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revision 1.67, Fri Sep 29 15:00:17 2006 UTC revision 1.99, Wed May 7 23:00:16 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 Warn);
24      @EXPORT_OK = qw(GetFile GetOptions Merge MergeOptions ParseCommand ParseRecord UnEscape Escape);      @EXPORT_OK = qw(GetFile GetOptions Merge MergeOptions ParseCommand ParseRecord UnEscape Escape PrintLine PutLine);
25      use strict;      use strict;
26      use Carp qw(longmess croak);      use Carp qw(longmess croak carp);
27      use CGI;      use CGI;
28      use Cwd;      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        use POSIX qw(strftime);
40        use Time::Zone;
41    
42    
43  =head1 Tracing and Debugging Helpers  =head1 Tracing and Debugging Helpers
44    
45  =head2 Introduction  =head2 Tracing
46    
47  This package provides simple tracing for debugging and reporting purposes. To use it simply call the  This package provides simple tracing for debugging and reporting purposes. To use it simply call the
48  L</TSetup> method to set the options and call L</Trace> to write out trace messages. Each trace  L</TSetup> or L</ETracing> method to set the options and call L</Trace> to write out trace messages.
49  message has a I<trace level> and I<category> associated with it. In addition, the tracing package itself  L</TSetup> and L</ETracing> both establish a I<trace level> and a list of I<categories>. Similarly,
50  has a list of categories and a single trace level set by the B<TSetup> method. Only messages whose trace  each trace message has a I<trace level> and I<category> associated with it. Only messages whose trace
51  level is less than or equal to this package's trace level and whose category is activated will  level is less than or equal to the setup trace level and whose category is activated will
52  be written. Thus, a higher trace level on a message indicates that the message  be written. Thus, a higher trace level on a message indicates that the message
53  is less likely to be seen. A higher trace level passed to B<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
54  appear. To generate a trace message, use the following syntax.  appear.
55    
56    =head3 Putting Trace Messages in Your Code
57    
58  C<< Trace($message) if T(errors => 4); >>  To generate a trace message, use the following syntax.
59    
60        Trace($message) if T(errors => 4);
61    
62  This statement will produce a trace message if the trace level is 4 or more and the C<errors>  This statement will produce a trace message if the trace level is 4 or more and the C<errors>
63  category is active. Note that the special category C<main> is always active, so  category is active. There is a special category C<main> that is always active, so
64    
65  C<< Trace($message) if T(main => 4); >>      Trace($message) if T(main => 4);
66    
67  will trace if the trace level is 4 or more.  will trace if the trace level is 4 or more.
68    
# Line 61  Line 70 
70  following call is made in the B<Sprout> package, it will appear if the C<Sprout> category is  following call is made in the B<Sprout> package, it will appear if the C<Sprout> category is
71  active and the trace level is 2 or more.  active and the trace level is 2 or more.
72    
73  C<< Trace($message) if T(2); >>      Trace($message) if T(2);
74    
75    In scripts, where no package name is available, the category defaults to C<main>.
76    
77    =head3 Custom Tracing
78    
79    Many programs have customized tracing configured using the L</TSetup> method. This is no longer
80    the preferred method, but a knowledge of how custom tracing works can make the more modern
81    L</Emergency Tracing> easier to understand.
82    
83  To set up tracing, you call the L</TSetup> method. The method takes as input a trace level, a list  To set up custom tracing, you call the L</TSetup> method. The method takes as input a trace level,
84  of category names, and a set of options. The trace level and list of category names are  a list of category names, and a destination. The trace level and list of category names are
85  specified as a space-delimited string. Thus  specified as a space-delimited string. Thus
86    
87  C<< TSetup('3 errors Sprout ERDB', 'HTML'); >>      TSetup('3 errors Sprout ERDB', 'TEXT');
88    
89  sets the trace level to 3, activates the C<errors>, C<Sprout>, and C<ERDB> categories, and  sets the trace level to 3, activates the C<errors>, C<Sprout>, and C<ERDB> categories, and
90  specifies that messages should be output as HTML paragraphs.  specifies that messages should be sent to the standard output.
91    
92  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
93  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
94  useful in a CGI environment.  useful in a CGI environment.
95    
96  C<< TSetup('3 *', 'WARN'); >>      TSetup('3 *', 'WARN');
97    
98  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
99  be queued. The messages can then be retrieved by calling the L</QTrace> method. This approach  be queued. The messages can then be retrieved by calling the L</QTrace> method. This approach
100  is useful if you are building a web page. Instead of having the trace messages interspersed with  is useful if you are building a web page. Instead of having the trace messages interspersed with
101  the page output, they can be gathered together and displayed at the end of the page. This makes  the page output, they can be gathered together and displayed at the end of the page. This makes
102  it easier to debug page formatting problems.  it easier to debug page formatting problems.
103    
104  Finally, you can specify that all trace messages be emitted as warnings.  Finally, you can specify that all trace messages be emitted to a file, or the standard output and
105    a file at the same time. To trace to a file, specify the filename with an output character in front
106    of it.
107    
108        TSetup('4 SQL', ">$fileName");
109    
110    To trace to the standard output and a file at the same time, put a C<+> in front of the angle
111    bracket.
112    
113        TSetup('3 *', "+>$fileName");
114    
115  The flexibility of tracing makes it superior to simple use of directives like C<die> and C<warn>.  The flexibility of tracing makes it superior to simple use of directives like C<die> and C<warn>.
116  Tracer calls can be left in the code with minimal overhead and then turned on only when needed.  Tracer calls can be left in the code with minimal overhead and then turned on only when needed.
117  Thus, debugging information is available and easily retrieved even when the application is  Thus, debugging information is available and easily retrieved even when the application is
118  being used out in the field.  being used out in the field.
119    
120    =head3 Trace Levels
121    
122  There is no hard and fast rule on how to use trace levels. The following is therefore only  There is no hard and fast rule on how to use trace levels. The following is therefore only
123  a suggestion.  a suggestion.
124    
# Line 121  Line 149 
149    
150  =back  =back
151    
152    The format of trace messages is important because some utilities analyze trace files.
153    There are three fields-- the time stamp, the category name, and the text.
154    The time stamp is between square brackets and the category name between angle brackets.
155    After the category name there is a colon (C<:>) followed by the message text.
156    If the square brackets or angle brackets are missing, then the trace management
157    utilities assume that they are encountering a set of pre-formatted lines.
158    
159    Note, however, that this formatting is done automatically by the tracing functions. You
160    only need to know about it if you want to parse a trace file.
161    
162    =head3 Emergency Tracing
163    
164    Sometimes, you need a way for tracing to happen automatically without putting parameters
165    in a form or on the command line. Emergency tracing does this. You invoke emergency tracing
166    from the debug form, which is accessed from the [[DebugConsole]]. Emergency tracing requires
167    that you specify a tracing key. For command-line tools, the key is
168    taken from the C<TRACING> environment variable. For web services, the key is taken from
169    a cookie. Either way, the key tells the tracing facility who you are, so that you control
170    the tracing in your environment without stepping on other users.
171    
172    The key can be anything you want. If you don't have a key, the C<SetPassword> page will
173    generate one for you.
174    
175    You can activate and de-activate emergency tracing from the debugging control panel, as
176    well as display the trace file itself.
177    
178    To enable emergency tracing in your code, call
179    
180        ETracing($cgi)
181    
182    from a web script and
183    
184        ETracing()
185    
186    from a command-line script.
187    
188    The web script will look for the tracing key in the cookies, and the command-line
189    script will look for it in the C<TRACING> environment variable. If you are
190    using the L</StandardSetup> method or a [[WebApplication]], emergency tracing
191    will be configured automatically.
192    
193  =cut  =cut
194    
195  # Declare the configuration variables.  # Declare the configuration variables.
196    
197  my $Destination = "NONE";   # Description of where to send the trace output.  my $Destination = "WARN";   # Description of where to send the trace output.
198  my $TeeFlag = 0;            # TRUE if output is going to a file and to the  my $TeeFlag = 0;            # TRUE if output is going to a file and to the
199                              # standard output                              # standard output
200  my %Categories = ( main => 1 );  my %Categories = ( main => 1 );
201                              # hash of active category names                              # hash of active category names
202    my @LevelNames = qw(error warn notice info detail);
203  my $TraceLevel = 0;         # trace level; a higher trace level produces more  my $TraceLevel = 0;         # trace level; a higher trace level produces more
204                              # messages                              # messages
205  my @Queue = ();             # queued list of trace messages.  my @Queue = ();             # queued list of trace messages.
206  my $LastCategory = "main";  # name of the last category interrogated  my $LastCategory = "main";  # name of the last category interrogated
207    my $LastLevel = 0;          # level of the last test call
208  my $SetupCount = 0;         # number of times TSetup called  my $SetupCount = 0;         # number of times TSetup called
209  my $AllTrace = 0;           # TRUE if we are tracing all categories.  my $AllTrace = 0;           # TRUE if we are tracing all categories.
210    my $SavedCGI;               # CGI object passed to ETracing
211    umask 2;                    # Fix the damn umask so everything is group-writable.
212    
213    =head2 Tracing Methods
214    
215    =head3 Setups
216    
217        my $count = Tracer::Setups();
218    
219    Return the number of times L</TSetup> has been called.
220    
221    This method allows for the creation of conditional tracing setups where, for example, we
222    may want to set up tracing if nobody else has done it before us.
223    
224    =cut
225    
226  =head2 Public Methods  sub Setups {
227        return $SetupCount;
228    }
229    
230  =head3 TSetup  =head3 TSetup
231    
232  C<< TSetup($categoryList, $target); >>      TSetup($categoryList, $target);
233    
234  This method is used to specify the trace options. The options are stored as package data  This method is used to specify the trace options. The options are stored as package data
235  and interrogated by the L</Trace> and L</T> methods.  and interrogated by the L</Trace> and L</T> methods.
# Line 191  Line 279 
279          }          }
280      }      }
281      # Now we need to process the destination information. The most important special      # Now we need to process the destination information. The most important special
282      # cases are the single ">", which requires we clear the file first, and the      # case is when we're writing to a file. This is indicated by ">" (overwrite) and
283      # "+" prefix which indicates a double echo.      # ">>" (append). A leading "+" for either indicates that we are also writing to
284        # the standard output (tee mode).
285      if ($target =~ m/^\+?>>?/) {      if ($target =~ m/^\+?>>?/) {
286          if ($target =~ m/^\+/) {          if ($target =~ m/^\+/) {
287              $TeeFlag = 1;              $TeeFlag = 1;
288              $target = substr($target, 1);              $target = substr($target, 1);
289          }          }
290          if ($target =~ m/^>[^>]/) {          if ($target =~ m/^>[^>]/) {
291                # We need to initialize the file (which clears it).
292              open TRACEFILE, $target;              open TRACEFILE, $target;
293              print TRACEFILE Now() . " Tracing initialized.\n";              print TRACEFILE "[" . Now() . "] [notice] [Tracer] Tracing initialized.\n";
294              close TRACEFILE;              close TRACEFILE;
295                # Set to append mode now that the file has been cleared.
296              $Destination = ">$target";              $Destination = ">$target";
297          } else {          } else {
298              $Destination = $target;              $Destination = $target;
# Line 213  Line 304 
304      $SetupCount++;      $SetupCount++;
305  }  }
306    
307  =head3 StandardSetup  =head3 SetLevel
308    
309  C<< my ($options, @parameters) = StandardSetup(\@categories, \%options, $parmHelp, @ARGV); >>      Tracer::SetLevel($newLevel);
310    
311  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.  
312    
313  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.  
314    
315  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  
316    
317      ["Sprout", "SproutLoad", "ERDB"]  Proposed new trace level.
318    
319  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.  
320    
321  =over 4  =cut
322    
323  =item FIG  sub SetLevel {
324        $TraceLevel = $_[0];
325    }
326    
327  Turns on trace messages inside the B<FIG> package.  =head3 ParseDate
328    
329  =item SQL      my $time = Tracer::ParseDate($dateString);
330    
331  Traces SQL commands and activity.  Convert a date into a PERL time number. This method expects a date-like string
332    and parses it into a number. The string must be vaguely date-like or it will
333    return an undefined value. Our requirement is that a month and day be
334    present and that three pieces of the date string (time of day, month and day,
335    year) be separated by likely delimiters, such as spaces, commas, and such-like.
336    
337  =item Tracer  If a time of day is present, it must be in military time with two digits for
338    everything but the hour.
339    
340  Traces error messages and call stacks.  The year must be exactly four digits.
341    
342  =back  Additional stuff can be in the string. We presume it's time zones or weekdays or something
343    equally innocuous. This means, however, that a sufficiently long sentence with date-like
344    parts in it may be interpreted as a date. Hopefully this will not be a problem.
345    
346  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.  
347    
348      TransactFeatures -trace=3 -sql register ../xacts IDs.tbl  The parameters are as follows.
349    
350  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  
351    
352  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.  
353    
354      TransactFeatures -trace=3 -sql -user=Bruce register ../xacts IDs.tbl  The date string to convert.
355    
356  would send the trace output to C<traceBruce.log> in the temporary directory.  =item RETURN
357    
358  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
359  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.  
360    
361  You can specify a different default trace level by setting C<$options->{trace}>  =back
 prior to calling this method.  
362    
363  An example at this point would help. Consider, for example, the command-line utility  =cut
 C<TransactFeatures>. It accepts a list of positional parameters plus the options  
 C<safe>, C<noAlias>, C<start>, and C<tblFiles>. To start up this command, we execute  
 the following code.  
364    
365      my ($options, @parameters) = Tracer::StandardSetup(["DocUtils"],  # Universal month conversion table.
366                          { safe => [0, "use database transactions"],  use constant MONTHS => {    Jan =>  0, January   =>  0, '01' =>  0,  '1' =>  0,
367                            noAlias => [0, "do not expect aliases in CHANGE transactions"],                              Feb =>  1, February  =>  1, '02' =>  1,  '2' =>  1,
368                            start => [' ', "start with this genome"],                              Mar =>  2, March     =>  2, '03' =>  2,  '3' =>  2,
369                            tblFiles => [0, "output TBL files containing the corrected IDs"] },                              Apr =>  3, April     =>  3, '04' =>  3,  '4' =>  3,
370                          "command transactionDirectory IDfile",                              May =>  4, May       =>  4, '05' =>  4,  '5' =>  4,
371                        @ARGV);                              Jun =>  5, June      =>  5, '06' =>  5,  '6' =>  5,
372                                Jul =>  6, July      =>  6, '07' =>  6,  '7' =>  6,
373                                Aug =>  7, August    =>  7, '08' =>  7,  '8' =>  7,
374                                Sep =>  8, September =>  8, '09' =>  8,  '9' =>  8,
375                                Oct =>  9, October  =>   9, '10' =>  9,
376                                Nov => 10, November =>  10, '11' => 10,
377                                Dec => 11, December =>  11, '12' => 11
378                            };
379    
380    sub ParseDate {
381        # Get the parameters.
382        my ($dateString) = @_;
383        # Declare the return variable.
384        my $retVal;
385        # Find the month and day of month. There are two ways that can happen. We check for the
386        # numeric style first. That way, if the user's done something like "Sun 12/22", then we
387        # won't be fooled into thinking the month is Sunday.
388        if ($dateString =~ m#\b(\d{1,2})/(\d{1,2})\b# || $dateString =~ m#\b(\w+)\s(\d{1,2})\b#) {
389            my ($mon, $mday) = (MONTHS->{$1}, $2);
390            # Insist that the month and day are valid.
391            if (defined($mon) && $2 >= 1 && $2 <= 31) {
392                # Find the time.
393                my ($hour, $min, $sec) = (0, 0, 0);
394                if ($dateString =~ /\b(\d{1,2}):(\d{2}):(\d{2})\b/) {
395                    ($hour, $min, $sec) = ($1, $2, $3);
396                }
397                # Find the year.
398                my $year;
399                if ($dateString =~ /\b(\d{4})\b/) {
400                    $year = $1;
401                } else {
402                    # Get the default year, which is this one. Note we must convert it to
403                    # the four-digit value expected by "timelocal".
404                    (undef, undef, undef, undef, undef, $year) = localtime();
405                    $year += 1900;
406                }
407                $retVal = timelocal($sec, $min, $hour, $mday, $mon, $year);
408            }
409        }
410        # Return the result.
411        return $retVal;
412    }
413    
414  The call to C<ParseCommand> specifies the default values for the options and  =head3 LogErrors
 stores the actual options in a hash that is returned as C<$options>. The  
 positional parameters are returned in C<@parameters>.  
415    
416  The following is a sample command line for C<TransactFeatures>.      Tracer::LogErrors($fileName);
417    
418      TransactFeatures -trace=2 -noAlias register ../xacts IDs.tbl  Route the standard error output to a log file.
419    
420  In this case, C<register>, C<../xacts>, and C<IDs.tbl> are the positional  =over 4
 parameters, and would find themselves in I<@parameters> after executing the  
 above code fragment. The tracing would be set to level 2, and the categories  
 would be C<FIG>, C<Tracer>, and <DocUtils>. C<FIG> and C<Tracer> are standard,  
 and C<DocUtils> was included because it came in within the first parameter  
 to this method. The I<$options> hash would be  
421    
422      { trace => 2, sql => 0, safe => 0,  =item fileName
       noAlias => 1, start => ' ', tblFiles => 0 }  
423    
424  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.  
425    
426  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  
427    
428      -user=Bruce -background  =cut
429    
430  then the trace output would go to C<traceBruce.log>, the standard output to  sub LogErrors {
431  C<outBruce.log>, and the error output to C<errBruce.log>. This is designed to      # Get the file name.
432  simplify starting a command in the background.      my ($fileName) = @_;
433        # Open the file as the standard error output.
434        open STDERR, '>', $fileName;
435    }
436    
437  Finally, if the special option C<-h> is specified, the option names will  =head3 Trace
 be traced at level 0 and the program will exit without processing.  
 This provides a limited help capability. For example, if the user enters  
438    
439      TransactFeatures -h      Trace($message);
440    
441  he would see the following output.  Write a trace message to the target location specified in L</TSetup>. If there has not been
442    any prior call to B<TSetup>.
443    
444      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  
445    
446  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,  
447    
448      { trace => [0, "tracing level (default 0)"],  Message to write.
        ...  
449    
450  would set the default trace level to 0 instead of 2, while  =back
451    
452      { trace => ["2-", "tracing level (default 2)"],  =cut
        ...  
453    
454  would leave the default at 2, but trace only to the log file, not to the  sub Trace {
455  standard output.      # Get the parameters.
456        my ($message) = @_;
457        # Strip off any line terminators at the end of the message. We will add
458        # new-line stuff ourselves.
459        my $stripped = Strip($message);
460        # Compute the caller information.
461        my ($callPackage, $callFile, $callLine) = caller();
462        my $callFileTitle = basename($callFile);
463        # Check the caller.
464        my $callerInfo = ($callFileTitle ne "Tracer.pm" ? " [$callFileTitle $callLine]" : "");
465        # Get the timestamp.
466        my $timeStamp = Now();
467        # Build the prefix.
468        my $level = $LevelNames[$LastLevel] || "($LastLevel)";
469        my $prefix = "[$timeStamp] [$level] [$LastCategory]$callerInfo";
470        # Format the message.
471        my $formatted = "$prefix $stripped";
472        # Process according to the destination.
473        if ($Destination eq "TEXT") {
474            # Write the message to the standard output.
475            print "$formatted\n";
476        } elsif ($Destination eq "ERROR") {
477            # Write the message to the error output. Here, we want our prefix fields.
478            print STDERR "$formatted\n";
479        } elsif ($Destination eq "WARN") {
480            # Emit the message to the standard error output. It is presumed that the
481            # error logger will add its own prefix fields, the notable exception being
482            # the caller info.
483            print STDERR "$callerInfo$stripped\n";
484        } elsif ($Destination eq "QUEUE") {
485            # Push the message into the queue.
486            push @Queue, "$formatted";
487        } elsif ($Destination eq "HTML") {
488            # Convert the message to HTML and write it to the standard output.
489            my $escapedMessage = CGI::escapeHTML($stripped);
490            print "<p>$timeStamp $LastCategory $LastLevel: $escapedMessage</p>\n";
491        } elsif ($Destination =~ m/^>>/) {
492            # Write the trace message to an output file.
493            open(TRACING, $Destination) || die "Tracing open for \"$Destination\" failed: $!";
494            print TRACING "$formatted\n";
495            close TRACING;
496            # If the Tee flag is on, echo it to the standard output.
497            if ($TeeFlag) {
498                print "$formatted\n";
499            }
500        }
501    }
502    
503  The parameters to this method are as follows.  =head3 T
504    
505  =over 4      my $switch = T($category, $traceLevel);
506    
507  =item categories      or
508    
509  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.  
510    
511  =item options  Return TRUE if the trace level is at or above a specified value and the specified category
512    is active, else FALSE. If no category is specified, the caller's package name is used.
513    
514  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).  
515    
516  =item parmHelp  =item category
517    
518  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
519  if the user specifies the C<-h> option.  used.
520    
521  =item argv  =item traceLevel
522    
523  List of command line parameters, including the option switches, which must  Relevant tracing level.
 precede the positional parameters and be prefixed by a hyphen.  
524    
525  =item RETURN  =item RETURN
526    
527  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.  
528    
529  =back  =back
530    
531  =cut  =cut
532    
533  sub StandardSetup {  sub T {
534        # Declare the return variable.
535        my $retVal = 0;
536        # Only proceed if tracing is turned on.
537        if ($Destination ne "NONE") {
538      # Get the parameters.      # Get the parameters.
539      my ($categories, $options, $parmHelp, @argv) = @_;          my ($category, $traceLevel) = @_;
540      # Add the tracing options.          if (!defined $traceLevel) {
541      if (! exists $options->{trace}) {              # Here we have no category, so we need to get the calling package.
542          $options->{trace} = [2, "tracing level"];              # The calling package is normally the first parameter. If it is
543      }              # omitted, the first parameter will be the tracelevel. So, the
544      $options->{sql} = [0, "turn on SQL tracing"];              # first thing we do is shift the so-called category into the
545      $options->{h} = [0, "display command-line options"];              # $traceLevel variable where it belongs.
546      $options->{user} = [$$, "trace log file name suffix"];              $traceLevel = $category;
547      $options->{background} = [0, "spool standard and error output"];              my ($package, $fileName, $line) = caller;
548      # Create a parsing hash from the options hash. The parsing hash              # If there is no calling package, we default to "main".
549      # contains the default values rather than the default value              if (!$package) {
550      # 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";  
551          } else {          } else {
552              $traceMode = "WARN";                  my @cats = split /::/, $package;
553                    $category = $cats[$#cats];
554          }          }
555      }      }
556      # Now set up the tracing.          # Save the category name and level.
557      TSetup("$traceLevel $cats", $traceMode);          $LastCategory = $category;
558      # Check for the "h" option. If it is specified, dump the command-line          $LastLevel = $traceLevel;
559      # options and exit the program.          # Convert it to lower case before we hash it.
560      if ($retOptions->{h}) {          $category = lc $category;
561          $0 =~ m#[/\\](\w+)(\.pl)?$#i;          # Use the category and tracelevel to compute the result.
562          Trace("$1 [options] $parmHelp") if T(0);          if (ref $traceLevel) {
563          for my $key (sort keys %{$options}) {              Confess("Bad trace level.");
564              my $name = Pad($key, $longestName, 0, ' ');          } elsif (ref $TraceLevel) {
565              my $desc = $options->{$key}->[1];              Confess("Bad trace config.");
             if ($options->{$key}->[0]) {  
                 $desc .= " (default " . $options->{$key}->[0] . ")";  
             }  
             Trace("  $name $desc") if T(0);  
566          }          }
567          exit(0);          $retVal = ($traceLevel <= $TraceLevel && ($AllTrace || exists $Categories{$category}));
568      }      }
569      # Return the parsed parameters.      # Return the computed result.
570      return ($retOptions, @retParameters);      return $retVal;
571  }  }
572    
573  =head3 Setups  =head3 QTrace
574    
575  C<< my $count = Tracer::Setups(); >>      my $data = QTrace($format);
576    
577  Return the number of times L</TSetup> has been called.  Return the queued trace data in the specified format.
578    
579  This method allows for the creation of conditional tracing setups where, for example, we  =over 4
580  may want to set up tracing if nobody else has done it before us.  
581    =item format
582    
583    C<html> to format the data as an HTML list, C<text> to format it as straight text.
584    
585    =back
586    
587  =cut  =cut
588    
589  sub Setups {  sub QTrace {
590      return $SetupCount;      # Get the parameter.
591        my ($format) = @_;
592        # Create the return variable.
593        my $retVal = "";
594        # Only proceed if there is an actual queue.
595        if (@Queue) {
596            # Process according to the format.
597            if ($format =~ m/^HTML$/i) {
598                # Convert the queue into an HTML list.
599                $retVal = "<ul>\n";
600                for my $line (@Queue) {
601                    my $escapedLine = CGI::escapeHTML($line);
602                    $retVal .= "<li>$escapedLine</li>\n";
603                }
604                $retVal .= "</ul>\n";
605            } elsif ($format =~ m/^TEXT$/i) {
606                # Convert the queue into a list of text lines.
607                $retVal = join("\n", @Queue) . "\n";
608            }
609            # Clear the queue.
610            @Queue = ();
611        }
612        # Return the formatted list.
613        return $retVal;
614  }  }
615    
616  =head3 Open  =head3 Confess
   
 C<< my $handle = Open($fileHandle, $fileSpec, $message); >>  
617    
618  Open a file.      Confess($message);
619    
620  The I<$fileSpec> is essentially the second argument of the PERL C<open>  Trace the call stack and abort the program with the specified message. When used with
621  function. The mode is specified using Unix-like shell information. So, for  the OR operator and the L</Assert> method, B<Confess> can function as a debugging assert.
622  example,  So, for example
623    
624      Open(\*LOGFILE, '>>/usr/spool/news/twitlog', "Could not open twit log.");      Assert($recNum >= 0) || Confess("Invalid record number $recNum.");
625    
626  would open for output appended to the specified file, and  Will abort the program with a stack trace if the value of C<$recNum> is negative.
627    
628      Open(\*DATASTREAM, "| sort -u >$outputFile", "Could not open $outputFile.");  =over 4
629    
630  would open a pipe that sorts the records written and removes duplicates. Note  =item message
 the use of file handle syntax in the Open call. To use anonymous file handles,  
 code as follows.  
631    
632      my $logFile = Open(undef, '>>/usr/spool/news/twitlog', "Could not open twit log.");  Message to include in the trace.
633    
634  The I<$message> parameter is used if the open fails. If it is set to C<0>, then  =back
 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.  
635    
636      Could not open "/usr/spool/news/twitlog"  =cut
637    
638  Note that the mode characters are automatically cleaned from the file name.  sub Confess {
639  The actual error message from the file system will be captured and appended to the      # Get the parameters.
640  message in any case.      my ($message) = @_;
641        # Set up the category and level.
642        $LastCategory = "(confess)";
643        $LastLevel = 0;
644        if (! defined($FIG_Config::no_tool_hdr)) {
645            # Here we have a tool header. Display its length so that the user can adjust the line numbers.
646            my $toolHeaderFile = "$FIG_Config::fig_disk/dist/releases/current/$FIG_Config::arch/tool_hdr";
647            # Only proceed if the tool header file is actually present.
648            if (-f $toolHeaderFile) {
649                my $fh;
650                if (open $fh, "<$toolHeaderFile") {
651                    my @lines = <$fh>;
652                    Trace("Tool header has " . scalar(@lines) . " lines.");
653                }
654            }
655        }
656        # Trace the call stack.
657        Cluck($message);
658        # Abort the program.
659        croak(">>> $message");
660    }
661    
662      Could not open "/usr/spool/news/twitlog": file not found.  =head3 Warn
663    
664  In some versions of PERL the only error message we get is a number, which      Warn($message);
 corresponds to the C++ C<errno> value.  
665    
666      Could not open "/usr/spool/news/twitlog": 6.  This method traces an important message. If an RSS feed is configured
667    (via I<FIG_Config::error_feed>) and the tracing destination is C<WARN>,
668    then the message will be echoed to the feed. In general, a tracing
669    destination of C<WARN> indicates that the caller is running as a web
670    service in a production environment; however, this is not a requirement.
671    
672    The L</Cluck> method calls this one for its final message. Since
673    L</Confess> calls L</Cluck>, this means that any error which is caught
674    and confessed will put something in the feed. This insures that someone
675    will be alerted relatively quickly when a failure occurs.
676    
677  =over 4  =over 4
678    
679  =item fileHandle  =item message
680    
681  File handle. If this parameter is C<undef>, a file handle will be generated  Message to be traced.
 and returned as the value of this method.  
682    
683  =item fileSpec  =back
684    
685  File name and mode, as per the PERL C<open> function.  =cut
686    
687  =item message (optional)  sub Warn {
688        # Get the parameters.
689        my ($message) = @_;
690        # Trace the message.
691        Trace($message);
692        # An error here would be disastrous. Note, however, that we aren't too worried
693        # about losing events. The error log is always available for the occasions where
694        # we mess up.
695        eval {
696            # Do we need to put this in the RSS feed?
697            if ($FIG_Config::error_feed && $Destination eq 'WARN') {
698                # Yes. We now need to compute the date, the link, and the title.
699                # First, the date, in a very specific format.
700                my $date = strftime("%a, %02e %b %H:%M:%S %Y ", localtime) .
701                    (tz_local_offset() / 30);
702                # We'll put the link and title in here.
703                my ($link, $title);
704                # Environment data goes in here.
705                my $environment;
706                # HTML-escape the message.
707                my $escaped = CGI::escapeHTML($message);
708                # If we have a CGI object, then this is a web error. Otherwise, it's
709                # command-line.
710                if (defined $SavedCGI) {
711                    # We're in a web service. The title is the user's IP, and the link
712                    # is the URL that got us here.
713                    my $key = $ENV{HTTP_X_FORWARDED_FOR} || $ENV{REMOTE_ADDR};
714                    $title = "Event Reported at IP address $key: $escaped";
715                    $link = $SavedCGI->url(-full => 1, -query => 1);
716                    # We need the user agent string.
717                    $environment = "User Agent $ENV{HTTP_USER_AGENT}."
718                } else {
719                    # No CGI object, so we're a command-line tool. Use the tracing
720                    # key and the PID as the user identifier.
721                    my $key = EmergencyKey();
722                    $title = "Event Reported by $key Process $$: $escaped";
723                    # Set the link to the development NMPDR. There is really no good
724                    # choice here.
725                    $link = "http://$FIG_Config::dev_server";
726                    # We need the command
727                    $environment = "Command $ENV{_}.";
728                }
729                # Build a GUID. We use the current time, the title, and the process ID,
730                # then digest the result.
731                my $guid = Digest::MD5::md5_base64(gettimeofday(), $title, $$);
732                # Finally, the description. This is a stack trace plus various environmental stuff.
733                my @trace = LongMess();
734                my $trace = join "; ", @trace;
735                my $description = CGI::escapeHTML("$environment Stack trace: $trace");
736                # Okay, we have all the pieces. Create a hash of the new event.
737                my $newItem = { title => $title,
738                                description => $description,
739                                link => $link,
740                                category => $LastCategory,
741                                pubDate => $date,
742                                guid => $guid,
743                               };
744                # We need XML capability for this.
745                require XML::Simple;
746                # The RSS document goes in here.
747                my $rss;
748                # Get the name of the RSS file. It's in the FIG temporary directory.
749                my $fileName = "$FIG_Config::temp/$FIG_Config::error_feed";
750                # Does it exist?
751                if (-s $fileName) {
752                    # Slurp it in.
753                    $rss = XML::Simple::XMLin($fileName, ForceArray => ['item']);
754                } else {
755                    my $size = -s $fileName;
756                    # Create an empty channel.
757                    $rss = {
758                        channel => {
759                            title => 'NMPDR Warning Feed',
760                            link => "$FIG_Config::temp_url/$FIG_Config::error_feed",
761                            description => "Important messages regarding the status of the NMPDR.",
762                            generator => "NMPDR Trace Facility",
763                            docs => "http://blogs.law.harvard.edu/tech/rss",
764                            item => []
765                        },
766                    };
767                }
768                # Get the channel object.
769                my $channel = $rss->{channel};
770                # Update the last-build date.
771                $channel->{lastBuildDate} = $date;
772                # Get the item array.
773                my $items = $channel->{item};
774                # Insure it has only 100 entries.
775                while (scalar @{$items} > 100) {
776                    pop @{$items};
777                }
778                # Add our new item at the front.
779                unshift @{$items}, $newItem;
780                # Replace the file.
781                my $xml = XML::Simple::XMLout($rss, NoAttr => 1, RootName => 'rss', XmlDecl => '<?xml version="1.0" encoding="utf-8"?>',
782                                              NoEscape => 1);
783                # We don't use Open here because we can't afford an error.
784                if (open XMLOUT, ">$fileName") {
785                    print XMLOUT $xml;
786                    close XMLOUT;
787                }
788            }
789        };
790        # There's no "if ($@)" here, because putting an error message in the log
791        # saying that we missed putting an error message in the feed of messages
792        # in the log is not going to help anybody.
793    }
794    
795  Error message to use if the open fails. If omitted, a standard error message  =head3 Assert
 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>.  
796    
797  =item RETURN      Assert($condition1, $condition2, ... $conditionN);
798    
799  Returns the name of the file handle assigned to the file, or C<undef> if the  Return TRUE if all the conditions are true. This method can be used in conjunction with
800  open failed.  the OR operator and the L</Confess> method as a debugging assert.
801    So, for example
802    
803  =back      Assert($recNum >= 0) || Confess("Invalid record number $recNum.");
804    
805  =cut  Will abort the program with a stack trace if the value of C<$recNum> is negative.
806    
807  sub Open {  =cut
808      # Get the parameters.  sub Assert {
809      my ($fileHandle, $fileSpec, $message) = @_;      my $retVal = 1;
810      # Attempt to open the file.      LOOP: for my $condition (@_) {
811      my $rv = open $fileHandle, $fileSpec;          if (! $condition) {
812      # If the open failed, generate an error message.              $retVal = 0;
813      if (! $rv) {              last LOOP;
         # Save the system error message.  
         my $sysMessage = $!;  
         # See if we need a default message.  
         if (!$message) {  
             # Clean any obvious mode characters and leading spaces from the  
             # filename.  
             my ($fileName) = FindNamePart($fileSpec);  
             $message = "Could not open \"$fileName\"";  
814          }          }
         # Terminate with an error using the supplied message and the  
         # error message from the file system.  
         Confess("$message: $!");  
815      }      }
816      # Return the file handle.      return $retVal;
     return $fileHandle;  
817  }  }
818    
819  =head3 FindNamePart  =head3 Cluck
   
 C<< my ($fileName, $start, $len) = Tracer::FindNamePart($fileSpec); >>  
820    
821  Extract the portion of a file specification that contains the file name.      Cluck($message);
822    
823  A file specification is the string passed to an C<open> call. It specifies the file  Trace the call stack. Note that for best results, you should qualify the call with a
824  mode and name. In a truly complex situation, it can specify a pipe sequence. This  trace condition. For example,
 method assumes that the file name is whatever follows the first angle bracket  
 sequence.  So, for example, in the following strings the file name is  
 C</usr/fig/myfile.txt>.  
825    
826      >>/usr/fig/myfile.txt      Cluck("Starting record parse.") if T(3);
     </usr/fig/myfile.txt  
     | sort -u > /usr/fig/myfile.txt  
827    
828  If the method cannot find a file name using its normal methods, it will return the  will only trace the stack if the trace level for the package is 3 or more.
 whole incoming string.  
829    
830  =over 4  =over 4
831    
832  =item fileSpec  =item message
833    
834  File specification string from which the file name is to be extracted.  Message to include in the trace.
835    
836    =back
837    
838    =cut
839    
840    sub Cluck {
841        # Get the parameters.
842        my ($message) = @_;
843        # Trace what's happening.
844        Trace("Stack trace for event: $message");
845        # Get the stack trace.
846        my @trace = LongMess();
847        # Convert the trace to a series of messages.
848        for my $line (@trace) {
849            # Replace the tab at the beginning with spaces.
850            $line =~ s/^\t/    /;
851            # Trace the line.
852            Trace($line);
853        }
854        # Issue a warning. This displays the event message and inserts it into the RSS error feed.
855        Warn($message);
856    }
857    
858    =head3 LongMess
859    
860        my @lines = Tracer::LongMess();
861    
862    Return a stack trace with all tracing methods removed. The return will be in the form of a list
863    of message strings.
864    
865    =cut
866    
867    sub LongMess {
868        # Declare the return variable.
869        my @retVal = ();
870        my $confession = longmess("");
871        for my $line (split /\s*\n/, $confession) {
872            unless ($line =~ /Tracer\.pm/) {
873                # Here we have a line worth keeping. Push it onto the result list.
874                push @retVal, $line;
875            }
876        }
877        # Return the result.
878        return @retVal;
879    }
880    
881    =head3 ScriptSetup (deprecated)
882    
883        my ($cgi, $varHash) = ScriptSetup($noTrace);
884    
885    Perform standard tracing and debugging setup for scripts. The value returned is
886    the CGI object followed by a pre-built variable hash. At the end of the script,
887    the client should call L</ScriptFinish> to output the web page.
888    
889    This method calls L</ETracing> to configure tracing, which allows the tracing
890    to be configured via the emergency tracing form on the debugging control panel.
891    Tracing will then be turned on automatically for all programs that use the L</ETracing>
892    method, which includes every program that uses this method or L</StandardSetup>.
893    
894    =over 4
895    
896    =item noTrace (optional)
897    
898    If specified, tracing will be suppressed. This is useful if the script wants to set up
899    tracing manually.
900    
901  =item RETURN  =item RETURN
902    
903  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
904  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.  
905    
906  =back  =back
907    
908  =cut  =cut
909  #: Return Type $;  
910  sub FindNamePart {  sub ScriptSetup {
911      # Get the parameters.      # Get the parameters.
912      my ($fileSpec) = @_;      my ($noTrace) = @_;
913      # Default to the whole input string.      # Get the CGI query object.
914      my ($retVal, $pos, $len) = ($fileSpec, 0, length $fileSpec);      my $cgi = CGI->new();
915      # Parse out the file name if we can.      # Set up tracing if it's not suppressed.
916      if ($fileSpec =~ m/(<|>>?)(.+?)(\s*)$/) {      ETracing($cgi) unless $noTrace;
917          $retVal = $2;      # Create the variable hash.
918          $len = length $retVal;      my $varHash = { results => '' };
919          $pos = (length $fileSpec) - (length $3) - $len;      # Return the query object and variable hash.
920        return ($cgi, $varHash);
921    }
922    
923    =head3 ETracing
924    
925        ETracing($parameter);
926    
927    Set up emergency tracing. Emergency tracing is tracing that is turned
928    on automatically for any program that calls this method. The emergency
929    tracing parameters are stored in a a file identified by a tracing key.
930    If this method is called with a CGI object, then the tracing key is
931    taken from a cookie. If it is called with no parameters, then the tracing
932    key is taken from an environment variable. If it is called with a string,
933    the tracing key is that string.
934    
935    =over 4
936    
937    =item parameter
938    
939    A parameter from which the tracing key is computed. If it is a scalar,
940    that scalar is used as the tracing key. If it is a CGI object, the
941    tracing key is taken from the C<IP> cookie. If it is omitted, the
942    tracing key is taken from the C<TRACING> environment variable. If it
943    is a CGI object and emergency tracing is not on, the C<Trace> and
944    C<TF> parameters will be used to determine the type of tracing.
945    
946    =back
947    
948    =cut
949    
950    sub ETracing {
951        # Get the parameter.
952        my ($parameter) = @_;
953        # Check for CGI mode.
954        if (defined $parameter && ref $parameter eq 'CGI') {
955            $SavedCGI = $parameter;
956        } else {
957            $SavedCGI = undef;
958        }
959        # Default to no tracing except errors.
960        my ($tracing, $dest) = ("0", "WARN");
961        # Check for emergency tracing.
962        my $tkey = EmergencyKey($parameter);
963        my $emergencyFile = EmergencyFileName($tkey);
964        if (-e $emergencyFile) {
965            # We have the file. Read in the data.
966            my @tracing = GetFile($emergencyFile);
967            # Pull off the time limit.
968            my $expire = shift @tracing;
969            # Convert it to seconds.
970            $expire *= 3600;
971            # Check the file data.
972            my $stat = stat($emergencyFile);
973            my ($now) = gettimeofday;
974            if ($now - $stat->mtime > $expire) {
975                # Delete the expired file.
976                unlink $emergencyFile;
977            } else {
978                # Emergency tracing is on. Pull off the destination and
979                # the trace level;
980                $dest = shift @tracing;
981                my $level = shift @tracing;
982                # Convert the destination to a real tracing destination.
983                # temp directory.
984                $dest = EmergencyTracingDest($tkey, $dest);
985                # Insure Tracer is specified.
986                my %moduleHash = map { $_ => 1 } @tracing;
987                $moduleHash{Tracer} = 1;
988                # Set the trace parameter.
989                $tracing = join(" ", $level, sort keys %moduleHash);
990            }
991        } elsif (defined $SavedCGI) {
992            # There's no emergency tracing, but we have a CGI object, so check
993            # for tracing from the form parameters.
994            if ($SavedCGI->param('Trace')) {
995                # Here the user has requested tracing via a form.
996                $dest = ($SavedCGI->param('TF') ? ">$FIG_Config::temp/Trace$$.log" : "QUEUE");
997                $tracing = $SavedCGI->param('Trace') . " Tracer";
998            }
999        }
1000        # Setup the tracing we've determined from all the stuff above.
1001        TSetup($tracing, $dest);
1002        # Check to see if we're a web script.
1003        if (defined $SavedCGI) {
1004            # Yes we are. Trace the form and environment data.
1005            TraceParms($SavedCGI);
1006            # Check for RAW mode. In raw mode, we print a fake header so that we see everything
1007            # emitted by the script in its raw form.
1008            if (T(Raw => 3)) {
1009                print CGI::header(-type => 'text/plain', -tracing => 'Raw');
1010            }
1011      }      }
     # Return the result.  
     return ($retVal, $pos, $len);  
1012  }  }
1013    
1014  =head3 OpenDir  =head3 EmergencyFileName
1015    
1016  C<< my @files = OpenDir($dirName, $filtered, $flag); >>      my $fileName = Tracer::EmergencyFileName($tkey);
1017    
1018  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
1019  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,  
1020    
1021      my @files = OpenDir("/Volumes/fig/contigs", 1);  =over 4
1022    
1023  is effectively the same as  =item tkey
1024    
1025      opendir(TMP, "/Volumes/fig/contigs") || Confess("Could not open /Volumes/fig/contigs.");  Tracing key for the current program.
     my @files = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir(TMP);  
1026    
1027  Similarly, the following code  =item RETURN
1028    
1029      my @files = grep { $_ =~ /^\d/ } OpenDir("/Volumes/fig/orgs", 0, 1);  Returns the name of the file to contain the emergency tracing information.
1030    
1031  Returns the names of all files in C</Volumes/fig/orgs> that begin with digits and  =back
1032  automatically returns an empty list if the directory fails to open.  
1033    =cut
1034    
1035    sub EmergencyFileName {
1036        # Get the parameters.
1037        my ($tkey) = @_;
1038        # Compute the emergency tracing file name.
1039        return "$FIG_Config::temp/Emergency$tkey.txt";
1040    }
1041    
1042    =head3 EmergencyFileTarget
1043    
1044        my $fileName = Tracer::EmergencyFileTarget($tkey);
1045    
1046    Return the emergency tracing target file name. This is the file that receives
1047    the tracing output for file-based tracing.
1048    
1049  =over 4  =over 4
1050    
1051  =item dirName  =item tkey
1052    
1053  Name of the directory to open.  Tracing key for the current program.
1054    
1055  =item filtered  =item RETURN
1056    
1057  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.  
1058    
1059  =item flag  =back
1060    
1061  TRUE if a failure to open is okay, else FALSE  =cut
1062    
1063    sub EmergencyFileTarget {
1064        # Get the parameters.
1065        my ($tkey) = @_;
1066        # Compute the emergency tracing file name.
1067        return "$FIG_Config::temp/trace$tkey.log";
1068    }
1069    
1070    =head3 EmergencyTracingDest
1071    
1072        my $dest = Tracer::EmergencyTracingDest($tkey, $myDest);
1073    
1074    This method converts an emergency tracing destination to a real
1075    tracing destination. The main difference is that if the
1076    destination is C<FILE> or C<APPEND>, we convert it to file
1077    output. If the destination is C<DUAL>, we convert it to file
1078    and standard output.
1079    
1080    =over 4
1081    
1082    =item tkey
1083    
1084    Tracing key for this environment.
1085    
1086    =item myDest
1087    
1088    Destination from the emergency tracing file.
1089    
1090    =item RETURN
1091    
1092    Returns a destination that can be passed into L</TSetup>.
1093    
1094  =back  =back
1095    
1096  =cut  =cut
1097  #: Return Type @;  
1098  sub OpenDir {  sub EmergencyTracingDest {
1099      # Get the parameters.      # Get the parameters.
1100      my ($dirName, $filtered, $flag) = @_;      my ($tkey, $myDest) = @_;
1101      # Declare the return variable.      # Declare the return variable.
1102      my @retVal = ();      my $retVal = $myDest;
1103      # Open the directory.      # Process according to the destination value.
1104      if (opendir(my $dirHandle, $dirName)) {      if ($myDest eq 'FILE') {
1105          # The directory opened successfully. Get the appropriate list according to the          $retVal = ">" . EmergencyFileTarget($tkey);
1106          # strictures of the filter parameter.      } elsif ($myDest eq 'APPEND') {
1107          if ($filtered) {          $retVal = ">>" . EmergencyFileTarget($tkey);
1108              @retVal = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir $dirHandle;      } elsif ($myDest eq 'DUAL') {
1109          } else {          $retVal = "+>" . EmergencyFileTarget($tkey);
1110              @retVal = readdir $dirHandle;      } elsif ($myDest eq 'WARN') {
1111          }          $retVal = "WARN";
     } elsif (! $flag) {  
         # Here the directory would not open and it's considered an error.  
         Confess("Could not open directory $dirName.");  
1112      }      }
1113      # Return the result.      # Return the result.
1114      return @retVal;      return $retVal;
1115  }  }
1116    
1117  =head3 SetLevel  =head3 Emergency
1118    
1119  C<< Tracer::SetLevel($newLevel); >>      Emergency($key, $hours, $dest, $level, @modules);
1120    
1121  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
1122    a debugging console, but it can also be called by the C<trace.pl> script.
1123    The caller specifies the duration of the emergency in hours, the desired tracing
1124    destination, the trace level, and a list of the trace modules to activate.
1125    For the length of the duration, when a program in an environment with the
1126    specified tracing key active invokes a Sprout CGI script, tracing will be
1127    turned on automatically. See L</TSetup> for more about tracing setup and
1128    L</ETracing> for more about emergency tracing.
1129    
1130  =over 4  =over 4
1131    
1132  =item newLevel  =item tkey
1133    
1134  Proposed new trace level.  The tracing key. This is used to identify the control file and the trace file.
1135    
1136    =item hours
1137    
1138    Number of hours to keep emergency tracing alive.
1139    
1140    =item dest
1141    
1142    Tracing destination. If no path information is specified for a file
1143    destination, it is put in the FIG temporary directory.
1144    
1145    =item level
1146    
1147    Tracing level. A higher level means more trace messages.
1148    
1149    =item modules
1150    
1151    A list of the tracing modules to activate.
1152    
1153  =back  =back
1154    
1155  =cut  =cut
1156    
1157  sub SetLevel {  sub Emergency {
1158      $TraceLevel = $_[0];      # Get the parameters.
1159        my ($tkey, $hours, $dest, $level, @modules) = @_;
1160        # Create the emergency file.
1161        my $specFile = EmergencyFileName($tkey);
1162        my $outHandle = Open(undef, ">$specFile");
1163        print $outHandle join("\n", $hours, $dest, $level, @modules, "");
1164  }  }
1165    
1166  =head3 Now  =head3 EmergencyKey
1167    
1168        my $tkey = EmergencyKey($parameter);
1169    
1170    Return the Key to be used for emergency tracing. This could be an IP address,
1171     a session ID, or a user name, depending on the environment.
1172    
1173  C<< my $string = Tracer::Now(); >>  =over 4
1174    
1175    =item parameter
1176    
1177    Parameter defining the method for finding the tracing key. If it is a scalar,
1178    then it is presumed to be the tracing key itself. If it is a CGI object, then
1179    the tracing key is taken from the C<IP> cookie. Otherwise, the tracing key is
1180    taken from the C<TRACING> environment variable.
1181    
1182    =item RETURN
1183    
1184    Returns the key to be used for labels in emergency tracing.
1185    
1186  Return a displayable time stamp containing the local time.  =back
1187    
1188  =cut  =cut
1189    
1190  sub Now {  sub EmergencyKey {
1191      my ($sec,$min,$hour,$mday,$mon,$year,$wday,$yday,$isdst) = localtime(time);      # Get the parameters.
1192      my $retVal = _p2($mon+1) . "/" . _p2($mday) . "/" . ($year + 1900) . " " .      my ($parameter) = @_;
1193                   _p2($hour) . ":" . _p2($min) . ":" . _p2($sec);      # Declare the return variable.
1194        my $retVal;
1195        # Determine the parameter type.
1196        if (! defined $parameter) {
1197            # Here we're supposed to check the environment. If that fails, we
1198            # get the effective login ID.
1199            $retVal = $ENV{TRACING} || scalar getpwuid($<);
1200        } else {
1201            my $ptype = ref $parameter;
1202            if ($ptype eq 'CGI') {
1203                # Here we were invoked from a web page. Look for a cookie.
1204                $retVal = $parameter->cookie('IP');
1205            } elsif (! $ptype) {
1206                # Here the key was passed in.
1207                $retVal = $parameter;
1208            }
1209        }
1210        # If no luck finding a key, use the PID.
1211        if (! defined $retVal) {
1212            $retVal = $$;
1213        }
1214        # Return the result.
1215      return $retVal;      return $retVal;
1216  }  }
1217    
1218  # Pad a number to 2 digits.  
1219  sub _p2 {  =head3 TraceParms
1220      my ($value) = @_;  
1221      $value = "0$value" if ($value < 10);      Tracer::TraceParms($cgi);
1222      return $value;  
1223    Trace the CGI parameters at trace level CGI => 3 and the environment variables
1224    at level CGI => 4. A self-referencing URL is traced at level CGI => 2.
1225    
1226    =over 4
1227    
1228    =item cgi
1229    
1230    CGI query object containing the parameters to trace.
1231    
1232    =back
1233    
1234    =cut
1235    
1236    sub TraceParms {
1237        # Get the parameters.
1238        my ($cgi) = @_;
1239        if (T(CGI => 2)) {
1240            # Here we trace the GET-style URL for the script.
1241            Trace("[URL] " . $cgi->url(-relative => 1, -query => 1));
1242        }
1243        if (T(CGI => 3)) {
1244            # Here we want to trace the parameter data.
1245            my @names = $cgi->param;
1246            for my $parmName (sort @names) {
1247                # Note we skip the Trace parameters, which are for our use only.
1248                if ($parmName ne 'Trace' && $parmName ne 'TF') {
1249                    my @values = $cgi->param($parmName);
1250                    Trace("[CGI] $parmName = " . join(", ", @values));
1251                }
1252            }
1253            # Display the request method.
1254            my $method = $cgi->request_method();
1255            Trace("Method: $method");
1256        }
1257        if (T(CGI => 4)) {
1258            # Here we want the environment data too.
1259            for my $envName (sort keys %ENV) {
1260                Trace("[ENV] $envName = $ENV{$envName}");
1261            }
1262        }
1263    }
1264    
1265    =head3 TraceImages
1266    
1267        Tracer::TraceImages($htmlString);
1268    
1269    Trace information about all of an html document's images. The tracing
1270    will be for type "IMG" at level 3. The image's source string
1271    will be displayed. This is generally either the URL of the image or
1272    raw data for the image itself. If the source is too long, only the first 300
1273    characters will be shown at trace level 3. The entire source will be shown,
1274    however, at trace level 4. This method is not very smart, and might catch
1275    Javascript code, but it is still useful when debugging the arcane
1276    behavior of images in multiple browser environments.
1277    
1278    =over 4
1279    
1280    =item htmlString
1281    
1282    HTML text for an outgoing web page.
1283    
1284    =back
1285    
1286    =cut
1287    
1288    sub TraceImages {
1289        # Only proceed if we're at the proper trace level.
1290        if (T(IMG => 3)) {
1291            # For performance reasons we're manipulating $_[0] instead of retrieving the string
1292            # into a variable called "$htmlString". This is because we expect html strings to be
1293            # long, and don't want to copy them any more than we have to.
1294            Trace(length($_[0]) . " characters in web page.");
1295            # Loop through the HTML, culling image tags.
1296            while ($_[0] =~ /<img\s+[^>]+?src="([^"]+)"/sgi) {
1297                # Extract the source string and determine whether or not it's too long.
1298                my $srcString = $1;
1299                my $pos = pos($_[0]) - length($srcString);
1300                my $excess = length($srcString) - 300;
1301                # We'll put the display string in here.
1302                my $srcDisplay = $srcString;
1303                # If it's a data string, split it at the comma.
1304                $srcDisplay =~ s/^(data[^,]+,)/$1\n/;
1305                # If there's no excess or we're at trace level 4, we're done. At level 3 with
1306                # a long string, however, we only show the first 300 characters.
1307                if ($excess > 0 && ! T(IMG => 4)) {
1308                    $srcDisplay = substr($srcDisplay,0,300) . "\nplus $excess characters.";
1309                }
1310                # Output the trace message.
1311                Trace("Image tag at position $pos:\n$srcDisplay");
1312            }
1313        }
1314    }
1315    
1316    
1317    =head3 ScriptFinish (deprecated)
1318    
1319        ScriptFinish($webData, $varHash);
1320    
1321    Output a web page at the end of a script. Either the string to be output or the
1322    name of a template file can be specified. If the second parameter is omitted,
1323    it is assumed we have a string to be output; otherwise, it is assumed we have the
1324    name of a template file. The template should have the variable C<DebugData>
1325    specified in any form that invokes a standard script. If debugging mode is turned
1326    on, a form field will be put in that allows the user to enter tracing data.
1327    Trace messages will be placed immediately before the terminal C<BODY> tag in
1328    the output, formatted as a list.
1329    
1330    A typical standard script would loook like the following.
1331    
1332        BEGIN {
1333            # Print the HTML header.
1334            print "CONTENT-TYPE: text/html\n\n";
1335        }
1336        use Tracer;
1337        use CGI;
1338        use FIG;
1339        # ... more uses ...
1340    
1341        my ($cgi, $varHash) = ScriptSetup();
1342        eval {
1343            # ... get data from $cgi, put it in $varHash ...
1344        };
1345        if ($@) {
1346            Trace("Script Error: $@") if T(0);
1347        }
1348        ScriptFinish("Html/MyTemplate.html", $varHash);
1349    
1350    The idea here is that even if the script fails, you'll see trace messages and
1351    useful output.
1352    
1353    =over 4
1354    
1355    =item webData
1356    
1357    A string containing either the full web page to be written to the output or the
1358    name of a template file from which the page is to be constructed. If the name
1359    of a template file is specified, then the second parameter must be present;
1360    otherwise, it must be absent.
1361    
1362    =item varHash (optional)
1363    
1364    If specified, then a reference to a hash mapping variable names for a template
1365    to their values. The template file will be read into memory, and variable markers
1366    will be replaced by data in this hash reference.
1367    
1368    =back
1369    
1370    =cut
1371    
1372    sub ScriptFinish {
1373        # Get the parameters.
1374        my ($webData, $varHash) = @_;
1375        # Check for a template file situation.
1376        my $outputString;
1377        if (defined $varHash) {
1378            # Here we have a template file. We need to determine the template type.
1379            my $template;
1380            if ($FIG_Config::template_url && $webData =~ /\.php$/) {
1381                $template = "$FIG_Config::template_url/$webData";
1382            } else {
1383                $template = "<<$webData";
1384            }
1385            $outputString = PageBuilder::Build($template, $varHash, "Html");
1386        } else {
1387            # Here the user gave us a raw string.
1388            $outputString = $webData;
1389        }
1390        # Check for trace messages.
1391        if ($Destination ne "NONE" && $TraceLevel > 0) {
1392            # We have trace messages, so we want to put them at the end of the body. This
1393            # is either at the end of the whole string or at the beginning of the BODY
1394            # end-tag.
1395            my $pos = length $outputString;
1396            if ($outputString =~ m#</body>#gi) {
1397                $pos = (pos $outputString) - 7;
1398            }
1399            # If the trace messages were queued, we unroll them. Otherwise, we display the
1400            # destination.
1401            my $traceHtml;
1402            if ($Destination eq "QUEUE") {
1403                $traceHtml = QTrace('Html');
1404            } elsif ($Destination =~ /^>>(.+)$/) {
1405                # Here the tracing output it to a file. We code it as a hyperlink so the user
1406                # can copy the file name into the clipboard easily.
1407                my $actualDest = $1;
1408                $traceHtml = "<p>Tracing output to $actualDest.</p>\n";
1409            } else {
1410                # Here we have one of the special destinations.
1411                $traceHtml = "<P>Tracing output type is $Destination.</p>\n";
1412            }
1413            substr $outputString, $pos, 0, $traceHtml;
1414        }
1415        # Write the output string.
1416        print $outputString;
1417    }
1418    
1419    =head2 Command-Line Utility Methods
1420    
1421    =head3 SendSMS
1422    
1423        my $msgID = Tracer::SendSMS($phoneNumber, $msg);
1424    
1425    Send a text message to a phone number using Clickatell. The FIG_Config file must contain the
1426    user name, password, and API ID for the relevant account in the hash reference variable
1427    I<$FIG_Config::phone>, using the keys C<user>, C<password>, and C<api_id>. For
1428    example, if the user name is C<BruceTheHumanPet>, the password is C<silly>, and the API ID
1429    is C<2561022>, then the FIG_Config file must contain
1430    
1431        $phone =  { user => 'BruceTheHumanPet',
1432                    password => 'silly',
1433                    api_id => '2561022' };
1434    
1435    The original purpose of this method was to insure Bruce would be notified immediately when the
1436    Sprout Load terminates. Care should be taken if you do not wish Bruce to be notified immediately
1437    when you call this method.
1438    
1439    The message ID will be returned if successful, and C<undef> if an error occurs.
1440    
1441    =over 4
1442    
1443    =item phoneNumber
1444    
1445    Phone number to receive the message, in international format. A United States phone number
1446    would be prefixed by "1". A British phone number would be prefixed by "44".
1447    
1448    =item msg
1449    
1450    Message to send to the specified phone.
1451    
1452    =item RETURN
1453    
1454    Returns the message ID if successful, and C<undef> if the message could not be sent.
1455    
1456    =back
1457    
1458    =cut
1459    
1460    sub SendSMS {
1461        # Get the parameters.
1462        my ($phoneNumber, $msg) = @_;
1463        # Declare the return variable. If we do not change it, C<undef> will be returned.
1464        my $retVal;
1465        # Only proceed if we have phone support.
1466        if (! defined $FIG_Config::phone) {
1467            Trace("Phone support not present in FIG_Config.") if T(1);
1468        } else {
1469            # Get the phone data.
1470            my $parms = $FIG_Config::phone;
1471            # Get the Clickatell URL.
1472            my $url = "http://api.clickatell.com/http/";
1473            # Create the user agent.
1474            my $ua = LWP::UserAgent->new;
1475            # Request a Clickatell session.
1476            my $resp = $ua->post("$url/sendmsg", { user => $parms->{user},
1477                                         password => $parms->{password},
1478                                         api_id => $parms->{api_id},
1479                                         to => $phoneNumber,
1480                                         text => $msg});
1481            # Check for an error.
1482            if (! $resp->is_success) {
1483                Trace("Alert failed.") if T(1);
1484            } else {
1485                # Get the message ID.
1486                my $rstring = $resp->content;
1487                if ($rstring =~ /^ID:\s+(.*)$/) {
1488                    $retVal = $1;
1489                } else {
1490                    Trace("Phone attempt failed with $rstring") if T(1);
1491                }
1492            }
1493        }
1494        # Return the result.
1495        return $retVal;
1496    }
1497    
1498    =head3 StandardSetup
1499    
1500        my ($options, @parameters) = StandardSetup(\@categories, \%options, $parmHelp, @ARGV);
1501    
1502    This method performs standard command-line parsing and tracing setup. The return
1503    values are a hash of the command-line options and a list of the positional
1504    parameters. Tracing is automatically set up and the command-line options are
1505    validated.
1506    
1507    This is a complex method that does a lot of grunt work. The parameters can
1508    be more easily understood, however, once they are examined individually.
1509    
1510    The I<categories> parameter is the most obtuse. It is a reference to a list of
1511    special-purpose tracing categories. Most tracing categories are PERL package
1512    names. So, for example, if you wanted to turn on tracing inside the B<Sprout>,
1513    B<ERDB>, and B<SproutLoad> packages, you would specify the categories
1514    
1515        ["Sprout", "SproutLoad", "ERDB"]
1516    
1517    This would cause trace messages in the specified three packages to appear in
1518    the output. There are two special tracing categories that are automatically
1519    handled by this method. In other words, if you used L</TSetup> you would need
1520    to include these categories manually, but if you use this method they are turned
1521    on automatically.
1522    
1523    =over 4
1524    
1525    =item SQL
1526    
1527    Traces SQL commands and activity.
1528    
1529    =item Tracer
1530    
1531    Traces error messages and call stacks.
1532    
1533    =back
1534    
1535    C<SQL> is only turned on if the C<-sql> option is specified in the command line.
1536    The trace level is specified using the C<-trace> command-line option. For example,
1537    the following command line for C<TransactFeatures> turns on SQL tracing and runs
1538    all tracing at level 3.
1539    
1540        TransactFeatures -trace=3 -sql register ../xacts IDs.tbl
1541    
1542    Standard tracing is output to the standard output and echoed to the file
1543    C<trace>I<$$>C<.log> in the FIG temporary directory, where I<$$> is the
1544    process ID. You can also specify the C<user> parameter to put a user ID
1545    instead of a process ID in the trace file name. So, for example
1546    
1547    The default trace level is 2. To get all messages, specify a trace level of 4.
1548    For a genome-by-genome update, use 3.
1549    
1550        TransactFeatures -trace=3 -sql -user=Bruce register ../xacts IDs.tbl
1551    
1552    would send the trace output to C<traceBruce.log> in the temporary directory.
1553    
1554    The I<options> parameter is a reference to a hash containing the command-line
1555    options, their default values, and an explanation of what they mean. Command-line
1556    options may be in the form of switches or keywords. In the case of a switch, the
1557    option value is 1 if it is specified and 0 if it is not specified. In the case
1558    of a keyword, the value is separated from the option name by an equal sign. You
1559    can see this last in the command-line example above.
1560    
1561    You can specify a different default trace level by setting C<$options->{trace}>
1562    prior to calling this method.
1563    
1564    An example at this point would help. Consider, for example, the command-line utility
1565    C<TransactFeatures>. It accepts a list of positional parameters plus the options
1566    C<safe>, C<noAlias>, C<start>, and C<tblFiles>. To start up this command, we execute
1567    the following code.
1568    
1569        my ($options, @parameters) = Tracer::StandardSetup(["DocUtils"],
1570                            { safe => [0, "use database transactions"],
1571                              noAlias => [0, "do not expect aliases in CHANGE transactions"],
1572                              start => [' ', "start with this genome"],
1573                              tblFiles => [0, "output TBL files containing the corrected IDs"] },
1574                            "<command> <transactionDirectory> <IDfile>",
1575                          @ARGV);
1576    
1577    
1578    The call to C<ParseCommand> specifies the default values for the options and
1579    stores the actual options in a hash that is returned as C<$options>. The
1580    positional parameters are returned in C<@parameters>.
1581    
1582    The following is a sample command line for C<TransactFeatures>.
1583    
1584        TransactFeatures -trace=2 -noAlias register ../xacts IDs.tbl
1585    
1586    Single and double hyphens are equivalent. So, you could also code the
1587    above command as
1588    
1589        TransactFeatures --trace=2 --noAlias register ../xacts IDs.tbl
1590    
1591    In this case, C<register>, C<../xacts>, and C<IDs.tbl> are the positional
1592    parameters, and would find themselves in I<@parameters> after executing the
1593    above code fragment. The tracing would be set to level 2, and the categories
1594    would be C<Tracer>, and <DocUtils>. C<Tracer> is standard,
1595    and C<DocUtils> was included because it came in within the first parameter
1596    to this method. The I<$options> hash would be
1597    
1598        { trace => 2, sql => 0, safe => 0,
1599          noAlias => 1, start => ' ', tblFiles => 0 }
1600    
1601    Use of C<StandardSetup> in this way provides a simple way of performing
1602    standard tracing setup and command-line parsing. Note that the caller is
1603    not even aware of the command-line switches C<-trace> and C<-sql>, which
1604    are used by this method to control the tracing. If additional tracing features
1605    need to be added in the future, they can be processed by this method without
1606    upsetting the command-line utilities.
1607    
1608    If the C<background> option is specified on the command line, then the
1609    standard and error outputs will be directed to files in the temporary
1610    directory, using the same suffix as the trace file. So, if the command
1611    line specified
1612    
1613        -user=Bruce -background
1614    
1615    then the trace output would go to C<traceBruce.log>, the standard output to
1616    C<outBruce.log>, and the error output to C<errBruce.log>. This is designed to
1617    simplify starting a command in the background.
1618    
1619    The user name is also used as the tracing key for L</Emergency Tracing>.
1620    Specifying a value of C<E> for the trace level causes emergency tracing to
1621    be used instead of custom tracing. If the user name is not specified,
1622    the tracing key is taken from the C<Tracing> environment variable. If there
1623    is no value for that variable, the tracing key will be computed from the PID.
1624    
1625    Finally, if the special option C<-help> is specified, the option
1626    names will be traced at level 0 and the program will exit without processing.
1627    This provides a limited help capability. For example, if the user enters
1628    
1629        TransactFeatures -help
1630    
1631    he would see the following output.
1632    
1633        TransactFeatures [options] <command> <transactionDirectory> <IDfile>
1634            -trace    tracing level (default E)
1635            -sql      trace SQL commands
1636            -safe     use database transactions
1637            -noAlias  do not expect aliases in CHANGE transactions
1638            -start    start with this genome
1639            -tblFiles output TBL files containing the corrected IDs
1640    
1641    The caller has the option of modifying the tracing scheme by placing a value
1642    for C<trace> in the incoming options hash. The default value can be overridden,
1643    or the tracing to the standard output can be turned off by suffixing a minus
1644    sign to the trace level. So, for example,
1645    
1646        { trace => [0, "tracing level (default 0)"],
1647           ...
1648    
1649    would set the default trace level to 0 instead of E, while
1650    
1651        { trace => ["2-", "tracing level (default 2)"],
1652           ...
1653    
1654    would set the default to 2, but trace only to the log file, not to the
1655    standard output.
1656    
1657    The parameters to this method are as follows.
1658    
1659    =over 4
1660    
1661    =item categories
1662    
1663    Reference to a list of tracing category names. These should be names of
1664    packages whose internal workings will need to be debugged to get the
1665    command working.
1666    
1667    =item options
1668    
1669    Reference to a hash containing the legal options for the current command mapped
1670    to their default values and descriptions. The user can override the defaults
1671    by specifying the options as command-line switches prefixed by a hyphen.
1672    Tracing-related options may be added to this hash. If the C<-h> option is
1673    specified on the command line, the option descriptions will be used to
1674    explain the options. To turn off tracing to the standard output, add a
1675    minus sign to the value for C<trace> (see above).
1676    
1677    =item parmHelp
1678    
1679    A string that vaguely describes the positional parameters. This is used
1680    if the user specifies the C<-h> option.
1681    
1682    =item argv
1683    
1684    List of command line parameters, including the option switches, which must
1685    precede the positional parameters and be prefixed by a hyphen.
1686    
1687    =item RETURN
1688    
1689    Returns a list. The first element of the list is the reference to a hash that
1690    maps the command-line option switches to their values. These will either be the
1691    default values or overrides specified on the command line. The remaining
1692    elements of the list are the position parameters, in order.
1693    
1694    =back
1695    
1696    =cut
1697    
1698    sub StandardSetup {
1699        # Get the parameters.
1700        my ($categories, $options, $parmHelp, @argv) = @_;
1701        # Get the default tracing key.
1702        my $tkey = EmergencyKey();
1703        # Add the tracing options.
1704        if (! exists $options->{trace}) {
1705            $options->{trace} = ['2', "tracing level (E for emergency tracing)"];
1706        }
1707        $options->{sql} = [0, "turn on SQL tracing"];
1708        $options->{help} = [0, "display command-line options"];
1709        $options->{user} = [$tkey, "tracing key"];
1710        $options->{background} = [0, "spool standard and error output"];
1711        # Create a parsing hash from the options hash. The parsing hash
1712        # contains the default values rather than the default value
1713        # and the description. While we're at it, we'll memorize the
1714        # length of the longest option name.
1715        my $longestName = 0;
1716        my %parseOptions = ();
1717        for my $key (keys %{$options}) {
1718            if (length $key > $longestName) {
1719                $longestName = length $key;
1720            }
1721            $parseOptions{$key} = $options->{$key}->[0];
1722        }
1723        # Parse the command line.
1724        my ($retOptions, @retParameters) = ParseCommand(\%parseOptions, @argv);
1725        # Get the logfile suffix.
1726        my $suffix = $retOptions->{user};
1727        # Check for background mode.
1728        if ($retOptions->{background}) {
1729            my $outFileName = "$FIG_Config::temp/out$suffix.log";
1730            my $errFileName = "$FIG_Config::temp/err$suffix.log";
1731            open STDOUT, ">$outFileName";
1732            open STDERR, ">$errFileName";
1733            # Check for phone support. If we have phone support and a phone number,
1734            # we want to turn it on.
1735            if ($ENV{PHONE} && defined($FIG_Config::phone)) {
1736                $retOptions->{phone} = $ENV{PHONE};
1737            }
1738        }
1739        # Now we want to set up tracing. First, we need to know if the user
1740        # wants emergency tracing.
1741        if ($retOptions->{trace} eq 'E') {
1742            ETracing($retOptions->{user});
1743        } else {
1744            # Here the tracing is controlled from the command line.
1745            my @cats = @{$categories};
1746            if ($retOptions->{sql}) {
1747                push @cats, "SQL";
1748            }
1749            # Add the default categories.
1750            push @cats, "Tracer";
1751            # Next, we create the category string by joining the categories.
1752            my $cats = join(" ", @cats);
1753            # Check to determine whether or not the caller wants to turn off tracing
1754            # to the standard output.
1755            my $traceLevel = $retOptions->{trace};
1756            my $textOKFlag = 1;
1757            if ($traceLevel =~ /^(.)-/) {
1758                $traceLevel = $1;
1759                $textOKFlag = 0;
1760            }
1761            # Now we set up the trace mode.
1762            my $traceMode;
1763            # Verify that we can open a file in the FIG temporary directory.
1764            my $traceFileName = "$FIG_Config::temp/trace$suffix.log";
1765            if (open TESTTRACE, ">$traceFileName") {
1766                # Here we can trace to a file.
1767                $traceMode = ">$traceFileName";
1768                if ($textOKFlag) {
1769                    # Echo to standard output if the text-OK flag is set.
1770                    $traceMode = "+$traceMode";
1771                }
1772                # Close the test file.
1773                close TESTTRACE;
1774            } else {
1775                # Here we can't trace to a file. Complain about this.
1776                warn "Could not open trace file $traceFileName: $!\n";
1777                # We trace to the standard output if it's
1778                # okay, and the error log otherwise.
1779                if ($textOKFlag) {
1780                    $traceMode = "TEXT";
1781                } else {
1782                    $traceMode = "WARN";
1783                }
1784            }
1785            # Now set up the tracing.
1786            TSetup("$traceLevel $cats", $traceMode);
1787        }
1788        # Check for the "help" option. If it is specified, dump the command-line
1789        # options and exit the program.
1790        if ($retOptions->{help}) {
1791            $0 =~ m#[/\\](\w+)(\.pl)?$#i;
1792            print "$1 [options] $parmHelp\n";
1793            for my $key (sort keys %{$options}) {
1794                my $name = Pad($key, $longestName, 0, ' ');
1795                my $desc = $options->{$key}->[1];
1796                if ($options->{$key}->[0]) {
1797                    $desc .= " (default " . $options->{$key}->[0] . ")";
1798  }  }
1799                print "  $name $desc\n";
1800  =head3 LogErrors          }
1801            exit(0);
1802  C<< Tracer::LogErrors($fileName); >>      }
1803        # Trace the options, if applicable.
1804  Route the standard error output to a log file.      if (T(3)) {
1805            my @parms = grep { $retOptions->{$_} } keys %{$retOptions};
1806  =over 4          Trace("Selected options: " . join(", ", sort @parms) . ".");
1807        }
1808  =item fileName      # Return the parsed parameters.
1809        return ($retOptions, @retParameters);
 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, '>', $fileName;  
1810  }  }
1811    
1812  =head3 ReadOptions  =head3 ReadOptions
1813    
1814  C<< my %options = Tracer::ReadOptions($fileName); >>      my %options = Tracer::ReadOptions($fileName);
1815    
1816  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
1817  format  format
# Line 853  Line 1872 
1872    
1873  =head3 GetOptions  =head3 GetOptions
1874    
1875  C<< Tracer::GetOptions(\%defaults, \%options); >>      Tracer::GetOptions(\%defaults, \%options);
1876    
1877  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
1878  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 1881 
1881    
1882  Consider the following example.  Consider the following example.
1883    
1884  C<< my $optionTable = GetOptions({ dbType => 'mySQL', trace => 0 }, $options); >>      my $optionTable = GetOptions({ dbType => 'mySQL', trace => 0 }, $options);
1885    
1886  In this example, the variable B<$options> is expected to contain at most two options-- B<dbType> and  In this example, the variable B<$options> is expected to contain at most two options-- B<dbType> and
1887  B<trace>. The default database type is C<mySQL> and the default trace level is C<0>. If the value of  B<trace>. The default database type is C<mySQL> and the default trace level is C<0>. If the value of
# Line 870  Line 1889 
1889  the trace level will remain at 0. If B<$options> is undefined, then the database type and trace level  the trace level will remain at 0. If B<$options> is undefined, then the database type and trace level
1890  will remain C<mySQL> and C<0>. If, on the other hand, B<$options> is defined as  will remain C<mySQL> and C<0>. If, on the other hand, B<$options> is defined as
1891    
1892  C<< {databaseType => 'Oracle'} >>      {databaseType => 'Oracle'}
1893    
1894  an error will occur because the B<databaseType> option does not exist.  an error will occur because the B<databaseType> option does not exist.
1895    
# Line 914  Line 1933 
1933    
1934  =head3 MergeOptions  =head3 MergeOptions
1935    
1936  C<< Tracer::MergeOptions(\%table, \%defaults); >>      Tracer::MergeOptions(\%table, \%defaults);
1937    
1938  Merge default values into a hash table. This method looks at the key-value pairs in the  Merge default values into a hash table. This method looks at the key-value pairs in the
1939  second (default) hash, and if a matching key is not found in the first hash, the default  second (default) hash, and if a matching key is not found in the first hash, the default
# Line 946  Line 1965 
1965      }      }
1966  }  }
1967    
1968  =head3 Trace  =head3 ParseCommand
1969    
1970        my ($options, @arguments) = Tracer::ParseCommand(\%optionTable, @inputList);
1971    
1972    Parse a command line consisting of a list of parameters. The initial parameters may be option
1973    specifiers of the form C<->I<option> or C<->I<option>C<=>I<value>. The options are stripped
1974    off and merged into a table of default options. The remainder of the command line is
1975    returned as a list of positional arguments. For example, consider the following invocation.
1976    
1977        my ($options, @arguments) = ParseCommand({ errors => 0, logFile => 'trace.log'}, @words);
1978    
1979    In this case, the list @words will be treated as a command line and there are two options available,
1980    B<errors> and B<logFile>. If @words has the following format
1981    
1982        -logFile=error.log apple orange rutabaga
1983    
1984    then at the end of the invocation, C<$options> will be
1985    
1986        { errors => 0, logFile => 'error.log' }
1987    
1988    and C<@arguments> will contain
1989    
1990        apple orange rutabaga
1991    
1992    The parser allows for some escape sequences. See L</UnEscape> for a description. There is no
1993    support for quote characters. Options can be specified with single or double hyphens.
1994    
1995    =over 4
1996    
1997    =item optionTable
1998    
1999    Table of default options.
2000    
2001    =item inputList
2002    
2003    List of words on the command line.
2004    
2005    =item RETURN
2006    
2007    Returns a reference to the option table and a list of the positional arguments.
2008    
2009    =back
2010    
2011    =cut
2012    
2013    sub ParseCommand {
2014        # Get the parameters.
2015        my ($optionTable, @inputList) = @_;
2016        # Process any options in the input list.
2017        my %overrides = ();
2018        while ((@inputList > 0) && ($inputList[0] =~ /^--?/)) {
2019            # Get the current option.
2020            my $arg = shift @inputList;
2021            # Pull out the option name.
2022            $arg =~ /^--?([^=]*)/g;
2023            my $name = $1;
2024            # Check for an option value.
2025            if ($arg =~ /\G=(.*)$/g) {
2026                # Here we have a value for the option.
2027                $overrides{$name} = UnEscape($1);
2028            } else {
2029                # Here there is no value, so we use 1.
2030                $overrides{$name} = 1;
2031            }
2032        }
2033        # Merge the options into the defaults.
2034        GetOptions($optionTable, \%overrides);
2035        # Translate the remaining parameters.
2036        my @retVal = ();
2037        for my $inputParm (@inputList) {
2038            push @retVal, UnEscape($inputParm);
2039        }
2040        # Return the results.
2041        return ($optionTable, @retVal);
2042    }
2043    
2044    
2045    =head2 File Utility Methods
2046    
2047    =head3 GetFile
2048    
2049        my @fileContents = Tracer::GetFile($fileName);
2050    
2051        or
2052    
2053        my $fileContents = Tracer::GetFile($fileName);
2054    
2055    Return the entire contents of a file. In list context, line-ends are removed and
2056    each line is a list element. In scalar context, line-ends are replaced by C<\n>.
2057    
2058    =over 4
2059    
2060    =item fileName
2061    
2062    Name of the file to read.
2063    
2064    =item RETURN
2065    
2066    In a list context, returns the entire file as a list with the line terminators removed.
2067    In a scalar context, returns the entire file as a string. If an error occurs opening
2068    the file, an empty list will be returned.
2069    
2070    =back
2071    
2072    =cut
2073    
2074    sub GetFile {
2075        # Get the parameters.
2076        my ($fileName) = @_;
2077        # Declare the return variable.
2078        my @retVal = ();
2079        # Open the file for input.
2080        my $handle = Open(undef, "<$fileName");
2081        # Read the whole file into the return variable, stripping off any terminator
2082        # characters.
2083        my $lineCount = 0;
2084        while (my $line = <$handle>) {
2085            $lineCount++;
2086            $line = Strip($line);
2087            push @retVal, $line;
2088        }
2089        # Close it.
2090        close $handle;
2091        my $actualLines = @retVal;
2092        Trace("$actualLines lines read from file $fileName.") if T(File => 2);
2093        # Return the file's contents in the desired format.
2094        if (wantarray) {
2095            return @retVal;
2096        } else {
2097            return join "\n", @retVal;
2098        }
2099    }
2100    
2101    =head3 PutFile
2102    
2103        Tracer::PutFile($fileName, \@lines);
2104    
2105    Write out a file from a list of lines of text.
2106    
2107    =over 4
2108    
2109    =item fileName
2110    
2111    Name of the output file.
2112    
2113    =item lines
2114    
2115    Reference to a list of text lines. The lines will be written to the file in order, with trailing
2116    new-line characters. Alternatively, may be a string, in which case the string will be written without
2117    modification.
2118    
2119    =back
2120    
2121    =cut
2122    
2123    sub PutFile {
2124        # Get the parameters.
2125        my ($fileName, $lines) = @_;
2126        # Open the output file.
2127        my $handle = Open(undef, ">$fileName");
2128        # Count the lines written.
2129        if (ref $lines ne 'ARRAY') {
2130            # Here we have a scalar, so we write it raw.
2131            print $handle $lines;
2132            Trace("Scalar put to file $fileName.") if T(File => 3);
2133        } else {
2134            # Write the lines one at a time.
2135            my $count = 0;
2136            for my $line (@{$lines}) {
2137                print $handle "$line\n";
2138                $count++;
2139            }
2140            Trace("$count lines put to file $fileName.") if T(File => 3);
2141        }
2142        # Close the output file.
2143        close $handle;
2144    }
2145    
2146    =head3 ParseRecord
2147    
2148        my @fields = Tracer::ParseRecord($line);
2149    
2150    Parse a tab-delimited data line. The data line is split into field values. Embedded tab
2151    and new-line characters in the data line must be represented as C<\t> and C<\n>, respectively.
2152    These will automatically be converted.
2153    
2154    =over 4
2155    
2156    =item line
2157    
2158    Line of data containing the tab-delimited fields.
2159    
2160    =item RETURN
2161    
2162    Returns a list of the fields found in the data line.
2163    
2164    =back
2165    
2166    =cut
2167    
2168    sub ParseRecord {
2169        # Get the parameter.
2170        my ($line) = @_;
2171        # Remove the trailing new-line, if any.
2172        chomp $line;
2173        # Split the line read into pieces using the tab character.
2174        my @retVal = split /\t/, $line;
2175        # Trim and fix the escapes in each piece.
2176        for my $value (@retVal) {
2177            # Trim leading whitespace.
2178            $value =~ s/^\s+//;
2179            # Trim trailing whitespace.
2180            $value =~ s/\s+$//;
2181            # Delete the carriage returns.
2182            $value =~ s/\r//g;
2183            # Convert the escapes into their real values.
2184            $value =~ s/\\t/"\t"/ge;
2185            $value =~ s/\\n/"\n"/ge;
2186        }
2187        # Return the result.
2188        return @retVal;
2189    }
2190    
2191    =head3 Merge
2192    
2193        my @mergedList = Tracer::Merge(@inputList);
2194    
2195    Sort a list of strings and remove duplicates.
2196    
2197    =over 4
2198    
2199    =item inputList
2200    
2201    List of scalars to sort and merge.
2202    
2203    =item RETURN
2204    
2205    Returns a list containing the same elements sorted in ascending order with duplicates
2206    removed.
2207    
2208    =back
2209    
2210    =cut
2211    
2212    sub Merge {
2213        # Get the input list in sort order.
2214        my @inputList = sort @_;
2215        # Only proceed if the list has at least two elements.
2216        if (@inputList > 1) {
2217            # Now we want to move through the list splicing out duplicates.
2218            my $i = 0;
2219            while ($i < @inputList) {
2220                # Get the current entry.
2221                my $thisEntry = $inputList[$i];
2222                # Find out how many elements duplicate the current entry.
2223                my $j = $i + 1;
2224                my $dup1 = $i + 1;
2225                while ($j < @inputList && $inputList[$j] eq $thisEntry) { $j++; };
2226                # If the number is nonzero, splice out the duplicates found.
2227                if ($j > $dup1) {
2228                    splice @inputList, $dup1, $j - $dup1;
2229                }
2230                # Now the element at position $dup1 is different from the element before it
2231                # at position $i. We push $i forward one position and start again.
2232                $i++;
2233            }
2234        }
2235        # Return the merged list.
2236        return @inputList;
2237    }
2238    
2239    =head3 Open
2240    
2241  C<< Trace($message); >>      my $handle = Open($fileHandle, $fileSpec, $message);
2242    
2243  Write a trace message to the target location specified in L</TSetup>. If there has not been  Open a file.
 any prior call to B<TSetup>.  
2244    
2245  =over 4  The I<$fileSpec> is essentially the second argument of the PERL C<open>
2246    function. The mode is specified using Unix-like shell information. So, for
2247    example,
2248    
2249  =item message      Open(\*LOGFILE, '>>/usr/spool/news/twitlog', "Could not open twit log.");
2250    
2251  Message to write.  would open for output appended to the specified file, and
2252    
2253  =back      Open(\*DATASTREAM, "| sort -u >$outputFile", "Could not open $outputFile.");
2254    
2255  =cut  would open a pipe that sorts the records written and removes duplicates. Note
2256    the use of file handle syntax in the Open call. To use anonymous file handles,
2257    code as follows.
2258    
2259  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";  
         }  
     }  
 }  
2260    
2261  =head3 T  The I<$message> parameter is used if the open fails. If it is set to C<0>, then
2262    the open returns TRUE if successful and FALSE if an error occurred. Otherwise, a
2263    failed open will throw an exception and the third parameter will be used to construct
2264    an error message. If the parameter is omitted, a standard message is constructed
2265    using the file spec.
2266    
2267  C<< my $switch = T($category, $traceLevel); >>      Could not open "/usr/spool/news/twitlog"
2268    
2269      or  Note that the mode characters are automatically cleaned from the file name.
2270    The actual error message from the file system will be captured and appended to the
2271    message in any case.
2272    
2273        Could not open "/usr/spool/news/twitlog": file not found.
2274    
2275  C<< my $switch = T($traceLevel); >>  In some versions of PERL the only error message we get is a number, which
2276    corresponds to the C++ C<errno> value.
2277    
2278  Return TRUE if the trace level is at or above a specified value and the specified category      Could not open "/usr/spool/news/twitlog": 6.
 is active, else FALSE. If no category is specified, the caller's package name is used.  
2279    
2280  =over 4  =over 4
2281    
2282  =item category  =item fileHandle
2283    
2284  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
2285  used.  and returned as the value of this method.
2286    
2287  =item traceLevel  =item fileSpec
2288    
2289  Relevant tracing level.  File name and mode, as per the PERL C<open> function.
2290    
2291    =item message (optional)
2292    
2293    Error message to use if the open fails. If omitted, a standard error message
2294    will be generated. In either case, the error information from the file system
2295    is appended to the message. To specify a conditional open that does not throw
2296    an error if it fails, use C<0>.
2297    
2298  =item RETURN  =item RETURN
2299    
2300  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
2301    open failed.
2302    
2303  =back  =back
2304    
2305  =cut  =cut
2306    
2307  sub T {  sub Open {
     # Declare the return variable.  
     my $retVal = 0;  
     # Only proceed if tracing is turned on.  
     if ($Destination ne "NONE") {  
2308          # Get the parameters.          # Get the parameters.
2309          my ($category, $traceLevel) = @_;      my ($fileHandle, $fileSpec, $message) = @_;
2310          if (!defined $traceLevel) {      # Attempt to open the file.
2311              # Here we have no category, so we need to get the calling package.      my $rv = open $fileHandle, $fileSpec;
2312              # The calling package is normally the first parameter. If it is      # If the open failed, generate an error message.
2313              # omitted, the first parameter will be the tracelevel. So, the      if (! $rv) {
2314              # first thing we do is shift the so-called category into the          # Save the system error message.
2315              # $traceLevel variable where it belongs.          my $sysMessage = $!;
2316              $traceLevel = $category;          # See if we need a default message.
2317              my ($package, $fileName, $line) = caller;          if (!$message) {
2318              # If there is no calling package, we default to "main".              # Clean any obvious mode characters and leading spaces from the
2319              if (!$package) {              # filename.
2320                  $category = "main";              my ($fileName) = FindNamePart($fileSpec);
2321              } 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.");  
2322          }          }
2323          $retVal = ($traceLevel <= $TraceLevel && ($AllTrace || exists $Categories{$category}));          # Terminate with an error using the supplied message and the
2324            # error message from the file system.
2325            Confess("$message: $!");
2326      }      }
2327      # Return the computed result.      # Return the file handle.
2328      return $retVal;      return $fileHandle;
2329  }  }
2330    
2331  =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 >>  
2332    
2333  then at the end of the invocation, C<$options> will be      my ($fileName, $start, $len) = Tracer::FindNamePart($fileSpec);
2334    
2335  C<< { errors => 0, logFile => 'error.log' } >>  Extract the portion of a file specification that contains the file name.
2336    
2337  and C<@arguments> will contain  A file specification is the string passed to an C<open> call. It specifies the file
2338    mode and name. In a truly complex situation, it can specify a pipe sequence. This
2339    method assumes that the file name is whatever follows the first angle bracket
2340    sequence.  So, for example, in the following strings the file name is
2341    C</usr/fig/myfile.txt>.
2342    
2343  C<< apple orange rutabaga >>      >>/usr/fig/myfile.txt
2344        </usr/fig/myfile.txt
2345        | sort -u > /usr/fig/myfile.txt
2346    
2347  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
2348  support for quote characters.  whole incoming string.
2349    
2350  =over 4  =over 4
2351    
2352  =item optionTable  =item fileSpec
   
 Table of default options.  
   
 =item inputList  
2353    
2354  List of words on the command line.  File specification string from which the file name is to be extracted.
2355    
2356  =item RETURN  =item RETURN
2357    
2358  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
2359    the specified string, or the whole string if a file name cannot be found via normal
2360    methods. The second element contains the start position of the file name portion and
2361    the third element contains the length.
2362    
2363  =back  =back
2364    
2365  =cut  =cut
2366    #: Return Type $;
2367  sub ParseCommand {  sub FindNamePart {
2368      # Get the parameters.      # Get the parameters.
2369      my ($optionTable, @inputList) = @_;      my ($fileSpec) = @_;
2370      # Process any options in the input list.      # Default to the whole input string.
2371      my %overrides = ();      my ($retVal, $pos, $len) = ($fileSpec, 0, length $fileSpec);
2372      while ((@inputList > 0) && ($inputList[0] =~ /^-/)) {      # Parse out the file name if we can.
2373          # Get the current option.      if ($fileSpec =~ m/(<|>>?)(.+?)(\s*)$/) {
2374          my $arg = shift @inputList;          $retVal = $2;
2375          # Pull out the option name.          $len = length $retVal;
2376          $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);  
2377      }      }
2378      # Return the results.      # Return the result.
2379      return ($optionTable, @retVal);      return ($retVal, $pos, $len);
2380  }  }
2381    
2382  =head3 Escape  =head3 OpenDir
2383    
2384  C<< my $codedString = Tracer::Escape($realString); >>      my @files = OpenDir($dirName, $filtered, $flag);
2385    
2386  Escape a string for use in a command length. Tabs will be replaced by C<\t>, new-lines  Open a directory and return all the file names. This function essentially performs
2387  replaced by C<\n>, carriage returns will be deleted, and backslashes will be doubled. The  the functions of an C<opendir> and C<readdir>. If the I<$filtered> parameter is
2388  result is to reverse the effect of L</UnEscape>.  set to TRUE, all filenames beginning with a period (C<.>), dollar sign (C<$>),
2389    or pound sign (C<#>) and all filenames ending with a tilde C<~>) will be
2390    filtered out of the return list. If the directory does not open and I<$flag> is not
2391    set, an exception is thrown. So, for example,
2392    
2393        my @files = OpenDir("/Volumes/fig/contigs", 1);
2394    
2395    is effectively the same as
2396    
2397        opendir(TMP, "/Volumes/fig/contigs") || Confess("Could not open /Volumes/fig/contigs.");
2398        my @files = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir(TMP);
2399    
2400    Similarly, the following code
2401    
2402        my @files = grep { $_ =~ /^\d/ } OpenDir("/Volumes/fig/orgs", 0, 1);
2403    
2404    Returns the names of all files in C</Volumes/fig/orgs> that begin with digits and
2405    automatically returns an empty list if the directory fails to open.
2406    
2407  =over 4  =over 4
2408    
2409  =item realString  =item dirName
2410    
2411  String to escape.  Name of the directory to open.
2412    
2413  =item RETURN  =item filtered
2414    
2415  Escaped equivalent of the real string.  TRUE if files whose names begin with a period (C<.>) should be automatically removed
2416    from the list, else FALSE.
2417    
2418    =item flag
2419    
2420    TRUE if a failure to open is okay, else FALSE
2421    
2422  =back  =back
2423    
2424  =cut  =cut
2425    #: Return Type @;
2426  sub Escape {  sub OpenDir {
2427      # Get the parameter.      # Get the parameters.
2428      my ($realString) = @_;      my ($dirName, $filtered, $flag) = @_;
2429      # Initialize the return variable.      # Declare the return variable.
2430      my $retVal = "";      my @retVal = ();
2431      # Loop through the parameter string, looking for sequences to escape.      # Open the directory.
2432      while (length $realString > 0) {      if (opendir(my $dirHandle, $dirName)) {
2433          # Look for the first sequence to escape.          # The directory opened successfully. Get the appropriate list according to the
2434          if ($realString =~ /^(.*?)([\n\t\r\\])/) {          # strictures of the filter parameter.
2435              # Here we found it. The text preceding the sequence is in $1. The sequence          if ($filtered) {
2436              # 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;  
             }  
2437          } else {          } else {
2438              # Here there are no more escape sequences. The rest of the string is              @retVal = readdir $dirHandle;
             # transferred unmodified.  
             $retVal .= $realString;  
             $realString = "";  
2439          }          }
2440        } elsif (! $flag) {
2441            # Here the directory would not open and it's considered an error.
2442            Confess("Could not open directory $dirName.");
2443      }      }
2444      # Return the result.      # Return the result.
2445      return $retVal;      return @retVal;
2446  }  }
2447    
 =head3 UnEscape  
2448    
2449  C<< my $realString = Tracer::UnEscape($codedString); >>  =head3 Insure
2450    
2451  Replace escape sequences with their actual equivalents. C<\t> will be replaced by      Insure($dirName, $chmod);
2452  a tab, C<\n> by a new-line character, and C<\\> by a backslash. C<\r> codes will  
2453  be deleted.  Insure a directory is present.
2454    
2455  =over 4  =over 4
2456    
2457  =item codedString  =item dirName
2458    
2459  String to un-escape.  Name of the directory to check. If it does not exist, it will be created.
2460    
2461  =item RETURN  =item chmod (optional)
2462    
2463  Returns a copy of the original string with the escape sequences converted to their actual  Security privileges to be given to the directory if it is created.
 values.  
2464    
2465  =back  =back
2466    
2467  =cut  =cut
2468    
2469  sub UnEscape {  sub Insure {
2470      # Get the parameter.      my ($dirName, $chmod) = @_;
2471      my ($codedString) = @_;      if (! -d $dirName) {
2472      # Initialize the return variable.          Trace("Creating $dirName directory.") if T(2);
2473      my $retVal = "";          eval {
2474      # Only proceed if the incoming string is nonempty.              mkpath $dirName;
2475      if (defined $codedString) {              # If we have permissions specified, set them here.
2476          # Loop through the parameter string, looking for escape sequences. We can't do              if (defined($chmod)) {
2477          # 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;  
                 $codedString = "";  
2478              }              }
2479            };
2480            if ($@) {
2481                Confess("Error creating $dirName: $@");
2482          }          }
2483      }      }
     # Return the result.  
     return $retVal;  
2484  }  }
2485    
2486  =head3 ParseRecord  =head3 ChDir
2487    
2488  C<< my @fields = Tracer::ParseRecord($line); >>      ChDir($dirName);
2489    
2490  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.  
2491    
2492  =over 4  =over 4
2493    
2494  =item line  =item dirName
   
 Line of data containing the tab-delimited fields.  
   
 =item RETURN  
2495    
2496  Returns a list of the fields found in the data line.  Name of the directory to which we want to change.
2497    
2498  =back  =back
2499    
2500  =cut  =cut
2501    
2502  sub ParseRecord {  sub ChDir {
2503      # Get the parameter.      my ($dirName) = @_;
2504      my ($line) = @_;      if (! -d $dirName) {
2505      # Remove the trailing new-line, if any.          Confess("Cannot change to directory $dirName: no such directory.");
2506      chomp $line;      } else {
2507      # Split the line read into pieces using the tab character.          Trace("Changing to directory $dirName.") if T(File => 4);
2508      my @retVal = split /\t/, $line;          my $okFlag = chdir $dirName;
2509      # Trim and fix the escapes in each piece.          if (! $okFlag) {
2510      for my $value (@retVal) {              Confess("Error switching to directory $dirName.");
2511          # 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;  
         $value =~ s/\\n/"\n"/ge;  
2512      }      }
     # Return the result.  
     return @retVal;  
2513  }  }
2514    
2515  =head3 Merge  =head3 SetPermissions
2516    
2517  C<< my @mergedList = Tracer::Merge(@inputList); >>      Tracer::SetPermissions($dirName, $group, $mask, %otherMasks);
2518    
2519  Sort a list of strings and remove duplicates.  Set the permissions for a directory and all the files and folders inside it.
2520    In addition, the group ownership will be changed to the specified value.
2521    
2522    This method is more vulnerable than most to permission and compatability
2523    problems, so it does internal error recovery.
2524    
2525  =over 4  =over 4
2526    
2527  =item inputList  =item dirName
2528    
2529  List of scalars to sort and merge.  Name of the directory to process.
2530    
2531  =item RETURN  =item group
2532    
2533  Returns a list containing the same elements sorted in ascending order with duplicates  Name of the group to be assigned.
2534  removed.  
2535    =item mask
2536    
2537    Permission mask. Bits that are C<1> in this mask will be ORed into the
2538    permission bits of any file or directory that does not already have them
2539    set to 1.
2540    
2541    =item otherMasks
2542    
2543    Map of search patterns to permission masks. If a directory name matches
2544    one of the patterns, that directory and all its members and subdirectories
2545    will be assigned the new pattern. For example, the following would
2546    assign 01664 to most files, but would use 01777 for directories named C<tmp>.
2547    
2548        Tracer::SetPermissions($dirName, 'fig', 01664, '^tmp$' => 01777);
2549    
2550    The list is ordered, so the following would use 0777 for C<tmp1> and
2551    0666 for C<tmp>, C<tmp2>, or C<tmp3>.
2552    
2553        Tracer::SetPermissions($dirName, 'fig', 01664, '^tmp1' => 0777,
2554                                                       '^tmp' => 0666);
2555    
2556    Note that the pattern matches are all case-insensitive, and only directory
2557    names are matched, not file names.
2558    
2559  =back  =back
2560    
2561  =cut  =cut
2562    
2563  sub Merge {  sub SetPermissions {
2564      # Get the input list in sort order.      # Get the parameters.
2565      my @inputList = sort @_;      my ($dirName, $group, $mask, @otherMasks) = @_;
2566      # Only proceed if the list has at least two elements.      # Set up for error recovery.
2567      if (@inputList > 1) {      eval {
2568          # Now we want to move through the list splicing out duplicates.          # Switch to the specified directory.
2569          my $i = 0;          ChDir($dirName);
2570          while ($i < @inputList) {          # Get the group ID.
2571              # Get the current entry.          my $gid = getgrnam($group);
2572              my $thisEntry = $inputList[$i];          # Get the mask for tracing.
2573              # Find out how many elements duplicate the current entry.          my $traceMask = sprintf("%04o", $mask) . "($mask)";
2574              my $j = $i + 1;          Trace("Fixing permissions for directory $dirName using group $group($gid) and mask $traceMask.") if T(File => 2);
2575              my $dup1 = $i + 1;          my $fixCount = 0;
2576              while ($j < @inputList && $inputList[$j] eq $thisEntry) { $j++; };          my $lookCount = 0;
2577              # If the number is nonzero, splice out the duplicates found.          # @dirs will be a stack of directories to be processed.
2578              if ($j > $dup1) {          my @dirs = (getcwd());
2579                  splice @inputList, $dup1, $j - $dup1;          while (scalar(@dirs) > 0) {
2580                # Get the current directory.
2581                my $dir = pop @dirs;
2582                # Check for a match to one of the specified directory names. To do
2583                # that, we need to pull the individual part of the name off of the
2584                # whole path.
2585                my $simpleName = $dir;
2586                if ($dir =~ m!/([^/]+)$!) {
2587                    $simpleName = $1;
2588                }
2589                Trace("Simple directory name for $dir is $simpleName.") if T(File => 4);
2590                # Search for a match.
2591                my $match = 0;
2592                my $i;
2593                for ($i = 0; $i < $#otherMasks && ! $match; $i += 2) {
2594                    my $pattern = $otherMasks[$i];
2595                    if ($simpleName =~ /$pattern/i) {
2596                        $match = 1;
2597                    }
2598                }
2599                # Check for a match. Note we use $i-1 because the loop added 2
2600                # before terminating due to the match.
2601                if ($match && $otherMasks[$i-1] != $mask) {
2602                    # This directory matches one of the incoming patterns, and it's
2603                    # a different mask, so we process it recursively with that mask.
2604                    SetPermissions($dir, $group, $otherMasks[$i-1], @otherMasks);
2605                } else {
2606                    # Here we can process normally. Get all of the non-hidden members.
2607                    my @submems = OpenDir($dir, 1);
2608                    for my $submem (@submems) {
2609                        # Get the full name.
2610                        my $thisMem = "$dir/$submem";
2611                        Trace("Checking member $thisMem.") if T(4);
2612                        $lookCount++;
2613                        if ($lookCount % 1000 == 0) {
2614                            Trace("$lookCount members examined. Current is $thisMem. Mask is $traceMask") if T(File => 3);
2615              }              }
2616              # Now the element at position $dup1 is different from the element before it                      # Fix the group.
2617              # at position $i. We push $i forward one position and start again.                      chown -1, $gid, $thisMem;
2618              $i++;                      # Insure this member is not a symlink.
2619                        if (! -l $thisMem) {
2620                            # Get its info.
2621                            my $fileInfo = stat $thisMem;
2622                            # Only proceed if we got the info. Otherwise, it's a hard link
2623                            # and we want to skip it anyway.
2624                            if ($fileInfo) {
2625                                my $fileMode = $fileInfo->mode;
2626                                if (($fileMode & $mask) != $mask) {
2627                                    # Fix this member.
2628                                    $fileMode |= $mask;
2629                                    chmod $fileMode, $thisMem;
2630                                    $fixCount++;
2631          }          }
2632                                # If it's a subdirectory, stack it.
2633                                if (-d $thisMem) {
2634                                    push @dirs, $thisMem;
2635      }      }
     # Return the merged list.  
     return @inputList;  
2636  }  }
   
 =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;  
2637      }      }
2638      # Return the result.                  }
2639      return $retVal;              }
2640            }
2641            Trace("$lookCount files and directories processed, $fixCount fixed.") if T(File => 2);
2642        };
2643        # Check for an error.
2644        if ($@) {
2645            Confess("SetPermissions error: $@");
2646        }
2647  }  }
2648    
2649  =head3 GetFile  =head3 GetLine
   
 C<< my @fileContents = Tracer::GetFile($fileName); >>  
   
     or  
2650    
2651  C<< my $fileContents = Tracer::GetFile($fileName); >>      my @data = Tracer::GetLine($handle);
2652    
2653  Return the entire contents of a file. In list context, line-ends are removed and  Read a line of data from a tab-delimited file.
 each line is a list element. In scalar context, line-ends are replaced by C<\n>.  
2654    
2655  =over 4  =over 4
2656    
2657  =item fileName  =item handle
2658    
2659  Name of the file to read.  Open file handle from which to read.
2660    
2661  =item RETURN  =item RETURN
2662    
2663  In a list context, returns the entire file as a list with the line terminators removed.  Returns a list of the fields in the record read. The fields are presumed to be
2664  In a scalar context, returns the entire file as a string. If an error occurs opening  tab-delimited. If we are at the end of the file, then an empty list will be
2665  the file, an empty list will be returned.  returned. If an empty line is read, a single list item consisting of a null
2666    string will be returned.
2667    
2668  =back  =back
2669    
2670  =cut  =cut
2671    
2672  sub GetFile {  sub GetLine {
2673      # Get the parameters.      # Get the parameters.
2674      my ($fileName) = @_;      my ($handle) = @_;
2675      # Declare the return variable.      # Declare the return variable.
2676      my @retVal = ();      my @retVal = ();
2677      # Open the file for input.      Trace("File position is " . tell($handle) . ". EOF flag is " . eof($handle) . ".") if T(File => 4);
2678      my $handle = Open(undef, "<$fileName");      # Read from the file.
2679      # Read the whole file into the return variable, stripping off any terminator      my $line = <$handle>;
2680      # characters.      # Only proceed if we found something.
2681      my $lineCount = 0;      if (defined $line) {
2682      while (my $line = <$handle>) {          # Remove the new-line. We are a bit over-cautious here because the file may be coming in via an
2683          $lineCount++;          # upload control and have a nonstandard EOL combination.
2684          $line = Strip($line);          $line =~ s/(\r|\n)+$//;
2685          push @retVal, $line;          # Here we do some fancy tracing to help in debugging complicated EOL marks.
2686            if (T(File => 4)) {
2687                my $escapedLine = $line;
2688                $escapedLine =~ s/\n/\\n/g;
2689                $escapedLine =~ s/\r/\\r/g;
2690                $escapedLine =~ s/\t/\\t/g;
2691                Trace("Line read: -->$escapedLine<--");
2692      }      }
2693      # Close it.          # If the line is empty, return a single empty string; otherwise, parse
2694      close $handle;          # it into fields.
2695      my $actualLines = @retVal;          if ($line eq "") {
2696      # Return the file's contents in the desired format.              push @retVal, "";
     if (wantarray) {  
         return @retVal;  
2697      } else {      } else {
2698          return join "\n", @retVal;              push @retVal, split /\t/,$line;
2699            }
2700        } else {
2701            # Trace the reason the read failed.
2702            Trace("End of file: $!") if T(File => 3);
2703      }      }
2704        # Return the result.
2705        return @retVal;
2706  }  }
2707    
2708  =head3 PutFile  =head3 PutLine
2709    
2710  C<< Tracer::PutFile($fileName, \@lines); >>      Tracer::PutLine($handle, \@fields, $eol);
2711    
2712  Write out a file from a list of lines of text.  Write a line of data to a tab-delimited file. The specified field values will be
2713    output in tab-separated form, with a trailing new-line.
2714    
2715  =over 4  =over 4
2716    
2717  =item fileName  =item handle
2718    
2719  Name of the output file.  Output file handle.
2720    
2721  =item lines  =item fields
2722    
2723  Reference to a list of text lines. The lines will be written to the file in order, with trailing  List of field values.
2724  new-line characters. Alternatively, may be a string, in which case the string will be written without  
2725  modification.  =item eol (optional)
2726    
2727    End-of-line character (default is "\n").
2728    
2729  =back  =back
2730    
2731  =cut  =cut
2732    
2733  sub PutFile {  sub PutLine {
2734      # Get the parameters.      # Get the parameters.
2735      my ($fileName, $lines) = @_;      my ($handle, $fields, $eol) = @_;
2736      # Open the output file.      # Write the data.
2737      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;  
2738  }  }
2739    
 =head3 QTrace  
2740    
2741  C<< my $data = QTrace($format); >>  =head3 PrintLine
2742    
2743  Return the queued trace data in the specified format.      Tracer::PrintLine($line);
2744    
2745    Print a line of text with a trailing new-line.
2746    
2747  =over 4  =over 4
2748    
2749  =item format  =item line
2750    
2751  C<html> to format the data as an HTML list, C<text> to format it as straight text.  Line of text to print.
2752    
2753  =back  =back
2754    
2755  =cut  =cut
2756    
2757  sub QTrace {  sub PrintLine {
2758      # Get the parameter.      # Get the parameters.
2759      my ($format) = @_;      my ($line) = @_;
2760      # Create the return variable.      # Print the line.
2761      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 $retVal;  
2762  }  }
2763    
 =head3 Confess  
2764    
2765  C<< Confess($message); >>  =head2 Other Useful Methods
2766    
2767  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  
2768    
2769  C<< Assert($recNum >= 0) || Confess("Invalid record number $recNum."); >>      my $listValue = Tracer::ParseParm($string);
2770    
2771  Will abort the program with a stack trace if the value of C<$recNum> is negative.  Convert a parameter into a list reference. If the parameter is undefined,
2772    an undefined value will be returned. Otherwise, it will be parsed as a
2773    comma-separated list of values.
2774    
2775  =over 4  =over 4
2776    
2777  =item message  =item string
2778    
2779  Message to include in the trace.  Incoming string.
2780    
2781    =item RETURN
2782    
2783    Returns a reference to a list of values, or C<undef> if the incoming value
2784    was undefined.
2785    
2786  =back  =back
2787    
2788  =cut  =cut
2789    
2790  sub Confess {  sub ParseParm {
2791      # Get the parameters.      # Get the parameters.
2792      my ($message) = @_;      my ($string) = @_;
2793      # Trace the call stack.      # Declare the return variable.
2794      Cluck($message);      my $retVal;
2795      # Abort the program.      # Check for data.
2796      croak(">>> $message");      if (defined $string) {
2797  }          # We have some, so split it into a list.
2798            $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;  
         }  
2799      }      }
2800        # Return the result.
2801      return $retVal;      return $retVal;
2802  }  }
2803    
2804  =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  
2805    
2806  Message to include in the trace.      my $string = Tracer::Now();
2807    
2808  =back  Return a displayable time stamp containing the local time. Whatever format this
2809    method produces must be parseable by L</ParseDate>.
2810    
2811  =cut  =cut
2812    
2813  sub Cluck {  sub Now {
2814      # Get the parameters.      return DisplayTime(time);
     my ($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/);  
     }  
2815  }  }
2816    
2817  =head3 Min  =head3 DisplayTime
2818    
2819  C<< my $min = Min($value1, $value2, ... $valueN); >>      my $string = Tracer::DisplayTime($time);
2820    
2821  Return the minimum argument. The arguments are treated as numbers.  Convert a time value to a displayable time stamp. Whatever format this
2822    method produces must be parseable by L</ParseDate>.
2823    
2824  =over 4  =over 4
2825    
2826  =item $value1, $value2, ... $valueN  =item time
2827    
2828  List of numbers to compare.  Time to display, in seconds since the epoch, or C<undef> if the time is unknown.
2829    
2830  =item RETURN  =item RETURN
2831    
2832  Returns the lowest number in the list.  Returns a displayable time, or C<(n/a)> if the incoming time is undefined.
2833    
2834  =back  =back
2835    
2836  =cut  =cut
2837    
2838  sub Min {  sub DisplayTime {
2839      # Get the parameters. Note that we prime the return value with the first parameter.      my ($time) = @_;
2840      my ($retVal, @values) = @_;      my $retVal = "(n/a)";
2841      # Loop through the remaining parameters, looking for the lowest.      if (defined $time) {
2842      for my $value (@values) {          my ($sec,$min,$hour,$mday,$mon,$year,$wday,$yday,$isdst) = localtime($time);
2843          if ($value < $retVal) {          $retVal = _p2($mon+1) . "/" . _p2($mday) . "/" . ($year + 1900) . " " .
2844              $retVal = $value;                    _p2($hour) . ":" . _p2($min) . ":" . _p2($sec);
         }  
2845      }      }
     # Return the minimum found.  
2846      return $retVal;      return $retVal;
2847  }  }
2848    
2849  =head3 Max  # Pad a number to 2 digits.
2850    sub _p2 {
2851        my ($value) = @_;
2852        $value = "0$value" if ($value < 10);
2853        return $value;
2854    }
2855    
2856  C<< my $max = Max($value1, $value2, ... $valueN); >>  =head3 Escape
2857    
2858  Return the maximum argument. The arguments are treated as numbers.      my $codedString = Tracer::Escape($realString);
2859    
2860    Escape a string for use in a command. Tabs will be replaced by C<\t>, new-lines
2861    replaced by C<\n>, carriage returns will be deleted, and backslashes will be doubled. The
2862    result is to reverse the effect of L</UnEscape>.
2863    
2864  =over 4  =over 4
2865    
2866  =item $value1, $value2, ... $valueN  =item realString
2867    
2868  List of numbers to compare.  String to escape.
2869    
2870  =item RETURN  =item RETURN
2871    
2872  Returns the highest number in the list.  Escaped equivalent of the real string.
2873    
2874  =back  =back
2875    
2876  =cut  =cut
2877    
2878  sub Max {  sub Escape {
2879      # Get the parameters. Note that we prime the return value with the first parameter.      # Get the parameter.
2880      my ($retVal, @values) = @_;      my ($realString) = @_;
2881      # Loop through the remaining parameters, looking for the highest.      # Initialize the return variable.
2882      for my $value (@values) {      my $retVal = "";
2883          if ($value > $retVal) {      # Loop through the parameter string, looking for sequences to escape.
2884              $retVal = $value;      while (length $realString > 0) {
2885            # Look for the first sequence to escape.
2886            if ($realString =~ /^(.*?)([\n\t\r\\])/) {
2887                # Here we found it. The text preceding the sequence is in $1. The sequence
2888                # itself is in $2. First, move the clear text to the return variable.
2889                $retVal .= $1;
2890                # Strip the processed section off the real string.
2891                $realString = substr $realString, (length $2) + (length $1);
2892                # Get the matched character.
2893                my $char = $2;
2894                # If we have a CR, we are done.
2895                if ($char ne "\r") {
2896                    # It's not a CR, so encode the escape sequence.
2897                    $char =~ tr/\t\n/tn/;
2898                    $retVal .= "\\" . $char;
2899                }
2900            } else {
2901                # Here there are no more escape sequences. The rest of the string is
2902                # transferred unmodified.
2903                $retVal .= $realString;
2904                $realString = "";
2905          }          }
2906      }      }
2907      # Return the maximum found.      # Return the result.
2908      return $retVal;      return $retVal;
2909  }  }
2910    
2911  =head3 AddToListMap  =head3 UnEscape
2912    
2913  C<< Tracer::AddToListMap(\%hash, $key, $value1, $value2, ... valueN); >>      my $realString = Tracer::UnEscape($codedString);
2914    
2915  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
2916  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
2917    be deleted.
2918    
2919  =over 4  =over 4
2920    
2921  =item hash  =item codedString
   
 Reference to the target hash.  
   
 =item key  
2922    
2923  Key for which the value is to be added.  String to un-escape.
2924    
2925  =item value1, value2, ... valueN  =item RETURN
2926    
2927  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
2928    values.
2929    
2930  =back  =back
2931    
2932  =cut  =cut
2933    
2934  sub AddToListMap {  sub UnEscape {
2935      # Get the parameters.      # Get the parameter.
2936      my ($hash, $key, @values) = @_;      my ($codedString) = @_;
2937      # Process according to whether or not the key already has a value.      # Initialize the return variable.
2938      if (! exists $hash->{$key}) {      my $retVal = "";
2939          $hash->{$key} = [@values];      # Only proceed if the incoming string is nonempty.
2940        if (defined $codedString) {
2941            # Loop through the parameter string, looking for escape sequences. We can't do
2942            # translating because it causes problems with the escaped slash. ("\\t" becomes
2943            # "\<tab>" no matter what we do.)
2944            while (length $codedString > 0) {
2945                # Look for the first escape sequence.
2946                if ($codedString =~ /^(.*?)\\(\\|n|t|r)/) {
2947                    # Here we found it. The text preceding the sequence is in $1. The sequence
2948                    # itself is in $2. First, move the clear text to the return variable.
2949                    $retVal .= $1;
2950                    $codedString = substr $codedString, (2 + length $1);
2951                    # Get the escape value.
2952                    my $char = $2;
2953                    # If we have a "\r", we are done.
2954                    if ($char ne 'r') {
2955                        # Here it's not an 'r', so we convert it.
2956                        $char =~ tr/\\tn/\\\t\n/;
2957                        $retVal .= $char;
2958                    }
2959      } else {      } else {
2960          push @{$hash->{$key}}, @values;                  # Here there are no more escape sequences. The rest of the string is
2961                    # transferred unmodified.
2962                    $retVal .= $codedString;
2963                    $codedString = "";
2964      }      }
2965  }  }
   
 =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;  
2966      }      }
2967      # Return the determination indicator.      # Return the result.
2968      return $retVal;      return $retVal;
2969  }  }
2970    
2971  =head3 Strip  =head3 Percent
2972    
2973  C<< my $string = Tracer::Strip($line); >>      my $percent = Tracer::Percent($number, $base);
2974    
2975  Strip all line terminators off a string. This is necessary when dealing with files  Returns the percent of the base represented by the given number. If the base
2976  that may have been transferred back and forth several times among different  is zero, returns zero.
 operating environments.  
2977    
2978  =over 4  =over 4
2979    
2980  =item line  =item number
2981    
2982  Line of text to be stripped.  Percent numerator.
2983    
2984    =item base
2985    
2986    Percent base.
2987    
2988  =item RETURN  =item RETURN
2989    
2990  The same line of text with all the line-ending characters chopped from the end.  Returns the percentage of the base represented by the numerator.
2991    
2992  =back  =back
2993    
2994  =cut  =cut
2995    
2996  sub Strip {  sub Percent {
2997      # Get a copy of the parameter string.      # Get the parameters.
2998      my ($string) = @_;      my ($number, $base) = @_;
2999      my $retVal = (defined $string ? $string : "");      # Declare the return variable.
3000      # Strip the line terminator characters.      my $retVal = 0;
3001      $retVal =~ s/(\r|\n)+$//g;      # Compute the percent.
3002        if ($base != 0) {
3003            $retVal = $number * 100 / $base;
3004        }
3005      # Return the result.      # Return the result.
3006      return $retVal;      return $retVal;
3007  }  }
3008    
3009  =head3 Pad  =head3 Constrain
3010    
3011  C<< my $paddedString = Tracer::Pad($string, $len, $left, $padChar); >>      my $constrained = Constrain($value, $min, $max);
3012    
3013  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.  
3014    
3015  =over 4  =over 4
3016    
3017  =item string  =item value
   
 String to be padded.  
   
 =item len  
3018    
3019  Desired length of the padded string.  Value to constrain.
3020    
3021  =item left (optional)  =item min (optional)
3022    
3023  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.
3024    
3025  =item padChar (optional)  =item max (optional)
3026    
3027  Character to use for padding. The default is a space.  Maximum permissible value. If this parameter is undefined, no maximum constraint will be applied.
3028    
3029  =item RETURN  =item RETURN
3030    
3031  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.  
3032    
3033  =back  =back
3034    
3035  =cut  =cut
3036    
3037  sub Pad {  sub Constrain {
3038      # Get the parameters.      # Get the parameters.
3039      my ($string, $len, $left, $padChar) = @_;      my ($value, $min, $max) = @_;
3040      # Compute the padding character.      # Declare the return variable.
3041      if (! defined $padChar) {      my $retVal = $value;
3042          $padChar = " ";      # Apply the minimum constraint.
3043      }      if (defined $min && $retVal < $min) {
3044      # Compute the number of spaces needed.          $retVal = $min;
3045      my $needed = $len - length $string;      }
3046      # Copy the string into the return variable.      # Apply the maximum constraint.
3047      my $retVal = $string;      if (defined $max && $retVal > $max) {
3048      # 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;  
         }  
3049      }      }
3050      # Return the result.      # Return the result.
3051      return $retVal;      return $retVal;
3052  }  }
3053    
3054  =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  
3055    
3056      TICK("./protein.cgi")      my $min = Min($value1, $value2, ... $valueN);
3057    
3058  it will work correctly in both environments.  Return the minimum argument. The arguments are treated as numbers.
3059    
3060  =over 4  =over 4
3061    
3062  =item commandString  =item $value1, $value2, ... $valueN
3063    
3064  The command string to pass to the system.  List of numbers to compare.
3065    
3066  =item RETURN  =item RETURN
3067    
3068  Returns the standard output from the specified command, as a list.  Returns the lowest number in the list.
3069    
3070  =back  =back
3071    
3072  =cut  =cut
3073  #: Return Type @;  
3074  sub TICK {  sub Min {
3075      # Get the parameters.      # Get the parameters. Note that we prime the return value with the first parameter.
3076      my ($commandString) = @_;      my ($retVal, @values) = @_;
3077      # Chop off the dot-slash if this is Windows.      # Loop through the remaining parameters, looking for the lowest.
3078      if ($FIG_Config::win_mode) {      for my $value (@values) {
3079          $commandString =~ s!^\./!!;          if ($value < $retVal) {
3080                $retVal = $value;
3081      }      }
3082      # Activate the command and return the result.      }
3083      return `$commandString`;      # Return the minimum found.
3084        return $retVal;
3085  }  }
3086    
3087  =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  
3088    
3089  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, $varHash);  
 }  
3090    
3091  =head3 TraceParms  Return the maximum argument. The arguments are treated as numbers.
3092    
3093  C<< Tracer::TraceParms($query); >>  =over 4
3094    
3095  Trace the CGI parameters at trace level CGI => 3 and the environment variables  =item $value1, $value2, ... $valueN
 at level CGI => 4.  
3096    
3097  =over 4  List of numbers to compare.
3098    
3099  =item query  =item RETURN
3100    
3101  CGI query object containing the parameters to trace.  Returns the highest number in the list.
3102    
3103  =back  =back
3104    
3105  =cut  =cut
3106    
3107  sub TraceParms {  sub Max {
3108      # Get the parameters.      # Get the parameters. Note that we prime the return value with the first parameter.
3109      my ($query) = @_;      my ($retVal, @values) = @_;
3110      if (T(CGI => 3)) {      # Loop through the remaining parameters, looking for the highest.
3111          # Here we want to trace the parameter data.      for my $value (@values) {
3112          my @names = $query->param;          if ($value > $retVal) {
3113          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}");  
3114          }          }
3115      }      }
3116        # Return the maximum found.
3117        return $retVal;
3118  }  }
3119    
 =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.  
3120    
3121  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 ...  
3122    
3123      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", $varHash);  
3124    
3125  The idea here is that even if the script fails, you'll see trace messages and  Strip all line terminators off a string. This is necessary when dealing with files
3126  useful output.  that may have been transferred back and forth several times among different
3127    operating environments.
3128    
3129  =over 4  =over 4
3130    
3131  =item webData  =item line
3132    
3133  A string containing either the full web page to be written to the output or the  Line of text to be stripped.
 name of a template file from which the page is to be constructed. If the name  
 of a template file is specified, then the second parameter must be present;  
 otherwise, it must be absent.  
3134    
3135  =item varHash (optional)  =item RETURN
3136    
3137  If specified, then a reference to a hash mapping variable names for a template  The same line of text with all the line-ending characters chopped from the end.
 to their values. The template file will be read into memory, and variable markers  
 will be replaced by data in this hash reference.  
3138    
3139  =back  =back
3140    
3141  =cut  =cut
3142    
3143  sub ScriptFinish {  sub Strip {
3144      # Get the parameters.      # Get a copy of the parameter string.
3145      my ($webData, $varHash) = @_;      my ($string) = @_;
3146      # Check for a template file situation.      my $retVal = (defined $string ? $string : "");
3147      my $outputString;      # Strip the line terminator characters.
3148      if (defined $varHash) {      $retVal =~ s/(\r|\n)+$//g;
3149          # Here we have a template file. We need to determine the template type.      # Return the result.
3150          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 $outputString;  
3151  }  }
3152    
3153  =head3 Insure  =head3 Pad
3154    
3155  C<< Insure($dirName); >>      my $paddedString = Tracer::Pad($string, $len, $left, $padChar);
3156    
3157  Insure a directory is present.  Pad a string to a specified length. The pad character will be a
3158    space, and the padding will be on the right side unless specified
3159    in the third parameter.
3160    
3161  =over 4  =over 4
3162    
3163  =item dirName  =item string
   
 Name of the directory to check. If it does not exist, it will be created.  
3164    
3165  =back  String to be padded.
3166    
3167  =cut  =item len
3168    
3169  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: $@");  
         }  
     }  
 }  
3170    
3171  =head3 ChDir  =item left (optional)
3172    
3173  C<< ChDir($dirName); >>  TRUE if the string is to be left-padded; otherwise it will be padded on the right.
3174    
3175  Change to the specified directory.  =item padChar (optional)
3176    
3177  =over 4  Character to use for padding. The default is a space.
3178    
3179  =item dirName  =item RETURN
3180    
3181  Name of the directory to which we want to change.  Returns a copy of the original string with the pad character added to the
3182    specified end so that it achieves the desired length.
3183    
3184  =back  =back
3185    
3186  =cut  =cut
3187    
3188  sub ChDir {  sub Pad {
3189      my ($dirName) = @_;      # Get the parameters.
3190      if (! -d $dirName) {      my ($string, $len, $left, $padChar) = @_;
3191          Confess("Cannot change to directory $dirName: no such directory.");      # Compute the padding character.
3192        if (! defined $padChar) {
3193            $padChar = " ";
3194        }
3195        # Compute the number of spaces needed.
3196        my $needed = $len - length $string;
3197        # Copy the string into the return variable.
3198        my $retVal = $string;
3199        # Only proceed if padding is needed.
3200        if ($needed > 0) {
3201            # Create the pad string.
3202            my $pad = $padChar x $needed;
3203            # Affix it to the return value.
3204            if ($left) {
3205                $retVal = $pad . $retVal;
3206      } else {      } else {
3207          Trace("Changing to directory $dirName.") if T(4);              $retVal .= $pad;
         my $okFlag = chdir $dirName;  
         if (! $okFlag) {  
             Confess("Error switching to directory $dirName.");  
3208          }          }
3209      }      }
3210        # Return the result.
3211        return $retVal;
3212  }  }
3213    
3214  =head3 SendSMS  =head3 EOF
3215    
3216  C<< my $msgID = Tracer::SendSMS($phoneNumber, $msg); >>  This is a constant that is lexically greater than any useful string.
3217    
3218  Send a text message to a phone number using Clickatell. The FIG_Config file must contain the  =cut
 user name, password, and API ID for the relevant account in the hash reference variable  
 I<$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  
3219    
3220      $phone =  { user => 'BruceTheHumanPet',  sub EOF {
3221                  password => 'silly',      return "\xFF\xFF\xFF\xFF\xFF";
3222                  api_id => '2561022' };  }
3223    
3224  The original purpose of this method was to insure Bruce would be notified immediately when the  =head3 TICK
 Sprout Load terminates. Care should be taken if you do not wish Bruce to be notified immediately  
 when you call this method.  
3225    
3226  The message ID will be returned if successful, and C<undef> if an error occurs.      my @results = TICK($commandString);
3227    
3228  =over 4  Perform a back-tick operation on a command. If this is a Windows environment, any leading
3229    dot-slash (C<./> will be removed. So, for example, if you were doing
3230    
3231  =item phoneNumber      `./protein.cgi`
3232    
3233  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
3234  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
3235    
3236  =item msg      TICK("./protein.cgi")
3237    
3238  Message to send to the specified phone.  it will work correctly in both environments.
3239    
3240    =over 4
3241    
3242    =item commandString
3243    
3244    The command string to pass to the system.
3245    
3246  =item RETURN  =item RETURN
3247    
3248  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.
3249    
3250  =back  =back
3251    
3252  =cut  =cut
3253    #: Return Type @;
3254  sub SendSMS {  sub TICK {
3255      # Get the parameters.      # Get the parameters.
3256      my ($phoneNumber, $msg) = @_;      my ($commandString) = @_;
3257      # Declare the return variable. If we do not change it, C<undef> will be returned.      # Chop off the dot-slash if this is Windows.
3258      my $retVal;      if ($FIG_Config::win_mode) {
3259      # 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);  
             }  
         }  
3260      }      }
3261      # Return the result.      # Activate the command and return the result.
3262      return $retVal;      return `$commandString`;
3263  }  }
3264    
3265    
3266  =head3 CommaFormat  =head3 CommaFormat
3267    
3268  C<< my $formatted = Tracer::CommaFormat($number); >>      my $formatted = Tracer::CommaFormat($number);
3269    
3270  Insert commas into a number.  Insert commas into a number.
3271    
# Line 2234  Line 3298 
3298      # Return the result.      # Return the result.
3299      return $retVal;      return $retVal;
3300  }  }
 =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  
3301    
 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: $@");  
     }  
 }  
3302    
3303  =head3 CompareLists  =head3 CompareLists
3304    
3305  C<< my ($inserted, $deleted) = Tracer::CompareLists(\@newList, \@oldList, $keyIndex); >>      my ($inserted, $deleted) = Tracer::CompareLists(\@newList, \@oldList, $keyIndex);
3306    
3307  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
3308  are presumed to be sorted alphabetically by the value in the $keyIndex column.  are presumed to be sorted alphabetically by the value in the $keyIndex column.
# Line 2435  Line 3367 
3367      return ($inserted, $deleted);      return ($inserted, $deleted);
3368  }  }
3369    
3370  =head3 GetLine  =head3 GenerateURL
3371    
3372  C<< my @data = Tracer::GetLine($handle); >>      my $queryUrl = Tracer::GenerateURL($page, %parameters);
3373    
3374  Read a line of data from a tab-delimited file.  Generate a GET-style URL for the specified page with the specified parameter
3375    names and values. The values will be URL-escaped automatically. So, for
3376    example
3377    
3378        Tracer::GenerateURL("form.cgi", type => 1, string => "\"high pass\" or highway")
3379    
3380    would return
3381    
3382        form.cgi?type=1;string=%22high%20pass%22%20or%20highway
3383    
3384  =over 4  =over 4
3385    
3386  =item handle  =item page
3387    
3388  Open file handle from which to read.  Page URL.
3389    
3390    =item parameters
3391    
3392    Hash mapping parameter names to parameter values.
3393    
3394  =item RETURN  =item RETURN
3395    
3396  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
3397  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.  
3398    
3399  =back  =back
3400    
3401