to be notified immediately
1271    when you call this method.
1272    
1273    The message ID will be returned if successful, and C<undef> if an error occurs.
1274    
1275    =over 4
1276    
1277    =item phoneNumber
1278    
1279    Phone number to receive the message, in international format. A United States phone number
1280    would be prefixed by "1". A British phone number would be prefixed by "44".
1281    
1282    =item msg
1283    
1284    Message to send to the specified phone.
1285    
1286    =item RETURN
1287    
1288    Returns the message ID if successful, and C<undef> if the message could not be sent.
1289    
1290    =back
1291    
1292    =cut
1293    
1294    sub SendSMS {
1295        # Get the parameters.
1296        my ($phoneNumber, $msg) = @_;
1297        # Declare the return variable. If we do not change it, C<undef> will be returned.
1298        my $retVal;
1299        # Only proceed if we have phone support.
1300        if (! defined $FIG_Config::phone) {
1301            Trace("Phone support not present in FIG_Config.") if T(1);
1302        } else {
1303            # Get the phone data.
1304            my $parms = $FIG_Config::phone;
1305            # Get the Clickatell URL.
1306            my $url = "http://api.clickatell.com/http/";
1307            # Create the user agent.
1308            my $ua = LWP::UserAgent->new;
1309            # Request a Clickatell session.
1310            my $resp = $ua->post("$url/sendmsg", { user => $parms->{user},
1311                                         password => $parms->{password},
1312                                         api_id => $parms->{api_id},
1313                                         to => $phoneNumber,
1314                                         text => $msg});
1315            # Check for an error.
1316            if (! $resp->is_success) {
1317                Trace("Alert failed.") if T(1);
1318            } else {
1319                # Get the message ID.
1320                my $rstring = $resp->content;
1321                if ($rstring =~ /^ID:\s+(.*)$/) {
1322                    $retVal = $1;
1323                } else {
1324                    Trace("Phone attempt failed with $rstring") if T(1);
1325                }
1326            }
1327        }
1328        # Return the result.
1329        return $retVal;
1330    }
1331    
1332    =head3 StandardSetup
1333    
1334        my ($options, @parameters) = StandardSetup(\@categories, \%options, $parmHelp, @ARGV);
1335    
1336    This method performs standard command-line parsing and tracing setup. The return
1337    values are a hash of the command-line options and a list of the positional
1338    parameters. Tracing is automatically set up and the command-line options are
1339    validated.
1340    
1341    This is a complex method that does a lot of grunt work. The parameters can
1342    be more easily understood, however, once they are examined individually.
1343    
1344    The I<categories> parameter is the most obtuse. It is a reference to a list of
1345    special-purpose tracing categories. Most tracing categories are PERL package
1346    names. So, for example, if you wanted to turn on tracing inside the B<Sprout>,
1347    B<ERDB>, and B<SproutLoad> packages, you would specify the categories
1348    
1349        ["Sprout", "SproutLoad", "ERDB"]
1350    
1351    This would cause trace messages in the specified three packages to appear in
1352    the output. There are two special tracing categories that are automatically
1353    handled by this method. In other words, if you used L</TSetup> you would need
1354    to include these categories manually, but if you use this method they are turned
1355    on automatically.
1356    
1357    =over 4
1358    
1359    =item SQL
1360    
1361    Traces SQL commands and activity.
1362    
1363    =item Tracer
1364    
1365    Traces error messages and call stacks.
1366    
1367    =back
1368    
1369    C<SQL> is only turned on if the C<-sql> option is specified in the command line.
1370    The trace level is specified using the C<-trace> command-line option. For example,
1371    the following command line for C<TransactFeatures> turns on SQL tracing and runs
1372    all tracing at level 3.
1373    
1374        TransactFeatures -trace=3 -sql register ../xacts IDs.tbl
1375    
1376    Standard tracing is output to the standard output and echoed to the file
1377    C<trace>I<$$>C<.log> in the FIG temporary directory, where I<$$> is the
1378    process ID. You can also specify the C<user> parameter to put a user ID
1379    instead of a process ID in the trace file name. So, for example
1380    
1381    The default trace level is 2. To get all messages, specify a trace level of 4.
1382    For a genome-by-genome update, use 3.
1383    
1384        TransactFeatures -trace=3 -sql -user=Bruce register ../xacts IDs.tbl
1385    
1386    would send the trace output to C<traceBruce.log> in the temporary directory.
1387    
1388    The I<options> parameter is a reference to a hash containing the command-line
1389    options, their default values, and an explanation of what they mean. Command-line
1390    options may be in the form of switches or keywords. In the case of a switch, the
1391    option value is 1 if it is specified and 0 if it is not specified. In the case
1392    of a keyword, the value is separated from the option name by an equal sign. You
1393    can see this last in the command-line example above.
1394    
1395    You can specify a different default trace level by setting C<$options->{trace}>
1396    prior to calling this method.
1397    
1398    An example at this point would help. Consider, for example, the command-line utility
1399    C<TransactFeatures>. It accepts a list of positional parameters plus the options
1400    C<safe>, C<noAlias>, C<start>, and C<tblFiles>. To start up this command, we execute
1401    the following code.
1402    
1403        my ($options, @parameters) = Tracer::StandardSetup(["DocUtils"],
1404                            { safe => [0, "use database transactions"],
1405                              noAlias => [0, "do not expect aliases in CHANGE transactions"],
1406                              start => [' ', "start with this genome"],
1407                              tblFiles => [0, "output TBL files containing the corrected IDs"] },
1408                            "<command> <transactionDirectory> <IDfile>",
1409                          @ARGV);
1410    
1411    
1412    The call to C<ParseCommand> specifies the default values for the options and
1413    stores the actual options in a hash that is returned as C<$options>. The
1414    positional parameters are returned in C<@parameters>.
1415    
1416    The following is a sample command line for C<TransactFeatures>.
1417    
1418        TransactFeatures -trace=2 -noAlias register ../xacts IDs.tbl
1419    
1420    Single and double hyphens are equivalent. So, you could also code the
1421    above command as
1422    
1423        TransactFeatures --trace=2 --noAlias register ../xacts IDs.tbl
1424    
1425    In this case, C<register>, C<../xacts>, and C<IDs.tbl> are the positional
1426    parameters, and would find themselves in I<@parameters> after executing the
1427    above code fragment. The tracing would be set to level 2, and the categories
1428    would be C<Tracer>, and <DocUtils>. C<Tracer> is standard,
1429    and C<DocUtils> was included because it came in within the first parameter
1430    to this method. The I<$options> hash would be
1431    
1432        { trace => 2, sql => 0, safe => 0,
1433          noAlias => 1, start => ' ', tblFiles => 0 }
1434    
1435    Use of C<StandardSetup> in this way provides a simple way of performing
1436    standard tracing setup and command-line parsing. Note that the caller is
1437    not even aware of the command-line switches C<-trace> and C<-sql>, which
1438    are used by this method to control the tracing. If additional tracing features
1439    need to be added in the future, they can be processed by this method without
1440    upsetting the command-line utilities.
1441    
1442    If the C<background> option is specified on the command line, then the
1443    standard and error outputs will be directed to files in the temporary
1444    directory, using the same suffix as the trace file. So, if the command
1445    line specified
1446    
1447        -user=Bruce -background
1448    
1449    then the trace output would go to C<traceBruce.log>, the standard output to
1450    C<outBruce.log>, and the error output to C<errBruce.log>. This is designed to
1451    simplify starting a command in the background.
1452    
1453    The user name is also used as the tracing key for L</Emergency Tracing>.
1454    Specifying a value of C<E> for the trace level causes emergency tracing to
1455    be used instead of custom tracing. If the user name is not specified,
1456    the tracing key is taken from the C<Tracing> environment variable. If there
1457    is no value for that variable, the tracing key will be computed from the PID.
1458    
1459    Finally, if the special option C<-help> is specified, the option
1460    names will be traced at level 0 and the program will exit without processing.
1461    This provides a limited help capability. For example, if the user enters
1462    
1463        TransactFeatures -help
1464    
1465    he would see the following output.
1466    
1467        TransactFeatures [options] <command> <transactionDirectory> <IDfile>
1468            -trace    tracing level (default E)
1469            -sql      trace SQL commands
1470            -safe     use database transactions
1471            -noAlias  do not expect aliases in CHANGE transactions
1472            -start    start with this genome
1473            -tblFiles output TBL files containing the corrected IDs
1474    
1475    The caller has the option of modifying the tracing scheme by placing a value
1476    for C<trace> in the incoming options hash. The default value can be overridden,
1477    or the tracing to the standard output can be turned off by suffixing a minus
1478    sign to the trace level. So, for example,
1479    
1480        { trace => [0, "tracing level (default 0)"],
1481           ...
1482    
1483    would set the default trace level to 0 instead of E, while
1484    
1485        { trace => ["2-", "tracing level (default 2)"],
1486           ...
1487    
1488    would set the default to 2, but trace only to the log file, not to the
1489    standard output.
1490    
1491    The parameters to this method are as follows.
1492    
1493    =over 4
1494    
1495    =item categories
1496    
1497    Reference to a list of tracing category names. These should be names of
1498    packages whose internal workings will need to be debugged to get the
1499    command working.
1500    
1501    =item options
1502    
1503    Reference to a hash containing the legal options for the current command mapped
1504    to their default values and descriptions. The user can override the defaults
1505    by specifying the options as command-line switches prefixed by a hyphen.
1506    Tracing-related options may be added to this hash. If the C<-h> option is
1507    specified on the command line, the option descriptions will be used to
1508    explain the options. To turn off tracing to the standard output, add a
1509    minus sign to the value for C<trace> (see above).
1510    
1511    =item parmHelp
1512    
1513    A string that vaguely describes the positional parameters. This is used
1514    if the user specifies the C<-h> option.
1515    
1516    =item argv
1517    
1518    List of command line parameters, including the option switches, which must
1519    precede the positional parameters and be prefixed by a hyphen.
1520    
1521    =item RETURN
1522    
1523    Returns a list. The first element of the list is the reference to a hash that
1524    maps the command-line option switches to their values. These will either be the
1525    default values or overrides specified on the command line. The remaining
1526    elements of the list are the position parameters, in order.
1527    
1528    =back
1529    
1530    =cut
1531    
1532    sub StandardSetup {
1533        # Get the parameters.
1534        my ($categories, $options, $parmHelp, @argv) = @_;
1535        # Get the default tracing key.
1536        my $tkey = EmergencyKey();
1537        # Add the tracing options.
1538        if (! exists $options->{trace}) {
1539            $options->{trace} = ['2', "tracing level (E for emergency tracing)"];
1540        }
1541        $options->{sql} = [0, "turn on SQL tracing"];
1542        $options->{help} = [0, "display command-line options"];
1543        $options->{user} = [$tkey, "tracing key"];
1544        $options->{background} = [0, "spool standard and error output"];
1545        # Create a parsing hash from the options hash. The parsing hash
1546        # contains the default values rather than the default value
1547        # and the description. While we're at it, we'll memorize the
1548        # length of the longest option name.
1549        my $longestName = 0;
1550        my %parseOptions = ();
1551        for my $key (keys %{$options}) {
1552            if (length $key > $longestName) {
1553                $longestName = length $key;
1554            }
1555            $parseOptions{$key} = $options->{$key}->[0];
1556        }
1557        # Parse the command line.
1558        my ($retOptions, @retParameters) = ParseCommand(\%parseOptions, @argv);
1559        # Get the logfile suffix.
1560        my $suffix = $retOptions->{user};
1561        # Check for background mode.
1562        if ($retOptions->{background}) {
1563            my $outFileName = "$FIG_Config::temp/out$suffix.log";
1564            my $errFileName = "$FIG_Config::temp/err$suffix.log";
1565            open STDOUT, ">$outFileName";
1566            open STDERR, ">$errFileName";
1567            # Check for phone support. If we have phone support and a phone number,
1568            # we want to turn it on.
1569            if ($ENV{PHONE} && defined($FIG_Config::phone)) {
1570                $retOptions->{phone} = $ENV{PHONE};
1571            }
1572        }
1573        # Now we want to set up tracing. First, we need to know if the user
1574        # wants emergency tracing.
1575        if ($retOptions->{trace} eq 'E') {
1576            ETracing($retOptions->{user});
1577        } else {
1578            # Here the tracing is controlled from the command line.
1579            my @cats = @{$categories};
1580            if ($retOptions->{sql}) {
1581                push @cats, "SQL";
1582            }
1583            # Add the default categories.
1584            push @cats, "Tracer";
1585            # Next, we create the category string by joining the categories.
1586            my $cats = join(" ", @cats);
1587            # Check to determine whether or not the caller wants to turn off tracing
1588            # to the standard output.
1589            my $traceLevel = $retOptions->{trace};
1590            my $textOKFlag = 1;
1591            if ($traceLevel =~ /^(.)-/) {
1592                $traceLevel = $1;
1593                $textOKFlag = 0;
1594            }
1595            # Now we set up the trace mode.
1596            my $traceMode;
1597            # Verify that we can open a file in the FIG temporary directory.
1598            my $traceFileName = "$FIG_Config::temp/trace$suffix.log";
1599            if (open TESTTRACE, ">$traceFileName") {
1600                # Here we can trace to a file.
1601                $traceMode = ">$traceFileName";
1602                if ($textOKFlag) {
1603                    # Echo to standard output if the text-OK flag is set.
1604                    $traceMode = "+$traceMode";
1605                }
1606                # Close the test file.
1607                close TESTTRACE;
1608            } else {
1609                # Here we can't trace to a file. Complain about this.
1610                warn "Could not open trace file $traceFileName: $!\n";
1611                # We trace to the standard output if it's
1612                # okay, and the error log otherwise.
1613                if ($textOKFlag) {
1614                    $traceMode = "TEXT";
1615                } else {
1616                    $traceMode = "WARN";
1617                }
1618            }
1619            # Now set up the tracing.
1620            TSetup("$traceLevel $cats", $traceMode);
1621        }
1622        # Check for the "help" option. If it is specified, dump the command-line
1623        # options and exit the program.
1624        if ($retOptions->{help}) {
1625            $0 =~ m#[/\\](\w+)(\.pl)?$#i;
1626            print "$1 [options] $parmHelp\n";
1627            for my $key (sort keys %{$options}) {
1628                my $name = Pad($key, $longestName, 0, ' ');
1629                my $desc = $options->{$key}->[1];
1630                if ($options->{$key}->[0]) {
1631                    $desc .= " (default " . $options->{$key}->[0] . ")";
1632                }
1633                print "  $name $desc\n";
1634  }  }
1635            exit(0);
1636  =head3 LogErrors      }
1637        # Trace the options, if applicable.
1638  C<< Tracer::LogErrors($fileName); >>      if (T(3)) {
1639            my @parms = grep { $retOptions->{$_} } keys %{$retOptions};
1640  Route the standard error output to a log file.          Trace("Selected options: " . join(", ", sort @parms) . ".");
1641        }
1642  =over 4      # Return the parsed parameters.
1643        return ($retOptions, @retParameters);
 =item fileName  
   
 Name of the file to receive the error output.  
   
 =back  
   
 =cut  
   
 sub LogErrors {  
     # Get the file name.  
     my ($fileName) = @_;  
     # Open the file as the standard error output.  
     open STDERR, '>', $fileName;  
1644  }  }
1645    
1646  =head3 ReadOptions  =head3 ReadOptions
1647    
1648  C<< my %options = Tracer::ReadOptions($fileName); >>      my %options = Tracer::ReadOptions($fileName);
1649    
1650  Read a set of options from a file. Each option is encoded in a line of text that has the  Read a set of options from a file. Each option is encoded in a line of text that has the
1651  format  format
# Line 853  Line 1706 
1706    
1707  =head3 GetOptions  =head3 GetOptions
1708    
1709  C<< Tracer::GetOptions(\%defaults, \%options); >>      Tracer::GetOptions(\%defaults, \%options);
1710    
1711  Merge a specified set of options into a table of defaults. This method takes two hash references  Merge a specified set of options into a table of defaults. This method takes two hash references
1712  as input and uses the data from the second to update the first. If the second does not exist,  as input and uses the data from the second to update the first. If the second does not exist,
# Line 862  Line 1715 
1715    
1716  Consider the following example.  Consider the following example.
1717    
1718  C<< my $optionTable = GetOptions({ dbType => 'mySQL', trace => 0 }, $options); >>      my $optionTable = GetOptions({ dbType => 'mySQL', trace => 0 }, $options);
1719    
1720  In this example, the variable B<$options> is expected to contain at most two options-- B<dbType> and  In this example, the variable B<$options> is expected to contain at most two options-- B<dbType> and
1721  B<trace>. The default database type is C<mySQL> and the default trace level is C<0>. If the value of  B<trace>. The default database type is C<mySQL> and the default trace level is C<0>. If the value of
# Line 870  Line 1723 
1723  the trace level will remain at 0. If B<$options> is undefined, then the database type and trace level  the trace level will remain at 0. If B<$options> is undefined, then the database type and trace level
1724  will remain C<mySQL> and C<0>. If, on the other hand, B<$options> is defined as  will remain C<mySQL> and C<0>. If, on the other hand, B<$options> is defined as
1725    
1726  C<< {databaseType => 'Oracle'} >>      {databaseType => 'Oracle'}
1727    
1728  an error will occur because the B<databaseType> option does not exist.  an error will occur because the B<databaseType> option does not exist.
1729    
# Line 914  Line 1767 
1767    
1768  =head3 MergeOptions  =head3 MergeOptions
1769    
1770  C<< Tracer::MergeOptions(\%table, \%defaults); >>      Tracer::MergeOptions(\%table, \%defaults);
1771    
1772  Merge default values into a hash table. This method looks at the key-value pairs in the  Merge default values into a hash table. This method looks at the key-value pairs in the
1773  second (default) hash, and if a matching key is not found in the first hash, the default  second (default) hash, and if a matching key is not found in the first hash, the default
# Line 946  Line 1799 
1799      }      }
1800  }  }
1801    
1802  =head3 Trace  =head3 ParseCommand
1803    
1804        my ($options, @arguments) = Tracer::ParseCommand(\%optionTable, @inputList);
1805    
1806    Parse a command line consisting of a list of parameters. The initial parameters may be option
1807    specifiers of the form C<->I<option> or C<->I<option>C<=>I<value>. The options are stripped
1808    off and merged into a table of default options. The remainder of the command line is
1809    returned as a list of positional arguments. For example, consider the following invocation.
1810    
1811        my ($options, @arguments) = ParseCommand({ errors => 0, logFile => 'trace.log'}, @words);
1812    
1813    In this case, the list @words will be treated as a command line and there are two options available,
1814    B<errors> and B<logFile>. If @words has the following format
1815    
1816        -logFile=error.log apple orange rutabaga
1817    
1818    then at the end of the invocation, C<$options> will be
1819    
1820        { errors => 0, logFile => 'error.log' }
1821    
1822    and C<@arguments> will contain
1823    
1824        apple orange rutabaga
1825    
1826    The parser allows for some escape sequences. See L</UnEscape> for a description. There is no
1827    support for quote characters. Options can be specified with single or double hyphens.
1828    
1829    =over 4
1830    
1831    =item optionTable
1832    
1833    Table of default options.
1834    
1835    =item inputList
1836    
1837    List of words on the command line.
1838    
1839    =item RETURN
1840    
1841    Returns a reference to the option table and a list of the positional arguments.
1842    
1843    =back
1844    
1845    =cut
1846    
1847    sub ParseCommand {
1848        # Get the parameters.
1849        my ($optionTable, @inputList) = @_;
1850        # Process any options in the input list.
1851        my %overrides = ();
1852        while ((@inputList > 0) && ($inputList[0] =~ /^--?/)) {
1853            # Get the current option.
1854            my $arg = shift @inputList;
1855            # Pull out the option name.
1856            $arg =~ /^--?([^=]*)/g;
1857            my $name = $1;
1858            # Check for an option value.
1859            if ($arg =~ /\G=(.*)$/g) {
1860                # Here we have a value for the option.
1861                $overrides{$name} = UnEscape($1);
1862            } else {
1863                # Here there is no value, so we use 1.
1864                $overrides{$name} = 1;
1865            }
1866        }
1867        # Merge the options into the defaults.
1868        GetOptions($optionTable, \%overrides);
1869        # Translate the remaining parameters.
1870        my @retVal = ();
1871        for my $inputParm (@inputList) {
1872            push @retVal, UnEscape($inputParm);
1873        }
1874        # Return the results.
1875        return ($optionTable, @retVal);
1876    }
1877    
1878    
1879    =head2 File Utility Methods
1880    
1881    =head3 GetFile
1882    
1883        my @fileContents = Tracer::GetFile($fileName);
1884    
1885        or
1886    
1887        my $fileContents = Tracer::GetFile($fileName);
1888    
1889    Return the entire contents of a file. In list context, line-ends are removed and
1890    each line is a list element. In scalar context, line-ends are replaced by C<\n>.
1891    
1892    =over 4
1893    
1894    =item fileName
1895    
1896    Name of the file to read.
1897    
1898    =item RETURN
1899    
1900    In a list context, returns the entire file as a list with the line terminators removed.
1901    In a scalar context, returns the entire file as a string. If an error occurs opening
1902    the file, an empty list will be returned.
1903    
1904    =back
1905    
1906    =cut
1907    
1908    sub GetFile {
1909        # Get the parameters.
1910        my ($fileName) = @_;
1911        # Declare the return variable.
1912        my @retVal = ();
1913        # Open the file for input.
1914        my $handle = Open(undef, "<$fileName");
1915        # Read the whole file into the return variable, stripping off any terminator
1916        # characters.
1917        my $lineCount = 0;
1918        while (my $line = <$handle>) {
1919            $lineCount++;
1920            $line = Strip($line);
1921            push @retVal, $line;
1922        }
1923        # Close it.
1924        close $handle;
1925        my $actualLines = @retVal;
1926        Trace("$actualLines lines read from file $fileName.") if T(File => 2);
1927        # Return the file's contents in the desired format.
1928        if (wantarray) {
1929            return @retVal;
1930        } else {
1931            return join "\n", @retVal;
1932        }
1933    }
1934    
1935    =head3 PutFile
1936    
1937        Tracer::PutFile($fileName, \@lines);
1938    
1939    Write out a file from a list of lines of text.
1940    
1941    =over 4
1942    
1943    =item fileName
1944    
1945    Name of the output file.
1946    
1947    =item lines
1948    
1949    Reference to a list of text lines. The lines will be written to the file in order, with trailing
1950    new-line characters. Alternatively, may be a string, in which case the string will be written without
1951    modification.
1952    
1953    =back
1954    
1955    =cut
1956    
1957    sub PutFile {
1958        # Get the parameters.
1959        my ($fileName, $lines) = @_;
1960        # Open the output file.
1961        my $handle = Open(undef, ">$fileName");
1962        # Count the lines written.
1963        if (ref $lines ne 'ARRAY') {
1964            # Here we have a scalar, so we write it raw.
1965            print $handle $lines;
1966            Trace("Scalar put to file $fileName.") if T(File => 3);
1967        } else {
1968            # Write the lines one at a time.
1969            my $count = 0;
1970            for my $line (@{$lines}) {
1971                print $handle "$line\n";
1972                $count++;
1973            }
1974            Trace("$count lines put to file $fileName.") if T(File => 3);
1975        }
1976        # Close the output file.
1977        close $handle;
1978    }
1979    
1980    =head3 ParseRecord
1981    
1982        my @fields = Tracer::ParseRecord($line);
1983    
1984    Parse a tab-delimited data line. The data line is split into field values. Embedded tab
1985    and new-line characters in the data line must be represented as C<\t> and C<\n>, respectively.
1986    These will automatically be converted.
1987    
1988    =over 4
1989    
1990    =item line
1991    
1992    Line of data containing the tab-delimited fields.
1993    
1994    =item RETURN
1995    
1996    Returns a list of the fields found in the data line.
1997    
1998    =back
1999    
2000    =cut
2001    
2002    sub ParseRecord {
2003        # Get the parameter.
2004        my ($line) = @_;
2005        # Remove the trailing new-line, if any.
2006        chomp $line;
2007        # Split the line read into pieces using the tab character.
2008        my @retVal = split /\t/, $line;
2009        # Trim and fix the escapes in each piece.
2010        for my $value (@retVal) {
2011            # Trim leading whitespace.
2012            $value =~ s/^\s+//;
2013            # Trim trailing whitespace.
2014            $value =~ s/\s+$//;
2015            # Delete the carriage returns.
2016            $value =~ s/\r//g;
2017            # Convert the escapes into their real values.
2018            $value =~ s/\\t/"\t"/ge;
2019            $value =~ s/\\n/"\n"/ge;
2020        }
2021        # Return the result.
2022        return @retVal;
2023    }
2024    
2025    =head3 Merge
2026    
2027        my @mergedList = Tracer::Merge(@inputList);
2028    
2029    Sort a list of strings and remove duplicates.
2030    
2031    =over 4
2032    
2033    =item inputList
2034    
2035    List of scalars to sort and merge.
2036    
2037    =item RETURN
2038    
2039    Returns a list containing the same elements sorted in ascending order with duplicates
2040    removed.
2041    
2042    =back
2043    
2044    =cut
2045    
2046    sub Merge {
2047        # Get the input list in sort order.
2048        my @inputList = sort @_;
2049        # Only proceed if the list has at least two elements.
2050        if (@inputList > 1) {
2051            # Now we want to move through the list splicing out duplicates.
2052            my $i = 0;
2053            while ($i < @inputList) {
2054                # Get the current entry.
2055                my $thisEntry = $inputList[$i];
2056                # Find out how many elements duplicate the current entry.
2057                my $j = $i + 1;
2058                my $dup1 = $i + 1;
2059                while ($j < @inputList && $inputList[$j] eq $thisEntry) { $j++; };
2060                # If the number is nonzero, splice out the duplicates found.
2061                if ($j > $dup1) {
2062                    splice @inputList, $dup1, $j - $dup1;
2063                }
2064                # Now the element at position $dup1 is different from the element before it
2065                # at position $i. We push $i forward one position and start again.
2066                $i++;
2067            }
2068        }
2069        # Return the merged list.
2070        return @inputList;
2071    }
2072    
2073    =head3 Open
2074    
2075  C<< Trace($message); >>      my $handle = Open($fileHandle, $fileSpec, $message);
2076    
2077  Write a trace message to the target location specified in L</TSetup>. If there has not been  Open a file.
 any prior call to B<TSetup>.  
2078    
2079  =over 4  The I<$fileSpec> is essentially the second argument of the PERL C<open>
2080    function. The mode is specified using Unix-like shell information. So, for
2081    example,
2082    
2083  =item message      Open(\*LOGFILE, '>>/usr/spool/news/twitlog', "Could not open twit log.");
2084    
2085  Message to write.  would open for output appended to the specified file, and
2086    
2087  =back      Open(\*DATASTREAM, "| sort -u >$outputFile", "Could not open $outputFile.");
2088    
2089  =cut  would open a pipe that sorts the records written and removes duplicates. Note
2090    the use of file handle syntax in the Open call. To use anonymous file handles,
2091    code as follows.
2092    
2093  sub Trace {      my $logFile = Open(undef, '>>/usr/spool/news/twitlog', "Could not open twit log.");
     # Get the parameters.  
     my ($message) = @_;  
     # Get the timestamp.  
     my $timeStamp = Now();  
     # Format the message. Note we strip off any line terminators at the end.  
     my $formatted = "$timeStamp <$LastCategory>: " . Strip($message);  
     # Process according to the destination.  
     if ($Destination eq "TEXT") {  
         # Write the message to the standard output.  
         print "$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";  
         }  
     }  
 }  
2094    
2095  =head3 T  The I<$message> parameter is used if the open fails. If it is set to C<0>, then
2096    the open returns TRUE if successful and FALSE if an error occurred. Otherwise, a
2097    failed open will throw an exception and the third parameter will be used to construct
2098    an error message. If the parameter is omitted, a standard message is constructed
2099    using the file spec.
2100    
2101  C<< my $switch = T($category, $traceLevel); >>      Could not open "/usr/spool/news/twitlog"
2102    
2103      or  Note that the mode characters are automatically cleaned from the file name.
2104    The actual error message from the file system will be captured and appended to the
2105    message in any case.
2106    
2107  C<< my $switch = T($traceLevel); >>      Could not open "/usr/spool/news/twitlog": file not found.
2108    
2109  Return TRUE if the trace level is at or above a specified value and the specified category  In some versions of PERL the only error message we get is a number, which
2110  is active, else FALSE. If no category is specified, the caller's package name is used.  corresponds to the C++ C<errno> value.
2111    
2112        Could not open "/usr/spool/news/twitlog": 6.
2113    
2114  =over 4  =over 4
2115    
2116  =item category  =item fileHandle
2117    
2118  Category to which the message belongs. If not specified, the caller's package name is  File handle. If this parameter is C<undef>, a file handle will be generated
2119  used.  and returned as the value of this method.
2120    
2121  =item traceLevel  =item fileSpec
2122    
2123  Relevant tracing level.  File name and mode, as per the PERL C<open> function.
2124    
2125    =item message (optional)
2126    
2127    Error message to use if the open fails. If omitted, a standard error message
2128    will be generated. In either case, the error information from the file system
2129    is appended to the message. To specify a conditional open that does not throw
2130    an error if it fails, use C<0>.
2131    
2132  =item RETURN  =item RETURN
2133    
2134  TRUE if a message at the specified trace level would appear in the trace, else FALSE.  Returns the name of the file handle assigned to the file, or C<undef> if the
2135    open failed.
2136    
2137  =back  =back
2138    
2139  =cut  =cut
2140    
2141  sub T {  sub Open {
     # Declare the return variable.  
     my $retVal = 0;  
     # Only proceed if tracing is turned on.  
     if ($Destination ne "NONE") {  
2142          # Get the parameters.          # Get the parameters.
2143          my ($category, $traceLevel) = @_;      my ($fileHandle, $fileSpec, $message) = @_;
2144          if (!defined $traceLevel) {      # Attempt to open the file.
2145              # Here we have no category, so we need to get the calling package.      my $rv = open $fileHandle, $fileSpec;
2146              # The calling package is normally the first parameter. If it is      # If the open failed, generate an error message.
2147              # omitted, the first parameter will be the tracelevel. So, the      if (! $rv) {
2148              # first thing we do is shift the so-called category into the          # Save the system error message.
2149              # $traceLevel variable where it belongs.          my $sysMessage = $!;
2150              $traceLevel = $category;          # See if we need a default message.
2151              my ($package, $fileName, $line) = caller;          if (!$message) {
2152              # If there is no calling package, we default to "main".              # Clean any obvious mode characters and leading spaces from the
2153              if (!$package) {              # filename.
2154                  $category = "main";              my ($fileName) = FindNamePart($fileSpec);
2155              } else {              $message = "Could not open \"$fileName\"";
                 $category = $package;  
             }  
         }  
         # 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.");  
2156          }          }
2157          $retVal = ($traceLevel <= $TraceLevel && ($AllTrace || exists $Categories{$category}));          # Terminate with an error using the supplied message and the
2158            # error message from the file system.
2159            Confess("$message: $!");
2160      }      }
2161      # Return the computed result.      # Return the file handle.
2162      return $retVal;      return $fileHandle;
2163  }  }
2164    
2165  =head3 ParseCommand  =head3 FindNamePart
   
 C<< my ($options, @arguments) = Tracer::ParseCommand(\%optionTable, @inputList); >>  
   
 Parse a command line consisting of a list of parameters. The initial parameters may be option  
 specifiers of the form C<->I<option> or C<->I<option>C<=>I<value>. The options are stripped  
 off and merged into a table of default options. The remainder of the command line is  
 returned as a list of positional arguments. For example, consider the following invocation.  
   
 C<< my ($options, @arguments) = ParseCommand({ errors => 0, logFile => 'trace.log'}, @words); >>  
   
 In this case, the list @words will be treated as a command line. There are two options available,  
 B<errors> and B<logFile>. If @words has the following format  
   
 C<< -logFile=error.log apple orange rutabaga >>  
2166    
2167  then at the end of the invocation, C<$options> will be      my ($fileName, $start, $len) = Tracer::FindNamePart($fileSpec);
2168    
2169  C<< { errors => 0, logFile => 'error.log' } >>  Extract the portion of a file specification that contains the file name.
2170    
2171  and C<@arguments> will contain  A file specification is the string passed to an C<open> call. It specifies the file
2172    mode and name. In a truly complex situation, it can specify a pipe sequence. This
2173    method assumes that the file name is whatever follows the first angle bracket
2174    sequence.  So, for example, in the following strings the file name is
2175    C</usr/fig/myfile.txt>.
2176    
2177  C<< apple orange rutabaga >>      >>/usr/fig/myfile.txt
2178        </usr/fig/myfile.txt
2179        | sort -u > /usr/fig/myfile.txt
2180    
2181  The parser allows for some escape sequences. See L</UnEscape> for a description. There is no  If the method cannot find a file name using its normal methods, it will return the
2182  support for quote characters.  whole incoming string.
2183    
2184  =over 4  =over 4
2185    
2186  =item optionTable  =item fileSpec
   
 Table of default options.  
   
 =item inputList  
2187    
2188  List of words on the command line.  File specification string from which the file name is to be extracted.
2189    
2190  =item RETURN  =item RETURN
2191    
2192  Returns a reference to the option table and a list of the positional arguments.  Returns a three-element list. The first element contains the file name portion of
2193    the specified string, or the whole string if a file name cannot be found via normal
2194    methods. The second element contains the start position of the file name portion and
2195    the third element contains the length.
2196    
2197  =back  =back
2198    
2199  =cut  =cut
2200    #: Return Type $;
2201  sub ParseCommand {  sub FindNamePart {
2202      # Get the parameters.      # Get the parameters.
2203      my ($optionTable, @inputList) = @_;      my ($fileSpec) = @_;
2204      # Process any options in the input list.      # Default to the whole input string.
2205      my %overrides = ();      my ($retVal, $pos, $len) = ($fileSpec, 0, length $fileSpec);
2206      while ((@inputList > 0) && ($inputList[0] =~ /^-/)) {      # Parse out the file name if we can.
2207          # Get the current option.      if ($fileSpec =~ m/(<|>>?)(.+?)(\s*)$/) {
2208          my $arg = shift @inputList;          $retVal = $2;
2209          # Pull out the option name.          $len = length $retVal;
2210          $arg =~ /^-([^=]*)/g;          $pos = (length $fileSpec) - (length $3) - $len;
         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;  
         }  
     }  
     # Merge the options into the defaults.  
     GetOptions($optionTable, \%overrides);  
     # Translate the remaining parameters.  
     my @retVal = ();  
     for my $inputParm (@inputList) {  
         push @retVal, UnEscape($inputParm);  
2211      }      }
2212      # Return the results.      # Return the result.
2213      return ($optionTable, @retVal);      return ($retVal, $pos, $len);
2214  }  }
2215    
2216  =head3 Escape  =head3 OpenDir
2217    
2218  C<< my $codedString = Tracer::Escape($realString); >>      my @files = OpenDir($dirName, $filtered, $flag);
2219    
2220  Escape a string for use in a command length. Tabs will be replaced by C<\t>, new-lines  Open a directory and return all the file names. This function essentially performs
2221  replaced by C<\n>, carriage returns will be deleted, and backslashes will be doubled. The  the functions of an C<opendir> and C<readdir>. If the I<$filtered> parameter is
2222  result is to reverse the effect of L</UnEscape>.  set to TRUE, all filenames beginning with a period (C<.>), dollar sign (C<$>),
2223    or pound sign (C<#>) and all filenames ending with a tilde C<~>) will be
2224    filtered out of the return list. If the directory does not open and I<$flag> is not
2225    set, an exception is thrown. So, for example,
2226    
2227        my @files = OpenDir("/Volumes/fig/contigs", 1);
2228    
2229    is effectively the same as
2230    
2231        opendir(TMP, "/Volumes/fig/contigs") || Confess("Could not open /Volumes/fig/contigs.");
2232        my @files = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir(TMP);
2233    
2234    Similarly, the following code
2235    
2236        my @files = grep { $_ =~ /^\d/ } OpenDir("/Volumes/fig/orgs", 0, 1);
2237    
2238    Returns the names of all files in C</Volumes/fig/orgs> that begin with digits and
2239    automatically returns an empty list if the directory fails to open.
2240    
2241  =over 4  =over 4
2242    
2243  =item realString  =item dirName
2244    
2245  String to escape.  Name of the directory to open.
2246    
2247  =item RETURN  =item filtered
2248    
2249  Escaped equivalent of the real string.  TRUE if files whose names begin with a period (C<.>) should be automatically removed
2250    from the list, else FALSE.
2251    
2252    =item flag
2253    
2254    TRUE if a failure to open is okay, else FALSE
2255    
2256  =back  =back
2257    
2258  =cut  =cut
2259    #: Return Type @;
2260  sub Escape {  sub OpenDir {
2261      # Get the parameter.      # Get the parameters.
2262      my ($realString) = @_;      my ($dirName, $filtered, $flag) = @_;
2263      # Initialize the return variable.      # Declare the return variable.
2264      my $retVal = "";      my @retVal = ();
2265      # Loop through the parameter string, looking for sequences to escape.      # Open the directory.
2266      while (length $realString > 0) {      if (opendir(my $dirHandle, $dirName)) {
2267          # Look for the first sequence to escape.          # The directory opened successfully. Get the appropriate list according to the
2268          if ($realString =~ /^(.*?)([\n\t\r\\])/) {          # strictures of the filter parameter.
2269              # Here we found it. The text preceding the sequence is in $1. The sequence          if ($filtered) {
2270              # itself is in $2. First, move the clear text to the return variable.              @retVal = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir $dirHandle;
             $retVal .= $1;  
             # Strip the processed section off the real string.  
             $realString = substr $realString, (length $2) + (length $1);  
             # Get the matched character.  
             my $char = $2;  
             # If we have a CR, we are done.  
             if ($char ne "\r") {  
                 # It's not a CR, so encode the escape sequence.  
                 $char =~ tr/\t\n/tn/;  
                 $retVal .= "\\" . $char;  
             }  
2271          } else {          } else {
2272              # Here there are no more escape sequences. The rest of the string is              @retVal = readdir $dirHandle;
             # transferred unmodified.  
             $retVal .= $realString;  
             $realString = "";  
2273          }          }
2274        } elsif (! $flag) {
2275            # Here the directory would not open and it's considered an error.
2276            Confess("Could not open directory $dirName.");
2277      }      }
2278      # Return the result.      # Return the result.
2279      return $retVal;      return @retVal;
2280  }  }
2281    
 =head3 UnEscape  
2282    
2283  C<< my $realString = Tracer::UnEscape($codedString); >>  =head3 Insure
2284    
2285        Insure($dirName, $chmod);
2286    
2287  Replace escape sequences with their actual equivalents. C<\t> will be replaced by  Insure a directory is present.
 a tab, C<\n> by a new-line character, and C<\\> by a backslash. C<\r> codes will  
 be deleted.  
2288    
2289  =over 4  =over 4
2290    
2291  =item codedString  =item dirName
2292    
2293  String to un-escape.  Name of the directory to check. If it does not exist, it will be created.
2294    
2295  =item RETURN  =item chmod (optional)
2296    
2297  Returns a copy of the original string with the escape sequences converted to their actual  Security privileges to be given to the directory if it is created.
 values.  
2298    
2299  =back  =back
2300    
2301  =cut  =cut
2302    
2303  sub UnEscape {  sub Insure {
2304      # Get the parameter.      my ($dirName, $chmod) = @_;
2305      my ($codedString) = @_;      if (! -d $dirName) {
2306      # Initialize the return variable.          Trace("Creating $dirName directory.") if T(2);
2307      my $retVal = "";          eval {
2308      # Only proceed if the incoming string is nonempty.              mkpath $dirName;
2309      if (defined $codedString) {              # If we have permissions specified, set them here.
2310          # Loop through the parameter string, looking for escape sequences. We can't do              if (defined($chmod)) {
2311          # translating because it causes problems with the escaped slash. ("\\t" becomes                  chmod $chmod, $dirName;
         # "\<tab>" no matter what we do.)  
         while (length $codedString > 0) {  
             # Look for the first escape sequence.  
             if ($codedString =~ /^(.*?)\\(\\|n|t|r)/) {  
                 # Here we found it. The text preceding the sequence is in $1. The sequence  
                 # itself is in $2. First, move the clear text to the return variable.  
                 $retVal .= $1;  
                 $codedString = substr $codedString, (2 + length $1);  
                 # Get the escape value.  
                 my $char = $2;  
                 # If we have a "\r", we are done.  
                 if ($char ne 'r') {  
                     # Here it's not an 'r', so we convert it.  
                     $char =~ tr/\\tn/\\\t\n/;  
                     $retVal .= $char;  
                 }  
             } else {  
                 # Here there are no more escape sequences. The rest of the string is  
                 # transferred unmodified.  
                 $retVal .= $codedString;  
                 $codedString = "";  
2312              }              }
2313            };
2314            if ($@) {
2315                Confess("Error creating $dirName: $@");
2316          }          }
2317      }      }
     # Return the result.  
     return $retVal;  
2318  }  }
2319    
2320  =head3 ParseRecord  =head3 ChDir
2321    
2322  C<< my @fields = Tracer::ParseRecord($line); >>      ChDir($dirName);
2323    
2324  Parse a tab-delimited data line. The data line is split into field values. Embedded tab  Change to the specified directory.
 and new-line characters in the data line must be represented as C<\t> and C<\n>, respectively.  
 These will automatically be converted.  
2325    
2326  =over 4  =over 4
2327    
2328  =item line  =item dirName
   
 Line of data containing the tab-delimited fields.  
   
 =item RETURN  
2329    
2330  Returns a list of the fields found in the data line.  Name of the directory to which we want to change.
2331    
2332  =back  =back
2333    
2334  =cut  =cut
2335    
2336  sub ParseRecord {  sub ChDir {
2337      # Get the parameter.      my ($dirName) = @_;
2338      my ($line) = @_;      if (! -d $dirName) {
2339      # Remove the trailing new-line, if any.          Confess("Cannot change to directory $dirName: no such directory.");
2340      chomp $line;      } else {
2341      # Split the line read into pieces using the tab character.          Trace("Changing to directory $dirName.") if T(File => 4);
2342      my @retVal = split /\t/, $line;          my $okFlag = chdir $dirName;
2343      # Trim and fix the escapes in each piece.          if (! $okFlag) {
2344      for my $value (@retVal) {              Confess("Error switching to directory $dirName.");
2345          # 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;  
         $value =~ s/\\n/"\n"/ge;  
2346      }      }
     # Return the result.  
     return @retVal;  
2347  }  }
2348    
2349  =head3 Merge  =head3 SetPermissions
2350    
2351  C<< my @mergedList = Tracer::Merge(@inputList); >>      Tracer::SetPermissions($dirName, $group, $mask, %otherMasks);
2352    
2353  Sort a list of strings and remove duplicates.  Set the permissions for a directory and all the files and folders inside it.
2354    In addition, the group ownership will be changed to the specified value.
2355    
2356    This method is more vulnerable than most to permission and compatability
2357    problems, so it does internal error recovery.
2358    
2359  =over 4  =over 4
2360    
2361  =item inputList  =item dirName
2362    
2363  List of scalars to sort and merge.  Name of the directory to process.
2364    
2365  =item RETURN  =item group
2366    
2367  Returns a list containing the same elements sorted in ascending order with duplicates  Name of the group to be assigned.
2368  removed.  
2369    =item mask
2370    
2371    Permission mask. Bits that are C<1> in this mask will be ORed into the
2372    permission bits of any file or directory that does not already have them
2373    set to 1.
2374    
2375    =item otherMasks
2376    
2377    Map of search patterns to permission masks. If a directory name matches
2378    one of the patterns, that directory and all its members and subdirectories
2379    will be assigned the new pattern. For example, the following would
2380    assign 01664 to most files, but would use 01777 for directories named C<tmp>.
2381    
2382        Tracer::SetPermissions($dirName, 'fig', 01664, '^tmp$' => 01777);
2383    
2384    The list is ordered, so the following would use 0777 for C<tmp1> and
2385    0666 for C<tmp>, C<tmp2>, or C<tmp3>.
2386    
2387        Tracer::SetPermissions($dirName, 'fig', 01664, '^tmp1' => 0777,
2388                                                       '^tmp' => 0666);
2389    
2390    Note that the pattern matches are all case-insensitive, and only directory
2391    names are matched, not file names.
2392    
2393  =back  =back
2394    
2395  =cut  =cut
2396    
2397  sub Merge {  sub SetPermissions {
2398      # Get the input list in sort order.      # Get the parameters.
2399      my @inputList = sort @_;      my ($dirName, $group, $mask, @otherMasks) = @_;
2400      # Only proceed if the list has at least two elements.      # Set up for error recovery.
2401      if (@inputList > 1) {      eval {
2402          # Now we want to move through the list splicing out duplicates.          # Switch to the specified directory.
2403          my $i = 0;          ChDir($dirName);
2404          while ($i < @inputList) {          # Get the group ID.
2405              # Get the current entry.          my $gid = getgrnam($group);
2406              my $thisEntry = $inputList[$i];          # Get the mask for tracing.
2407              # Find out how many elements duplicate the current entry.          my $traceMask = sprintf("%04o", $mask) . "($mask)";
2408              my $j = $i + 1;          Trace("Fixing permissions for directory $dirName using group $group($gid) and mask $traceMask.") if T(File => 2);
2409              my $dup1 = $i + 1;          my $fixCount = 0;
2410              while ($j < @inputList && $inputList[$j] eq $thisEntry) { $j++; };          my $lookCount = 0;
2411              # If the number is nonzero, splice out the duplicates found.          # @dirs will be a stack of directories to be processed.
2412              if ($j > $dup1) {          my @dirs = (getcwd());
2413                  splice @inputList, $dup1, $j - $dup1;          while (scalar(@dirs) > 0) {
2414                # Get the current directory.
2415                my $dir = pop @dirs;
2416                # Check for a match to one of the specified directory names. To do
2417                # that, we need to pull the individual part of the name off of the
2418                # whole path.
2419                my $simpleName = $dir;
2420                if ($dir =~ m!/([^/]+)$!) {
2421                    $simpleName = $1;
2422                }
2423                Trace("Simple directory name for $dir is $simpleName.") if T(File => 4);
2424                # Search for a match.
2425                my $match = 0;
2426                my $i;
2427                for ($i = 0; $i < $#otherMasks && ! $match; $i += 2) {
2428                    my $pattern = $otherMasks[$i];
2429                    if ($simpleName =~ /$pattern/i) {
2430                        $match = 1;
2431                    }
2432                }
2433                # Check for a match. Note we use $i-1 because the loop added 2
2434                # before terminating due to the match.
2435                if ($match && $otherMasks[$i-1] != $mask) {
2436                    # This directory matches one of the incoming patterns, and it's
2437                    # a different mask, so we process it recursively with that mask.
2438                    SetPermissions($dir, $group, $otherMasks[$i-1], @otherMasks);
2439                } else {
2440                    # Here we can process normally. Get all of the non-hidden members.
2441                    my @submems = OpenDir($dir, 1);
2442                    for my $submem (@submems) {
2443                        # Get the full name.
2444                        my $thisMem = "$dir/$submem";
2445                        Trace("Checking member $thisMem.") if T(4);
2446                        $lookCount++;
2447                        if ($lookCount % 1000 == 0) {
2448                            Trace("$lookCount members examined. Current is $thisMem. Mask is $traceMask") if T(File => 3);
2449              }              }
2450              # Now the element at position $dup1 is different from the element before it                      # Fix the group.
2451              # at position $i. We push $i forward one position and start again.                      chown -1, $gid, $thisMem;
2452              $i++;                      # Insure this member is not a symlink.
2453                        if (! -l $thisMem) {
2454                            # Get its info.
2455                            my $fileInfo = stat $thisMem;
2456                            # Only proceed if we got the info. Otherwise, it's a hard link
2457                            # and we want to skip it anyway.
2458                            if ($fileInfo) {
2459                                my $fileMode = $fileInfo->mode;
2460                                if (($fileMode & $mask) != $mask) {
2461                                    # Fix this member.
2462                                    $fileMode |= $mask;
2463                                    chmod $fileMode, $thisMem;
2464                                    $fixCount++;
2465          }          }
2466                                # If it's a subdirectory, stack it.
2467                                if (-d $thisMem) {
2468                                    push @dirs, $thisMem;
2469      }      }
     # Return the merged list.  
     return @inputList;  
2470  }  }
   
 =head3 Percent  
   
 C<< my $percent = Tracer::Percent($number, $base); >>  
   
 Returns the percent of the base represented by the given number. If the base  
 is zero, returns zero.  
   
 =over 4  
   
 =item number  
   
 Percent numerator.  
   
 =item base  
   
 Percent base.  
   
 =item RETURN  
   
 Returns the percentage of the base represented by the numerator.  
   
 =back  
   
 =cut  
   
 sub Percent {  
     # Get the parameters.  
     my ($number, $base) = @_;  
     # Declare the return variable.  
     my $retVal = 0;  
     # Compute the percent.  
     if ($base != 0) {  
         $retVal = $number * 100 / $base;  
2471      }      }
2472      # Return the result.                  }
2473      return $retVal;              }
2474            }
2475            Trace("$lookCount files and directories processed, $fixCount fixed.") if T(File => 2);
2476        };
2477        # Check for an error.
2478        if ($@) {
2479            Confess("SetPermissions error: $@");
2480        }
2481  }  }
2482    
2483  =head3 GetFile  =head3 GetLine
   
 C<< my @fileContents = Tracer::GetFile($fileName); >>  
   
     or  
2484    
2485  C<< my $fileContents = Tracer::GetFile($fileName); >>      my @data = Tracer::GetLine($handle);
2486    
2487  Return the entire contents of a file. In list context, line-ends are removed and  Read a line of data from a tab-delimited file.
 each line is a list element. In scalar context, line-ends are replaced by C<\n>.  
2488    
2489  =over 4  =over 4
2490    
2491  =item fileName  =item handle
2492    
2493  Name of the file to read.  Open file handle from which to read.
2494    
2495  =item RETURN  =item RETURN
2496    
2497  In a list context, returns the entire file as a list with the line terminators removed.  Returns a list of the fields in the record read. The fields are presumed to be
2498  In a scalar context, returns the entire file as a string. If an error occurs opening  tab-delimited. If we are at the end of the file, then an empty list will be
2499  the file, an empty list will be returned.  returned. If an empty line is read, a single list item consisting of a null
2500    string will be returned.
2501    
2502  =back  =back
2503    
2504  =cut  =cut
2505    
2506  sub GetFile {  sub GetLine {
2507      # Get the parameters.      # Get the parameters.
2508      my ($fileName) = @_;      my ($handle) = @_;
2509      # Declare the return variable.      # Declare the return variable.
2510      my @retVal = ();      my @retVal = ();
2511      # Open the file for input.      Trace("File position is " . tell($handle) . ". EOF flag is " . eof($handle) . ".") if T(File => 4);
2512      my $handle = Open(undef, "<$fileName");      # Read from the file.
2513      # Read the whole file into the return variable, stripping off any terminator      my $line = <$handle>;
2514      # characters.      # Only proceed if we found something.
2515      my $lineCount = 0;      if (defined $line) {
2516      while (my $line = <$handle>) {          # Remove the new-line. We are a bit over-cautious here because the file may be coming in via an
2517          $lineCount++;          # upload control and have a nonstandard EOL combination.
2518          $line = Strip($line);          $line =~ s/(\r|\n)+$//;
2519          push @retVal, $line;          # Here we do some fancy tracing to help in debugging complicated EOL marks.
2520            if (T(File => 4)) {
2521                my $escapedLine = $line;
2522                $escapedLine =~ s/\n/\\n/g;
2523                $escapedLine =~ s/\r/\\r/g;
2524                $escapedLine =~ s/\t/\\t/g;
2525                Trace("Line read: -->$escapedLine<--");
2526      }      }
2527      # Close it.          # If the line is empty, return a single empty string; otherwise, parse
2528      close $handle;          # it into fields.
2529      my $actualLines = @retVal;          if ($line eq "") {
2530      # Return the file's contents in the desired format.              push @retVal, "";
     if (wantarray) {  
         return @retVal;  
2531      } else {      } else {
2532          return join "\n", @retVal;              push @retVal, split /\t/,$line;
2533      }      }
2534        } else {
2535            # Trace the reason the read failed.
2536            Trace("End of file: $!") if T(File => 3);
2537        }
2538        # Return the result.
2539        return @retVal;
2540  }  }
2541    
2542  =head3 PutFile  =head3 PutLine
2543    
2544  C<< Tracer::PutFile($fileName, \@lines); >>      Tracer::PutLine($handle, \@fields, $eol);
2545    
2546  Write out a file from a list of lines of text.  Write a line of data to a tab-delimited file. The specified field values will be
2547    output in tab-separated form, with a trailing new-line.
2548    
2549  =over 4  =over 4
2550    
2551  =item fileName  =item handle
2552    
2553  Name of the output file.  Output file handle.
2554    
2555  =item lines  =item fields
2556    
2557  Reference to a list of text lines. The lines will be written to the file in order, with trailing  List of field values.
2558  new-line characters. Alternatively, may be a string, in which case the string will be written without  
2559  modification.  =item eol (optional)
2560    
2561    End-of-line character (default is "\n").
2562    
2563  =back  =back
2564    
2565  =cut  =cut
2566    
2567  sub PutFile {  sub PutLine {
2568      # Get the parameters.      # Get the parameters.
2569      my ($fileName, $lines) = @_;      my ($handle, $fields, $eol) = @_;
2570      # Open the output file.      # Write the data.
2571      my $handle = Open(undef, ">$fileName");      print $handle join("\t", @{$fields}) . ($eol || "\n");
     if (ref $lines ne 'ARRAY') {  
         # Here we have a scalar, so we write it raw.  
         print $handle $lines;  
     } else {  
         # Write the lines one at a time.  
         for my $line (@{$lines}) {  
             print $handle "$line\n";  
         }  
     }  
     # Close the output file.  
     close $handle;  
2572  }  }
2573    
 =head3 QTrace  
2574    
2575  C<< my $data = QTrace($format); >>  =head3 PrintLine
2576    
2577  Return the queued trace data in the specified format.      Tracer::PrintLine($line);
2578    
2579    Print a line of text with a trailing new-line.
2580    
2581  =over 4  =over 4
2582    
2583  =item format  =item line
2584    
2585  C<html> to format the data as an HTML list, C<text> to format it as straight text.  Line of text to print.
2586    
2587  =back  =back
2588    
2589  =cut  =cut
2590    
2591  sub QTrace {  sub PrintLine {
2592      # Get the parameter.      # Get the parameters.
2593      my ($format) = @_;      my ($line) = @_;
2594      # Create the return variable.      # Print the line.
2595      my $retVal = "";      print "$line\n";
     # 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";  
             }  
             $retVal .= "</ul>\n";  
         } elsif ($format =~ m/^TEXT$/i) {  
             # Convert the queue into a list of text lines.  
             $retVal = join("\n", @Queue) . "\n";  
         }  
         # Clear the queue.  
         @Queue = ();  
     }  
     # Return the formatted list.  
     return $retVal;  
2596  }  }
2597    
 =head3 Confess  
2598    
2599  C<< Confess($message); >>  =head2 Other Useful Methods
2600    
2601  Trace the call stack and abort the program with the specified message. When used with  =head3 ParseParm
 the OR operator and the L</Assert> method, B<Confess> can function as a debugging assert.  
 So, for example  
2602    
2603  C<< Assert($recNum >= 0) || Confess("Invalid record number $recNum."); >>      my $listValue = Tracer::ParseParm($string);
2604    
2605  Will abort the program with a stack trace if the value of C<$recNum> is negative.  Convert a parameter into a list reference. If the parameter is undefined,
2606    an undefined value will be returned. Otherwise, it will be parsed as a
2607    comma-separated list of values.
2608    
2609  =over 4  =over 4
2610    
2611  =item message  =item string
2612    
2613  Message to include in the trace.  Incoming string.
2614    
2615    =item RETURN
2616    
2617    Returns a reference to a list of values, or C<undef> if the incoming value
2618    was undefined.
2619    
2620  =back  =back
2621    
2622  =cut  =cut
2623    
2624  sub Confess {  sub ParseParm {
2625      # Get the parameters.      # Get the parameters.
2626      my ($message) = @_;      my ($string) = @_;
2627      # Trace the call stack.      # Declare the return variable.
2628      Cluck($message);      my $retVal;
2629      # Abort the program.      # Check for data.
2630      croak(">>> $message");      if (defined $string) {
2631  }          # We have some, so split it into a list.
2632            $retVal = [ split /\s*,\s*/, $string];
 =head3 Assert  
   
 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  
   
 C<< Assert($recNum >= 0) || Confess("Invalid record number $recNum."); >>  
   
 Will abort the program with a stack trace if the value of C<$recNum> is negative.  
   
 =cut  
 sub Assert {  
     my $retVal = 1;  
     LOOP: for my $condition (@_) {  
         if (! $condition) {  
             $retVal = 0;  
             last LOOP;  
         }  
2633      }      }
2634        # Return the result.
2635      return $retVal;      return $retVal;
2636  }  }
2637    
2638  =head3 Cluck  =head3 Now
   
 C<< Cluck($message); >>  
   
 Trace the call stack. Note that for best results, you should qualify the call with a  
 trace condition. For example,  
   
 C<< Cluck("Starting record parse.") if T(3); >>  
   
 will only trace the stack if the trace level for the package is 3 or more.  
   
 =over 4  
   
 =item message  
2639    
2640  Message to include in the trace.      my $string = Tracer::Now();
2641    
2642  =back  Return a displayable time stamp containing the local time. Whatever format this
2643    method produces must be parseable by L</ParseDate>.
2644    
2645  =cut  =cut
2646    
2647  sub Cluck {  sub Now {
2648      # Get the parameters.      return DisplayTime(time);
     my ($message) = @_;  
     # Trace what's happening.  
     Trace("Stack trace for event: $message");  
     my $confession = longmess($message);  
     # Convert the confession to a series of trace messages. Note we skip any  
     # messages relating to calls into Tracer.  
     for my $line (split /\s*\n/, $confession) {  
         Trace($line) if ($line !~ /Tracer\.pm/);  
     }  
2649  }  }
2650    
2651  =head3 Min  =head3 DisplayTime
2652    
2653  C<< my $min = Min($value1, $value2, ... $valueN); >>      my $string = Tracer::DisplayTime($time);
2654    
2655  Return the minimum argument. The arguments are treated as numbers.  Convert a time value to a displayable time stamp. Whatever format this
2656    method produces must be parseable by L</ParseDate>.
2657    
2658  =over 4  =over 4
2659    
2660  =item $value1, $value2, ... $valueN  =item time
2661    
2662  List of numbers to compare.  Time to display, in seconds since the epoch, or C<undef> if the time is unknown.
2663    
2664  =item RETURN  =item RETURN
2665    
2666  Returns the lowest number in the list.  Returns a displayable time, or C<(n/a)> if the incoming time is undefined.
2667    
2668  =back  =back
2669    
2670  =cut  =cut
2671    
2672  sub Min {  sub DisplayTime {
2673      # Get the parameters. Note that we prime the return value with the first parameter.      my ($time) = @_;
2674      my ($retVal, @values) = @_;      my $retVal = "(n/a)";
2675      # Loop through the remaining parameters, looking for the lowest.      if (defined $time) {
2676      for my $value (@values) {          my ($sec,$min,$hour,$mday,$mon,$year,$wday,$yday,$isdst) = localtime($time);
2677          if ($value < $retVal) {          $retVal = _p2($mon+1) . "/" . _p2($mday) . "/" . ($year + 1900) . " " .
2678              $retVal = $value;                    _p2($hour) . ":" . _p2($min) . ":" . _p2($sec);
         }  
2679      }      }
     # Return the minimum found.  
2680      return $retVal;      return $retVal;
2681  }  }
2682    
2683  =head3 Max  # Pad a number to 2 digits.
2684    sub _p2 {
2685        my ($value) = @_;
2686        $value = "0$value" if ($value < 10);
2687        return $value;
2688    }
2689    
2690  C<< my $max = Max($value1, $value2, ... $valueN); >>  =head3 Escape
2691    
2692  Return the maximum argument. The arguments are treated as numbers.      my $codedString = Tracer::Escape($realString);
2693    
2694    Escape a string for use in a command. Tabs will be replaced by C<\t>, new-lines
2695    replaced by C<\n>, carriage returns will be deleted, and backslashes will be doubled. The
2696    result is to reverse the effect of L</UnEscape>.
2697    
2698  =over 4  =over 4
2699    
2700  =item $value1, $value2, ... $valueN  =item realString
2701    
2702  List of numbers to compare.  String to escape.
2703    
2704  =item RETURN  =item RETURN
2705    
2706  Returns the highest number in the list.  Escaped equivalent of the real string.
2707    
2708  =back  =back
2709    
2710  =cut  =cut
2711    
2712  sub Max {  sub Escape {
2713      # Get the parameters. Note that we prime the return value with the first parameter.      # Get the parameter.
2714      my ($retVal, @values) = @_;      my ($realString) = @_;
2715      # Loop through the remaining parameters, looking for the highest.      # Initialize the return variable.
2716      for my $value (@values) {      my $retVal = "";
2717          if ($value > $retVal) {      # Loop through the parameter string, looking for sequences to escape.
2718              $retVal = $value;      while (length $realString > 0) {
2719            # Look for the first sequence to escape.
2720            if ($realString =~ /^(.*?)([\n\t\r\\])/) {
2721                # Here we found it. The text preceding the sequence is in $1. The sequence
2722                # itself is in $2. First, move the clear text to the return variable.
2723                $retVal .= $1;
2724                # Strip the processed section off the real string.
2725                $realString = substr $realString, (length $2) + (length $1);
2726                # Get the matched character.
2727                my $char = $2;
2728                # If we have a CR, we are done.
2729                if ($char ne "\r") {
2730                    # It's not a CR, so encode the escape sequence.
2731                    $char =~ tr/\t\n/tn/;
2732                    $retVal .= "\\" . $char;
2733                }
2734            } else {
2735                # Here there are no more escape sequences. The rest of the string is
2736                # transferred unmodified.
2737                $retVal .= $realString;
2738                $realString = "";
2739          }          }
2740      }      }
2741      # Return the maximum found.      # Return the result.
2742      return $retVal;      return $retVal;
2743  }  }
2744    
2745  =head3 AddToListMap  =head3 UnEscape
2746    
2747  C<< Tracer::AddToListMap(\%hash, $key, $value1, $value2, ... valueN); >>      my $realString = Tracer::UnEscape($codedString);
2748    
2749  Add a key-value pair to a hash of lists. If no value exists for the key, a singleton list  Replace escape sequences with their actual equivalents. C<\t> will be replaced by
2750  is created for the key. Otherwise, the new value is pushed onto the list.  a tab, C<\n> by a new-line character, and C<\\> by a backslash. C<\r> codes will
2751    be deleted.
2752    
2753  =over 4  =over 4
2754    
2755  =item hash  =item codedString
   
 Reference to the target hash.  
   
 =item key  
2756    
2757  Key for which the value is to be added.  String to un-escape.
2758    
2759  =item value1, value2, ... valueN  =item RETURN
2760    
2761  List of values to add to the key's value list.  Returns a copy of the original string with the escape sequences converted to their actual
2762    values.
2763    
2764  =back  =back
2765    
2766  =cut  =cut
2767    
2768  sub AddToListMap {  sub UnEscape {
2769      # Get the parameters.      # Get the parameter.
2770      my ($hash, $key, @values) = @_;      my ($codedString) = @_;
2771      # Process according to whether or not the key already has a value.      # Initialize the return variable.
2772      if (! exists $hash->{$key}) {      my $retVal = "";
2773          $hash->{$key} = [@values];      # Only proceed if the incoming string is nonempty.
2774        if (defined $codedString) {
2775            # Loop through the parameter string, looking for escape sequences. We can't do
2776            # translating because it causes problems with the escaped slash. ("\\t" becomes
2777            # "\<tab>" no matter what we do.)
2778            while (length $codedString > 0) {
2779                # Look for the first escape sequence.
2780                if ($codedString =~ /^(.*?)\\(\\|n|t|r)/) {
2781                    # Here we found it. The text preceding the sequence is in $1. The sequence
2782                    # itself is in $2. First, move the clear text to the return variable.
2783                    $retVal .= $1;
2784                    $codedString = substr $codedString, (2 + length $1);
2785                    # Get the escape value.
2786                    my $char = $2;
2787                    # If we have a "\r", we are done.
2788                    if ($char ne 'r') {
2789                        # Here it's not an 'r', so we convert it.
2790                        $char =~ tr/\\tn/\\\t\n/;
2791                        $retVal .= $char;
2792                    }
2793      } else {      } else {
2794          push @{$hash->{$key}}, @values;                  # Here there are no more escape sequences. The rest of the string is
2795                    # transferred unmodified.
2796                    $retVal .= $codedString;
2797                    $codedString = "";
2798      }      }
2799  }  }
   
 =head3 DebugMode  
   
 C<< if (Tracer::DebugMode) { ...code... } >>  
   
 Return TRUE if debug mode has been turned on, else output an error  
 page and return FALSE.  
   
 Certain CGI scripts are too dangerous to exist in the production  
 environment. This method provides a simple way to prevent them  
 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.  
   
 =cut  
   
 sub DebugMode {  
     # Declare the return variable.  
     my $retVal = 0;  
     # Check the debug configuration.  
     my $password = CGI::cookie("DebugMode");  
     my $encrypted = Digest::MD5::md5_hex($password);  
     if ($encrypted eq "252dec43280e0c0d6a75ffcec486e61d") {  
         $retVal = 1;  
     } else {  
         # Here debug mode is off, so we generate an error page.  
         my $pageString = PageBuilder::Build("<<Html/ErrorPage.html", {}, "Html");  
         print $pageString;  
2800      }      }
2801      # Return the determination indicator.      # Return the result.
2802      return $retVal;      return $retVal;
2803  }  }
2804    
2805  =head3 Strip  =head3 Percent
2806    
2807  C<< my $string = Tracer::Strip($line); >>      my $percent = Tracer::Percent($number, $base);
2808    
2809  Strip all line terminators off a string. This is necessary when dealing with files  Returns the percent of the base represented by the given number. If the base
2810  that may have been transferred back and forth several times among different  is zero, returns zero.
 operating environments.  
2811    
2812  =over 4  =over 4
2813    
2814  =item line  =item number
2815    
2816  Line of text to be stripped.  Percent numerator.
2817    
2818    =item base
2819    
2820    Percent base.
2821    
2822  =item RETURN  =item RETURN
2823    
2824  The same line of text with all the line-ending characters chopped from the end.  Returns the percentage of the base represented by the numerator.
2825    
2826  =back  =back
2827    
2828  =cut  =cut
2829    
2830  sub Strip {  sub Percent {
2831      # Get a copy of the parameter string.      # Get the parameters.
2832      my ($string) = @_;      my ($number, $base) = @_;
2833      my $retVal = (defined $string ? $string : "");      # Declare the return variable.
2834      # Strip the line terminator characters.      my $retVal = 0;
2835      $retVal =~ s/(\r|\n)+$//g;      # Compute the percent.
2836        if ($base != 0) {
2837            $retVal = $number * 100 / $base;
2838        }
2839      # Return the result.      # Return the result.
2840      return $retVal;      return $retVal;
2841  }  }
2842    
2843  =head3 Pad  =head3 Constrain
2844    
2845  C<< my $paddedString = Tracer::Pad($string, $len, $left, $padChar); >>      my $constrained = Constrain($value, $min, $max);
2846    
2847  Pad a string to a specified length. The pad character will be a  Modify a numeric value to bring it to a point in between a maximum and a minimum.
 space, and the padding will be on the right side unless specified  
 in the third parameter.  
2848    
2849  =over 4  =over 4
2850    
2851  =item string  =item value
   
 String to be padded.  
   
 =item len  
2852    
2853  Desired length of the padded string.  Value to constrain.
2854    
2855  =item left (optional)  =item min (optional)
2856    
2857  TRUE if the string is to be left-padded; otherwise it will be padded on the right.  Minimum permissible value. If this parameter is undefined, no minimum constraint will be applied.
2858    
2859  =item padChar (optional)  =item max (optional)
2860    
2861  Character to use for padding. The default is a space.  Maximum permissible value. If this parameter is undefined, no maximum constraint will be applied.
2862    
2863  =item RETURN  =item RETURN
2864    
2865  Returns a copy of the original string with the pad character added to the  Returns the incoming value, constrained according to the other parameters.
 specified end so that it achieves the desired length.  
2866    
2867  =back  =back
2868    
2869  =cut  =cut
2870    
2871  sub Pad {  sub Constrain {
2872      # Get the parameters.      # Get the parameters.
2873      my ($string, $len, $left, $padChar) = @_;      my ($value, $min, $max) = @_;
2874      # Compute the padding character.      # Declare the return variable.
2875      if (! defined $padChar) {      my $retVal = $value;
2876          $padChar = " ";      # Apply the minimum constraint.
2877      }      if (defined $min && $retVal < $min) {
2878      # Compute the number of spaces needed.          $retVal = $min;
2879      my $needed = $len - length $string;      }
2880      # Copy the string into the return variable.      # Apply the maximum constraint.
2881      my $retVal = $string;      if (defined $max && $retVal > $max) {
2882      # Only proceed if padding is needed.          $retVal = $max;
     if ($needed > 0) {  
         # Create the pad string.  
         my $pad = $padChar x $needed;  
         # Affix it to the return value.  
         if ($left) {  
             $retVal = $pad . $retVal;  
         } else {  
             $retVal .= $pad;  
         }  
2883      }      }
2884      # Return the result.      # Return the result.
2885      return $retVal;      return $retVal;
2886  }  }
2887    
2888  =head3 EOF  =head3 Min
   
 This is a constant that is lexically greater than any useful string.  
   
 =cut  
   
 sub EOF {  
     return "\xFF\xFF\xFF\xFF\xFF";  
 }  
   
 =head3 TICK  
   
 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  
   
     `./protein.cgi`  
   
 from inside a CGI script, it would work fine in Unix, but would issue an error message  
 in Windows complaining that C<'.'> is not a valid command. If instead you code  
2889    
2890      TICK("./protein.cgi")      my $min = Min($value1, $value2, ... $valueN);
2891    
2892  it will work correctly in both environments.  Return the minimum argument. The arguments are treated as numbers.
2893    
2894  =over 4  =over 4
2895    
2896  =item commandString  =item $value1, $value2, ... $valueN
2897    
2898  The command string to pass to the system.  List of numbers to compare.
2899    
2900  =item RETURN  =item RETURN
2901    
2902  Returns the standard output from the specified command, as a list.  Returns the lowest number in the list.
2903    
2904  =back  =back
2905    
2906  =cut  =cut
2907  #: Return Type @;  
2908  sub TICK {  sub Min {
2909      # Get the parameters.      # Get the parameters. Note that we prime the return value with the first parameter.
2910      my ($commandString) = @_;      my ($retVal, @values) = @_;
2911      # Chop off the dot-slash if this is Windows.      # Loop through the remaining parameters, looking for the lowest.
2912      if ($FIG_Config::win_mode) {      for my $value (@values) {
2913          $commandString =~ s!^\./!!;          if ($value < $retVal) {
2914                $retVal = $value;
2915      }      }
2916      # Activate the command and return the result.      }
2917      return `$commandString`;      # Return the minimum found.
2918        return $retVal;
2919  }  }
2920    
2921  =head3 ScriptSetup  =head3 Max
   
 C<< my ($query, $varHash) = ScriptSetup(); >>  
   
 Perform standard tracing and debugging setup for scripts. The value returned is  
 the CGI object followed by a pre-built variable hash.  
   
 The C<Trace> query parameter is used to determine whether or not tracing is active and  
 which trace modules (other than C<Tracer> and C<FIG>) should be turned on. Specifying  
 the C<CGI> trace module will trace parameter and environment information. Parameters are  
 traced at level 3 and environment variables at level 4. At the end of the script, the  
 client should call L</ScriptFinish> to output the web page.  
   
 =cut  
2922    
2923  sub ScriptSetup {      my $max = Max($value1, $value2, ... $valueN);
     # Get the CGI query object.  
     my $query = CGI->new();  
     # Check for tracing. Set it up if the user asked for it.  
     if ($query->param('Trace')) {  
         # Set up tracing.  
         my $ttype = ($query->param('TF') ? ">$FIG_Config::temp/Trace$$.log" : "QUEUE");  
         TSetup($query->param('Trace') . " FIG Tracer", $ttype);  
         # Trace the parameter and environment data.  
         TraceParms($query);  
     } else {  
         # Here tracing is to be turned off. All we allow is errors traced into the  
         # error log.  
         TSetup("0", "WARN");  
     }  
     # Create the variable hash.  
     my $varHash = { DebugData => '' };  
     # Return the query object and variable hash.  
     return ($query, $varHash);  
 }  
2924    
2925  =head3 TraceParms  Return the maximum argument. The arguments are treated as numbers.
2926    
2927  C<< Tracer::TraceParms($query); >>  =over 4
2928    
2929  Trace the CGI parameters at trace level CGI => 3 and the environment variables  =item $value1, $value2, ... $valueN
 at level CGI => 4.  
2930    
2931  =over 4  List of numbers to compare.
2932    
2933  =item query  =item RETURN
2934    
2935  CGI query object containing the parameters to trace.  Returns the highest number in the list.
2936    
2937  =back  =back
2938    
2939  =cut  =cut
2940    
2941  sub TraceParms {  sub Max {
2942      # Get the parameters.      # Get the parameters. Note that we prime the return value with the first parameter.
2943      my ($query) = @_;      my ($retVal, @values) = @_;
2944      if (T(CGI => 3)) {      # Loop through the remaining parameters, looking for the highest.
2945          # Here we want to trace the parameter data.      for my $value (@values) {
2946          my @names = $query->param;          if ($value > $retVal) {
2947          for my $parmName (sort @names) {              $retVal = $value;
             # Note we skip "Trace", which is for our use only.  
             if ($parmName ne 'Trace') {  
                 my @values = $query->param($parmName);  
                 Trace("CGI: $parmName = " . join(", ", @values));  
             }  
         }  
         # Now output a GET-style URL for this query.  
         my $getURL = $query->url(-relative => 1, -query => 1);  
         # Strip out the Trace parameters.  
         $getURL =~ s/Trace=\d[^;&]+[;&]//;  
         $getURL =~ s/TF=\d[;&]//;  
         # Output the URL.  
         Trace("URL: ../FIG/$getURL");  
         # Display the request method.  
         my $method = $query->request_method();  
         Trace("Method: $method");  
     }  
     if (T(CGI => 4)) {  
         # Here we want the environment data too.  
         for my $envName (sort keys %ENV) {  
             Trace("ENV: $envName = $ENV{$envName}");  
2948          }          }
2949      }      }
2950        # Return the maximum found.
2951        return $retVal;
2952  }  }
2953    
 =head3 ScriptFinish  
   
 C<< ScriptFinish($webData, $varHash); >>  
   
 Output a web page at the end of a script. Either the string to be output or the  
 name of a template file can be specified. If the second parameter is omitted,  
 it is assumed we have a string to be output; otherwise, it is assumed we have the  
 name of a template file. The template should have the variable C<DebugData>  
 specified in any form that invokes a standard script. If debugging mode is turned  
 on, a form field will be put in that allows the user to enter tracing data.  
 Trace messages will be placed immediately before the terminal C<BODY> tag in  
 the output, formatted as a list.  
2954    
2955  A typical standard script would loook like the following.  =head3 Strip
   
     BEGIN {  
         # Print the HTML header.  
         print "CONTENT-TYPE: text/html\n\n";  
     }  
     use Tracer;  
     use CGI;  
     use FIG;  
     # ... more uses ...  
2956    
2957      my ($query, $varHash) = ScriptSetup();      my $string = Tracer::Strip($line);
     eval {  
         # ... get data from $query, put it in $varHash ...  
     };  
     if ($@) {  
         Trace("Script Error: $@") if T(0);  
     }  
     ScriptFinish("Html/MyTemplate.html", $varHash);  
2958    
2959  The idea here is that even if the script fails, you'll see trace messages and  Strip all line terminators off a string. This is necessary when dealing with files
2960  useful output.  that may have been transferred back and forth several times among different
2961    operating environments.
2962    
2963  =over 4  =over 4
2964    
2965  =item webData  =item line
2966    
2967  A string containing either the full web page to be written to the output or the  Line of text to be stripped.
 name of a template file from which the page is to be constructed. If the name  
 of a template file is specified, then the second parameter must be present;  
 otherwise, it must be absent.  
2968    
2969  =item varHash (optional)  =item RETURN
2970    
2971  If specified, then a reference to a hash mapping variable names for a template  The same line of text with all the line-ending characters chopped from the end.
 to their values. The template file will be read into memory, and variable markers  
 will be replaced by data in this hash reference.  
2972    
2973  =back  =back
2974    
2975  =cut  =cut
2976    
2977  sub ScriptFinish {  sub Strip {
2978      # Get the parameters.      # Get a copy of the parameter string.
2979      my ($webData, $varHash) = @_;      my ($string) = @_;
2980      # Check for a template file situation.      my $retVal = (defined $string ? $string : "");
2981      my $outputString;      # Strip the line terminator characters.
2982      if (defined $varHash) {      $retVal =~ s/(\r|\n)+$//g;
2983          # Here we have a template file. We need to determine the template type.      # Return the result.
2984          my $template;      return $retVal;
         if ($FIG_Config::template_url && $webData =~ /\.php$/) {  
             $template = "$FIG_Config::template_url/$webData";  
         } else {  
             $template = "<<$webData";  
         }  
         $outputString = PageBuilder::Build($template, $varHash, "Html");  
     } else {  
         # Here the user gave us a raw string.  
         $outputString = $webData;  
     }  
     # Check for trace messages.  
     if ($Destination eq "QUEUE") {  
         # We have trace messages, so we want to put them at the end of the body. This  
         # is either at the end of the whole string or at the beginning of the BODY  
         # end-tag.  
         my $pos = length $outputString;  
         if ($outputString =~ m#</body>#gi) {  
             $pos = (pos $outputString) - 7;  
         }  
         substr $outputString, $pos, 0, QTrace('Html');  
     }  
     # Write the output string.  
     print $outputString;  
2985  }  }
2986    
2987  =head3 Insure  =head3 Pad
2988    
2989  C<< Insure($dirName); >>      my $paddedString = Tracer::Pad($string, $len, $left, $padChar);
2990    
2991  Insure a directory is present.  Pad a string to a specified length. The pad character will be a
2992    space, and the padding will be on the right side unless specified
2993    in the third parameter.
2994    
2995  =over 4  =over 4
2996    
2997  =item dirName  =item string
   
 Name of the directory to check. If it does not exist, it will be created.  
2998    
2999  =back  String to be padded.
3000    
3001  =cut  =item len
3002    
3003  sub Insure {  Desired length of the padded string.
     my ($dirName) = @_;  
     if (! -d $dirName) {  
         Trace("Creating $dirName directory.") if T(2);  
         eval { mkpath $dirName; };  
         if ($@) {  
             Confess("Error creating $dirName: $@");  
         }  
     }  
 }  
3004    
3005  =head3 ChDir  =item left (optional)
3006    
3007  C<< ChDir($dirName); >>  TRUE if the string is to be left-padded; otherwise it will be padded on the right.
3008    
3009  Change to the specified directory.  =item padChar (optional)
3010    
3011  =over 4  Character to use for padding. The default is a space.
3012    
3013  =item dirName  =item RETURN
3014    
3015  Name of the directory to which we want to change.  Returns a copy of the original string with the pad character added to the
3016    specified end so that it achieves the desired length.
3017    
3018  =back  =back
3019    
3020  =cut  =cut
3021    
3022  sub ChDir {  sub Pad {
3023      my ($dirName) = @_;      # Get the parameters.
3024      if (! -d $dirName) {      my ($string, $len, $left, $padChar) = @_;
3025          Confess("Cannot change to directory $dirName: no such directory.");      # Compute the padding character.
3026        if (! defined $padChar) {
3027            $padChar = " ";
3028        }
3029        # Compute the number of spaces needed.
3030        my $needed = $len - length $string;
3031        # Copy the string into the return variable.
3032        my $retVal = $string;
3033        # Only proceed if padding is needed.
3034        if ($needed > 0) {
3035            # Create the pad string.
3036            my $pad = $padChar x $needed;
3037            # Affix it to the return value.
3038            if ($left) {
3039                $retVal = $pad . $retVal;
3040      } else {      } else {
3041          Trace("Changing to directory $dirName.") if T(4);              $retVal .= $pad;
         my $okFlag = chdir $dirName;  
         if (! $okFlag) {  
             Confess("Error switching to directory $dirName.");  
3042          }          }
3043      }      }
3044        # Return the result.
3045        return $retVal;
3046  }  }
3047    
3048  =head3 SendSMS  =head3 EOF
3049    
3050  C<< my $msgID = Tracer::SendSMS($phoneNumber, $msg); >>  This is a constant that is lexically greater than any useful string.
3051    
3052  Send a text message to a phone number using Clickatell. The FIG_Config file must contain the  =cut
 user name, password, and API ID for the relevant account in the hash reference variable  
 I<$FIG_Config::phone>, using the keys C<user>, C<password>, and C<api_id>. For  
 example, if the user name is C<BruceTheHumanPet>, the password is C<silly>, and the API ID  
 is C<2561022>, then the FIG_Config file must contain  
3053    
3054      $phone =  { user => 'BruceTheHumanPet',  sub EOF {
3055                  password => 'silly',      return "\xFF\xFF\xFF\xFF\xFF";
3056                  api_id => '2561022' };  }
3057    
3058  The original purpose of this method was to insure Bruce would be notified immediately when the  =head3 TICK
 Sprout Load terminates. Care should be taken if you do not wish Bruce to be notified immediately  
 when you call this method.  
3059    
3060  The message ID will be returned if successful, and C<undef> if an error occurs.      my @results = TICK($commandString);
3061    
3062  =over 4  Perform a back-tick operation on a command. If this is a Windows environment, any leading
3063    dot-slash (C<./> will be removed. So, for example, if you were doing
3064    
3065  =item phoneNumber      `./protein.cgi`
3066    
3067  Phone number to receive the message, in international format. A United States phone number  from inside a CGI script, it would work fine in Unix, but would issue an error message
3068  would be prefixed by "1". A British phone number would be prefixed by "44".  in Windows complaining that C<'.'> is not a valid command. If instead you code
3069    
3070  =item msg      TICK("./protein.cgi")
3071    
3072  Message to send to the specified phone.  it will work correctly in both environments.
3073    
3074    =over 4
3075    
3076    =item commandString
3077    
3078    The command string to pass to the system.
3079    
3080  =item RETURN  =item RETURN
3081    
3082  Returns the message ID if successful, and C<undef> if the message could not be sent.  Returns the standard output from the specified command, as a list.
3083    
3084  =back  =back
3085    
3086  =cut  =cut
3087    #: Return Type @;
3088  sub SendSMS {  sub TICK {
3089      # Get the parameters.      # Get the parameters.
3090      my ($phoneNumber, $msg) = @_;      my ($commandString) = @_;
3091      # Declare the return variable. If we do not change it, C<undef> will be returned.      # Chop off the dot-slash if this is Windows.
3092      my $retVal;      if ($FIG_Config::win_mode) {
3093      # Only proceed if we have phone support.          $commandString =~ s!^\./!!;
     if (! defined $FIG_Config::phone) {  
         Trace("Phone support not present in FIG_Config.") if T(1);  
     } else {  
         # Get the phone data.  
         my $parms = $FIG_Config::phone;  
         # Get the Clickatell URL.  
         my $url = "http://api.clickatell.com/http/";  
         # Create the user agent.  
         my $ua = LWP::UserAgent->new;  
         # Request a Clickatell session.  
         my $resp = $ua->post("$url/sendmsg", { user => $parms->{user},  
                                      password => $parms->{password},  
                                      api_id => $parms->{api_id},  
                                      to => $phoneNumber,  
                                      text => $msg});  
         # Check for an error.  
         if (! $resp->is_success) {  
             Trace("Alert failed.") if T(1);  
         } else {  
             # Get the message ID.  
             my $rstring = $resp->content;  
             if ($rstring =~ /^ID:\s+(.*)$/) {  
                 $retVal = $1;  
             } else {  
                 Trace("Phone attempt failed with $rstring") if T(1);  
             }  
         }  
3094      }      }
3095      # Return the result.      # Activate the command and return the result.
3096      return $retVal;      return `$commandString`;
3097  }  }
3098    
3099    
3100  =head3 CommaFormat  =head3 CommaFormat
3101    
3102  C<< my $formatted = Tracer::CommaFormat($number); >>      my $formatted = Tracer::CommaFormat($number);
3103    
3104  Insert commas into a number.  Insert commas into a number.
3105    
# Line 2234  Line 3132 
3132      # Return the result.      # Return the result.
3133      return $retVal;      return $retVal;
3134  }  }
 =head3 SetPermissions  
   
 C<< Tracer::SetPermissions($dirName, $group, $mask, %otherMasks); >>  
   
 Set the permissions for a directory and all the files and folders inside it.  
 In addition, the group ownership will be changed to the specified value.  
   
 This method is more vulnerable than most to permission and compatability  
 problems, so it does internal error recovery.  
   
 =over 4  
   
 =item dirName  
   
 Name of the directory to process.  
   
 =item group  
   
 Name of the group to be assigned.  
   
 =item mask  
   
 Permission mask. Bits that are C<1> in this mask will be ORed into the  
 permission bits of any file or directory that does not already have them  
 set to 1.  
   
 =item otherMasks  
3135    
 Map of search patterns to permission masks. If a directory name matches  
 one of the patterns, that directory and all its members and subdirectories  
 will be assigned the new pattern. For example, the following would  
 assign 01664 to most files, but would use 01777 for directories named C<tmp>.  
   
     Tracer::SetPermissions($dirName, 'fig', 01664, '^tmp$' => 01777);  
   
 The list is ordered, so the following would use 0777 for C<tmp1> and  
 0666 for C<tmp>, C<tmp2>, or C<tmp3>.  
   
     Tracer::SetPermissions($dirName, 'fig', 01664, '^tmp1' => 0777,  
                                                    '^tmp' => 0666);  
   
 Note that the pattern matches are all case-insensitive, and only directory  
 names are matched, not file names.  
   
 =back  
   
 =cut  
   
 sub SetPermissions {  
     # Get the parameters.  
     my ($dirName, $group, $mask, @otherMasks) = @_;  
     # Set up for error recovery.  
     eval {  
         # Switch to the specified directory.  
         ChDir($dirName);  
         # Get the group ID.  
         my $gid = getgrnam($group);  
         # Get the mask for tracing.  
         my $traceMask = sprintf("%04o", $mask) . "($mask)";  
         Trace("Fixing permissions for directory $dirName using group $group($gid) and mask $traceMask.") if T(2);  
         my $fixCount = 0;  
         my $lookCount = 0;  
         # @dirs will be a stack of directories to be processed.  
         my @dirs = (getcwd());  
         while (scalar(@dirs) > 0) {  
             # Get the current directory.  
             my $dir = pop @dirs;  
             # Check for a match to one of the specified directory names. To do  
             # that, we need to pull the individual part of the name off of the  
             # whole path.  
             my $simpleName = $dir;  
             if ($dir =~ m!/([^/]+)$!) {  
                 $simpleName = $1;  
             }  
             Trace("Simple directory name for $dir is $simpleName.") if T(4);  
             # Search for a match.  
             my $match = 0;  
             my $i;  
             for ($i = 0; $i < $#otherMasks && ! $match; $i += 2) {  
                 my $pattern = $otherMasks[$i];  
                 if ($simpleName =~ /$pattern/i) {  
                     $match = 1;  
                 }  
             }  
             # Check for a match. Note we use $i-1 because the loop added 2  
             # before terminating due to the match.  
             if ($match && $otherMasks[$i-1] != $mask) {  
                 # This directory matches one of the incoming patterns, and it's  
                 # a different mask, so we process it recursively with that mask.  
                 SetPermissions($dir, $group, $otherMasks[$i-1], @otherMasks);  
             } else {  
                 # Here we can process normally. Get all of the non-hidden members.  
                 my @submems = OpenDir($dir, 1);  
                 for my $submem (@submems) {  
                     # Get the full name.  
                     my $thisMem = "$dir/$submem";  
                     Trace("Checking member $thisMem.") if T(4);  
                     $lookCount++;  
                     if ($lookCount % 1000 == 0) {  
                         Trace("$lookCount members examined. Current is $thisMem. Mask is $traceMask") if T(3);  
                     }  
                     # Fix the group.  
                     chown -1, $gid, $thisMem;  
                     # Insure this member is not a symlink.  
                     if (! -l $thisMem) {  
                         # Get its info.  
                         my $fileInfo = stat $thisMem;  
                         # Only proceed if we got the info. Otherwise, it's a hard link  
                         # and we want to skip it anyway.  
                         if ($fileInfo) {  
                             my $fileMode = $fileInfo->mode;  
                             if (($fileMode & $mask) != $mask) {  
                                 # Fix this member.  
                                 $fileMode |= $mask;  
                                 chmod $fileMode, $thisMem;  
                                 $fixCount++;  
                             }  
                             # If it's a subdirectory, stack it.  
                             if (-d $thisMem) {  
                                 push @dirs, $thisMem;  
                             }  
                         }  
                     }  
                 }  
             }  
         }  
         Trace("$lookCount files and directories processed, $fixCount fixed.") if T(2);  
     };  
     # Check for an error.  
     if ($@) {  
         Confess("SetPermissions error: $@");  
     }  
 }  
3136    
3137  =head3 CompareLists  =head3 CompareLists
3138    
3139  C<< my ($inserted, $deleted) = Tracer::CompareLists(\@newList, \@oldList, $keyIndex); >>      my ($inserted, $deleted) = Tracer::CompareLists(\@newList, \@oldList, $keyIndex);
3140    
3141  Compare two lists of tuples, and return a hash analyzing the differences. The lists  Compare two lists of tuples, and return a hash analyzing the differences. The lists
3142  are presumed to be sorted alphabetically by the value in the $keyIndex column.  are presumed to be sorted alphabetically by the value in the $keyIndex column.
# Line 2435  Line 3201 
3201      return ($inserted, $deleted);      return ($inserted, $deleted);
3202  }  }
3203    
3204  =head3 GetLine  =head3 GenerateURL
3205    
3206  C<< my @data = Tracer::GetLine($handle); >>      my $queryUrl = Tracer::GenerateURL($page, %parameters);
3207    
3208  Read a line of data from a tab-delimited file.  Generate a GET-style URL for the specified page with the specified parameter
3209    names and values. The values will be URL-escaped automatically. So, for
3210    example
3211    
3212        Tracer::GenerateURL("form.cgi", type => 1, string => "\"high pass\" or highway")
3213    
3214    would return
3215    
3216        form.cgi?type=1;string=%22high%20pass%22%20or%20highway
3217    
3218  =over 4  =over 4
3219    
3220  =item handle  =item page
3221    
3222  Open file handle from which to read.  Page URL.
3223    
3224    =item parameters
3225    
3226    Hash mapping parameter names to parameter values.
3227    
3228  =item RETURN  =item RETURN
3229    
3230  Returns a list of the fields in the record read. The fields are presumed to be  Returns a GET-style URL that goes to the specified page and passes in the
3231  tab-delimited. If we are at the end of the file, then an empty list will be  specified parameters and values.
 returned. If an empty line is read, a single list item consisting of a null  
 string will be returned.  
3232    
3233  =back  =back
3234    
3235  =cut  =cut
3236    
3237  sub GetLine {  sub GenerateURL {
3238      # Get the parameters.      # Get the parameters.
3239      my ($handle) = @_;      my ($page, %parameters) = @_;
3240      # Declare the return variable.      # Prime the return variable with the page URL.
3241      my @retVal = ();      my $retVal = $page;
3242      # Read from the file.      # Loop through the parameters, creating parameter elements in a list.
3243      my $line = <$handle>;      my @parmList = map { "$_=" . uri_escape($parameters{$_}) } keys %parameters;
3244      # Only proceed if we found something.      # If the list is nonempty, tack it on.
3245      if (defined $line) {      if (@parmList) {
3246          # Remove the new-line.          $retVal .= "?" . join(";", @parmList);
         chomp $line;  
         # If the line is empty, return a single empty string; otherwise, parse  
         # it into fields.  
         if ($line eq "") {  
             push @retVal, "";  
         } else {  
             push @retVal, split /\t/,$line;  
         }  
3247      }      }
3248      # Return the result.      # Return the result.
3249      return @retVal;      return $retVal;
3250  }  }
3251    
3252  =head3 PutLine  =head3 ApplyURL
3253    
3254  C<< Tracer::PutLine($handle, \@fields); >>      Tracer::ApplyURL($table, $target, $url);
3255    
3256  Write a line of data to a tab-delimited file. The specified field values will be  Run through a two-dimensional table (or more accurately, a list of lists), converting the
3257  output in tab-separated form, with a trailing new-line.  I<$target> column to HTML text having a hyperlink to a URL in the I<$url> column. The
3258    URL column will be deleted by this process and the target column will be HTML-escaped.
3259    
3260    This provides a simple way to process the results of a database query into something
3261    displayable by combining a URL with text.
3262    
3263  =over 4  =over 4
3264    
3265  =item handle  =item table
3266    
3267  Output file handle.  Reference to a list of lists. The elements in the containing list will be updated by
3268    this method.
3269    
3270  =item fields  =item target
3271    
3272  List of field values.  The index of the column to be converted into HTML.
3273    
3274    =item url
3275    
3276    The index of the column containing the URL. Note that the URL must have a recognizable
3277    C<http:> at the beginning.
3278    
3279  =back  =back
3280    
3281  =cut  =cut
3282    
3283  sub PutLine {  sub ApplyURL {
3284      # Get the parameters.      # Get the parameters.
3285      my ($handle, $fields) = @_;      my ($table, $target, $url) = @_;
3286      # Write the data.      # Loop through the table.
3287      print $handle join("\t", @{$fields}) . "\n";      for my $row (@{$table}) {
3288            # Apply the URL to the target cell.
3289            $row->[$target] = CombineURL($row->[$target], $row->[$url]);
3290            # Delete the URL from the row.
3291            delete $row->[$url];
3292        }
3293  }  }
3294    
3295  =head3 GenerateURL  =head3 CombineURL
3296    
3297  C<< my $queryUrl = Tracer::GenerateURL($page, %parameters); >>      my $combinedHtml = Tracer::CombineURL($text, $url);
3298    
3299  Generate a GET-style URL for the specified page with the specified parameter  This method will convert the specified text into HTML hyperlinked to the specified
3300  names and values. The values will be URL-escaped automatically. So, for  URL. The hyperlinking will only take place if the URL looks legitimate: that is, it
3301  example  is defined and begins with an C<http:> header.
3302    
3303      Tracer::GenerateURL("form.cgi", type => 1, string => "\"high pass\" or highway")  =over 4
3304    
3305  would return  =item text
3306    
3307    Text to return. This will be HTML-escaped automatically.
3308    
3309    =item url
3310    
3311    A URL to be hyperlinked to the text. If it does not look like a URL, then the text
3312    will be returned without any hyperlinking.
3313    
3314    =item RETURN
3315    
3316    Returns the original text, HTML-escaped, with the URL hyperlinked to it. If the URL
3317    doesn't look right, the HTML-escaped text will be returned without any further
3318    modification.
3319    
3320    =back
3321    
3322    =cut
3323    
3324    sub CombineURL {
3325        # Get the parameters.
3326        my ($text, $url) = @_;
3327        # Declare the return variable.
3328        my $retVal = CGI::escapeHTML($text);
3329        # Verify the URL.
3330        if (defined($url) && $url =~ m!http://!i) {
3331            # It's good, so we apply it to the text.
3332            $retVal = "<a href=\"$url\">$retVal</a>";
3333        }
3334        # Return the result.
3335        return $retVal;
3336    }
3337    
3338      form.cgi?type=1&string=%22high%20pass%22%20or%20highway  =head3 Cmp
3339    
3340        my $cmp = Tracer::Cmp($a, $b);
3341    
3342    This method performs a universal sort comparison. Each value coming in is
3343    separated into a leading text part and a trailing number part. The text
3344    part is string compared, and if both parts are equal, then the number
3345    parts are compared numerically. A stream of just numbers or a stream of
3346    just strings will sort correctly, and a mixed stream will sort with the
3347    numbers first. Strings with a label and a number will sort in the
3348    expected manner instead of lexically.
3349    
3350  =over 4  =over 4
3351    
3352  =item page  =item a
3353    
3354  Page URL.  First item to compare.
3355    
3356  =item parameters  =item b
3357    
3358  Hash mapping parameter names to parameter values.  Second item to compare.
3359    
3360  =item RETURN  =item RETURN
3361    
3362  Returns a GET-style URL that goes to the specified page and passes in the  Returns a negative number if the first item should sort first (is less), a positive
3363  specified parameters and values.  number if the first item should sort second (is greater), and a zero if the items are
3364    equal.
3365    
3366  =back  =back
3367    
3368  =cut  =cut
3369    
3370  sub GenerateURL {  sub Cmp {
3371      # Get the parameters.      # Get the parameters.
3372      my ($page, %parameters) = @_;      my ($a, $b) = @_;
3373      # Prime the return variable with the page URL.      # Declare the return value.
3374      my $retVal = $page;      my $retVal;
3375      # Loop through the parameters, creating parameter elements in a list.      # Check for nulls.
3376      my @parmList = map { "$_=" . uri_escape($parameters{$_}) } keys %parameters;      if (! defined($a)) {
3377      # If the list is nonempty, tack it on.          $retVal = (! defined($b) ? 0 : -1);
3378      if (@parmList) {      } elsif (! defined($b)) {
3379          $retVal .= "?" . join("&", @parmList);          $retVal = 1;
3380        } else {
3381            # Here we have two real values. Parse the two strings.
3382            $a =~ /^(\D*)(\d*)$/;
3383            my $aParsed = [$1, $2];
3384            $b =~ /^(\D*)(\d*)$/;
3385            my $bParsed = [$1, $2];
3386            # Compare the string parts.
3387            $retVal = $aParsed->[0] cmp $bParsed->[0];
3388            if (! $retVal) {
3389                $retVal = $aParsed->[1] <=> $bParsed->[1];
3390            }
3391      }      }
3392      # Return the result.      # Return the result.
3393      return $retVal;      return $retVal;
3394  }  }
3395    
3396    
3397    =head3 TrackingCode
3398    
3399        my $html = Tracer::TrackingCode();
3400    
3401    Returns the HTML code for doing web page traffic monitoring. If the
3402    current environment is a test system, then it returns a null string;
3403    otherwise, it returns a bunch of javascript containing code for turning
3404    on SiteMeter and Google Analytics.
3405    
3406    =cut
3407    
3408    sub TrackingC