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# Line 1  Line 1 
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        use Fcntl qw(:DEFAULT :flock);
42    
43    
44  =head1 Tracing and Debugging Helpers  =head1 Tracing and Debugging Helpers
45    
46  =head2 Introduction  =head2 Tracing
47    
48  This package provides simple tracing for debugging and reporting purposes. To use it simply call the  This package provides simple tracing for debugging and reporting purposes. To use it simply call the
49  L</TSetup> method to set the options and call L</Trace> to write out trace messages. Each trace  L</TSetup> or L</ETracing> method to set the options and call L</Trace> to write out trace messages.
50  message has a I<trace level> and I<category> associated with it. In addition, the tracing package itself  L</TSetup> and L</ETracing> both establish a I<trace level> and a list of I<categories>. Similarly,
51  has a list of categories and a single trace level set by the B<TSetup> method. Only messages whose trace  each trace message has a I<trace level> and I<category> associated with it. Only messages whose trace
52  level is less than or equal to this package's trace level and whose category is activated will  level is less than or equal to the setup trace level and whose category is activated will
53  be written. Thus, a higher trace level on a message indicates that the message  be written. Thus, a higher trace level on a message indicates that the message
54  is less likely to be seen. A higher trace level passed to B<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
55  appear. To generate a trace message, use the following syntax.  appear.
56    
57    =head3 Putting Trace Messages in Your Code
58    
59  C<< Trace($message) if T(errors => 4); >>  To generate a trace message, use the following syntax.
60    
61        Trace($message) if T(errors => 4);
62    
63  This statement will produce a trace message if the trace level is 4 or more and the C<errors>  This statement will produce a trace message if the trace level is 4 or more and the C<errors>
64  category is active. Note that the special category C<main> is always active, so  category is active. There is a special category C<main> that is always active, so
65    
66  C<< Trace($message) if T(main => 4); >>      Trace($message) if T(main => 4);
67    
68  will trace if the trace level is 4 or more.  will trace if the trace level is 4 or more.
69    
# Line 61  Line 71 
71  following call is made in the B<Sprout> package, it will appear if the C<Sprout> category is  following call is made in the B<Sprout> package, it will appear if the C<Sprout> category is
72  active and the trace level is 2 or more.  active and the trace level is 2 or more.
73    
74  C<< Trace($message) if T(2); >>      Trace($message) if T(2);
75    
76    In scripts, where no package name is available, the category defaults to C<main>.
77    
78    =head3 Custom Tracing
79    
80    Many programs have customized tracing configured using the L</TSetup> method. This is no longer
81    the preferred method, but a knowledge of how custom tracing works can make the more modern
82    L</Emergency Tracing> easier to understand.
83    
84  To set up 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,
85  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
86  specified as a space-delimited string. Thus  specified as a space-delimited string. Thus
87    
88  C<< TSetup('3 errors Sprout ERDB', 'HTML'); >>      TSetup('3 errors Sprout ERDB', 'TEXT');
89    
90  sets the trace level to 3, activates the C<errors>, C<Sprout>, and C<ERDB> categories, and  sets the trace level to 3, activates the C<errors>, C<Sprout>, and C<ERDB> categories, and
91  specifies that messages should be output as HTML paragraphs.  specifies that messages should be sent to the standard output.
92    
93  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
94  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
95  useful in a CGI environment.  useful in a CGI environment.
96    
97  C<< TSetup('3 *', 'WARN'); >>      TSetup('3 *', 'WARN');
98    
99  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
100  be queued. The messages can then be retrieved by calling the L</QTrace> method. This approach  be queued. The messages can then be retrieved by calling the L</QTrace> method. This approach
101  is useful if you are building a web page. Instead of having the trace messages interspersed with  is useful if you are building a web page. Instead of having the trace messages interspersed with
102  the page output, they can be gathered together and displayed at the end of the page. This makes  the page output, they can be gathered together and displayed at the end of the page. This makes
103  it easier to debug page formatting problems.  it easier to debug page formatting problems.
104    
105  Finally, you can specify that all trace messages be emitted as warnings.  Finally, you can specify that all trace messages be emitted to a file, or the standard output and
106    a file at the same time. To trace to a file, specify the filename with an output character in front
107    of it.
108    
109        TSetup('4 SQL', ">$fileName");
110    
111    To trace to the standard output and a file at the same time, put a C<+> in front of the angle
112    bracket.
113    
114        TSetup('3 *', "+>$fileName");
115    
116  The flexibility of tracing makes it superior to simple use of directives like C<die> and C<warn>.  The flexibility of tracing makes it superior to simple use of directives like C<die> and C<warn>.
117  Tracer calls can be left in the code with minimal overhead and then turned on only when needed.  Tracer calls can be left in the code with minimal overhead and then turned on only when needed.
118  Thus, debugging information is available and easily retrieved even when the application is  Thus, debugging information is available and easily retrieved even when the application is
119  being used out in the field.  being used out in the field.
120    
121    =head3 Trace Levels
122    
123  There is no hard and fast rule on how to use trace levels. The following is therefore only  There is no hard and fast rule on how to use trace levels. The following is therefore only
124  a suggestion.  a suggestion.
125    
# Line 121  Line 150 
150    
151  =back  =back
152    
153    The format of trace messages is important because some utilities analyze trace files.
154    There are three fields-- the time stamp, the category name, and the text.
155    The time stamp is between square brackets and the category name between angle brackets.
156    After the category name there is a colon (C<:>) followed by the message text.
157    If the square brackets or angle brackets are missing, then the trace management
158    utilities assume that they are encountering a set of pre-formatted lines.
159    
160    Note, however, that this formatting is done automatically by the tracing functions. You
161    only need to know about it if you want to parse a trace file.
162    
163    =head3 Emergency Tracing
164    
165    Sometimes, you need a way for tracing to happen automatically without putting parameters
166    in a form or on the command line. Emergency tracing does this. You invoke emergency tracing
167    from the debug form, which is accessed from the [[DebugConsole]]. Emergency tracing requires
168    that you specify a tracing key. For command-line tools, the key is
169    taken from the C<TRACING> environment variable. For web services, the key is taken from
170    a cookie. Either way, the key tells the tracing facility who you are, so that you control
171    the tracing in your environment without stepping on other users.
172    
173    The key can be anything you want. If you don't have a key, the C<SetPassword> page will
174    generate one for you.
175    
176    You can activate and de-activate emergency tracing from the debugging control panel, as
177    well as display the trace file itself.
178    
179    To enable emergency tracing in your code, call
180    
181        ETracing($cgi)
182    
183    from a web script and
184    
185        ETracing()
186    
187    from a command-line script.
188    
189    The web script will look for the tracing key in the cookies, and the command-line
190    script will look for it in the C<TRACING> environment variable. If you are
191    using the L</StandardSetup> method or a [[WebApplication]], emergency tracing
192    will be configured automatically.
193    
194  =cut  =cut
195    
196  # Declare the configuration variables.  # Declare the configuration variables.
197    
198  my $Destination = "NONE";   # Description of where to send the trace output.  my $Destination = "WARN";   # Description of where to send the trace output.
199  my $TeeFlag = 0;            # TRUE if output is going to a file and to the  my $TeeFlag = 0;            # TRUE if output is going to a file and to the
200                              # standard output                              # standard output
201  my %Categories = ( main => 1 );  my %Categories = ( main => 1 );
202                              # hash of active category names                              # hash of active category names
203    my @LevelNames = qw(error warn notice info detail);
204  my $TraceLevel = 0;         # trace level; a higher trace level produces more  my $TraceLevel = 0;         # trace level; a higher trace level produces more
205                              # messages                              # messages
206  my @Queue = ();             # queued list of trace messages.  my @Queue = ();             # queued list of trace messages.
207  my $LastCategory = "main";  # name of the last category interrogated  my $LastCategory = "main";  # name of the last category interrogated
208    my $LastLevel = 0;          # level of the last test call
209  my $SetupCount = 0;         # number of times TSetup called  my $SetupCount = 0;         # number of times TSetup called
210  my $AllTrace = 0;           # TRUE if we are tracing all categories.  my $AllTrace = 0;           # TRUE if we are tracing all categories.
211    my $SavedCGI;               # CGI object passed to ETracing
212    my $CommandLine;            # Command line passed to StandardSetup
213    umask 2;                    # Fix the damn umask so everything is group-writable.
214    
215    =head2 Tracing Methods
216    
217    =head3 Setups
218    
219        my $count = Tracer::Setups();
220    
221    Return the number of times L</TSetup> has been called.
222    
223    This method allows for the creation of conditional tracing setups where, for example, we
224    may want to set up tracing if nobody else has done it before us.
225    
226    =cut
227    
228  =head2 Public Methods  sub Setups {
229        return $SetupCount;
230    }
231    
232  =head3 TSetup  =head3 TSetup
233    
234  C<< TSetup($categoryList, $target); >>      TSetup($categoryList, $target);
235    
236  This method is used to specify the trace options. The options are stored as package data  This method is used to specify the trace options. The options are stored as package data
237  and interrogated by the L</Trace> and L</T> methods.  and interrogated by the L</Trace> and L</T> methods.
# Line 191  Line 281 
281          }          }
282      }      }
283      # Now we need to process the destination information. The most important special      # Now we need to process the destination information. The most important special
284      # cases are the single ">", which requires we clear the file first, and the      # case is when we're writing to a file. This is indicated by ">" (overwrite) and
285      # "+" prefix which indicates a double echo.      # ">>" (append). A leading "+" for either indicates that we are also writing to
286        # the standard output (tee mode).
287      if ($target =~ m/^\+?>>?/) {      if ($target =~ m/^\+?>>?/) {
288          if ($target =~ m/^\+/) {          if ($target =~ m/^\+/) {
289              $TeeFlag = 1;              $TeeFlag = 1;
290              $target = substr($target, 1);              $target = substr($target, 1);
291          }          }
292          if ($target =~ m/^>[^>]/) {          if ($target =~ m/^>[^>]/) {
293                # We need to initialize the file (which clears it).
294              open TRACEFILE, $target;              open TRACEFILE, $target;
295              print TRACEFILE Now() . " Tracing initialized.\n";              print TRACEFILE "[" . Now() . "] [notice] [Tracer] Tracing initialized.\n";
296              close TRACEFILE;              close TRACEFILE;
297                # Set to append mode now that the file has been cleared.
298              $Destination = ">$target";              $Destination = ">$target";
299          } else {          } else {
300              $Destination = $target;              $Destination = $target;
# Line 213  Line 306 
306      $SetupCount++;      $SetupCount++;
307  }  }
308    
309  =head3 StandardSetup  =head3 SetLevel
310    
311  C<< my ($options, @parameters) = StandardSetup(\@categories, \%options, $parmHelp, @ARGV); >>      Tracer::SetLevel($newLevel);
312    
313  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.  
314    
315  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.  
316    
317  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  
318    
319      ["Sprout", "SproutLoad", "ERDB"]  Proposed new trace level.
320    
321  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.  
322    
323  =over 4  =cut
324    
325  =item FIG  sub SetLevel {
326        $TraceLevel = $_[0];
327    }
328    
329  Turns on trace messages inside the B<FIG> package.  =head3 ParseDate
330    
331  =item SQL      my $time = Tracer::ParseDate($dateString);
332    
333  Traces SQL commands and activity.  Convert a date into a PERL time number. This method expects a date-like string
334    and parses it into a number. The string must be vaguely date-like or it will
335    return an undefined value. Our requirement is that a month and day be
336    present and that three pieces of the date string (time of day, month and day,
337    year) be separated by likely delimiters, such as spaces, commas, and such-like.
338    
339  =item Tracer  If a time of day is present, it must be in military time with two digits for
340    everything but the hour.
341    
342  Traces error messages and call stacks.  The year must be exactly four digits.
343    
344  =back  Additional stuff can be in the string. We presume it's time zones or weekdays or something
345    equally innocuous. This means, however, that a sufficiently long sentence with date-like
346    parts in it may be interpreted as a date. Hopefully this will not be a problem.
347    
348  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.  
349    
350      TransactFeatures -trace=3 -sql register ../xacts IDs.tbl  The parameters are as follows.
351    
352  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  
353    
354  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.  
355    
356      TransactFeatures -trace=3 -sql -user=Bruce register ../xacts IDs.tbl  The date string to convert.
357    
358  would send the trace output to C<traceBruce.log> in the temporary directory.  =item RETURN
359    
360  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
361  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.  
362    
363  You can specify a different default trace level by setting C<$options->{trace}>  =back
 prior to calling this method.  
364    
365  An example at this point would help. Consider, for example, the command-line utility  =cut
 C<TransactFeatures>. It accepts a list of positional parameters plus the options  
 C<safe>, C<noAlias>, C<start>, and C<tblFiles>. To start up this command, we execute  
 the following code.  
366    
367      my ($options, @parameters) = Tracer::StandardSetup(["DocUtils"],  # Universal month conversion table.
368                          { safe => [0, "use database transactions"],  use constant MONTHS => {    Jan =>  0, January   =>  0, '01' =>  0,  '1' =>  0,
369                            noAlias => [0, "do not expect aliases in CHANGE transactions"],                              Feb =>  1, February  =>  1, '02' =>  1,  '2' =>  1,
370                            start => [' ', "start with this genome"],                              Mar =>  2, March     =>  2, '03' =>  2,  '3' =>  2,
371                            tblFiles => [0, "output TBL files containing the corrected IDs"] },                              Apr =>  3, April     =>  3, '04' =>  3,  '4' =>  3,
372                          "command transactionDirectory IDfile",                              May =>  4, May       =>  4, '05' =>  4,  '5' =>  4,
373                        @ARGV);                              Jun =>  5, June      =>  5, '06' =>  5,  '6' =>  5,
374                                Jul =>  6, July      =>  6, '07' =>  6,  '7' =>  6,
375                                Aug =>  7, August    =>  7, '08' =>  7,  '8' =>  7,
376                                Sep =>  8, September =>  8, '09' =>  8,  '9' =>  8,
377                                Oct =>  9, October  =>   9, '10' =>  9,
378                                Nov => 10, November =>  10, '11' => 10,
379                                Dec => 11, December =>  11, '12' => 11
380                            };
381    
382    sub ParseDate {
383        # Get the parameters.
384        my ($dateString) = @_;
385        # Declare the return variable.
386        my $retVal;
387        # Find the month and day of month. There are two ways that can happen. We check for the
388        # numeric style first. That way, if the user's done something like "Sun 12/22", then we
389        # won't be fooled into thinking the month is Sunday.
390        if ($dateString =~ m#\b(\d{1,2})/(\d{1,2})\b# || $dateString =~ m#\b(\w+)\s(\d{1,2})\b#) {
391            my ($mon, $mday) = (MONTHS->{$1}, $2);
392            # Insist that the month and day are valid.
393            if (defined($mon) && $2 >= 1 && $2 <= 31) {
394                # Find the time.
395                my ($hour, $min, $sec) = (0, 0, 0);
396                if ($dateString =~ /\b(\d{1,2}):(\d{2}):(\d{2})\b/) {
397                    ($hour, $min, $sec) = ($1, $2, $3);
398                }
399                # Find the year.
400                my $year;
401                if ($dateString =~ /\b(\d{4})\b/) {
402                    $year = $1;
403                } else {
404                    # Get the default year, which is this one. Note we must convert it to
405                    # the four-digit value expected by "timelocal".
406                    (undef, undef, undef, undef, undef, $year) = localtime();
407                    $year += 1900;
408                }
409                $retVal = timelocal($sec, $min, $hour, $mday, $mon, $year);
410            }
411        }
412        # Return the result.
413        return $retVal;
414    }
415    
416  The call to C<ParseCommand> specifies the default values for the options and  =head3 LogErrors
 stores the actual options in a hash that is returned as C<$options>. The  
 positional parameters are returned in C<@parameters>.  
417    
418  The following is a sample command line for C<TransactFeatures>.      Tracer::LogErrors($fileName);
419    
420      TransactFeatures -trace=2 -noAlias register ../xacts IDs.tbl  Route the standard error output to a log file.
421    
422  In this case, C<register>, C<../xacts>, and C<IDs.tbl> are the positional  =over 4
 parameters, and would find themselves in I<@parameters> after executing the  
 above code fragment. The tracing would be set to level 2, and the categories  
 would be C<FIG>, C<Tracer>, and <DocUtils>. C<FIG> and C<Tracer> are standard,  
 and C<DocUtils> was included because it came in within the first parameter  
 to this method. The I<$options> hash would be  
423    
424      { trace => 2, sql => 0, safe => 0,  =item fileName
       noAlias => 1, start => ' ', tblFiles => 0 }  
425    
426  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.  
427    
428  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  
429    
430      -user=Bruce -background  =cut
431    
432  then the trace output would go to C<traceBruce.log>, the standard output to  sub LogErrors {
433  C<outBruce.log>, and the error output to C<errBruce.log>. This is designed to      # Get the file name.
434  simplify starting a command in the background.      my ($fileName) = @_;
435        # Open the file as the standard error output.
436        open STDERR, '>', $fileName;
437    }
438    
439  Finally, if the special option C<-h> is specified, the option names will  =head3 Trace
 be traced at level 0 and the program will exit without processing.  
 This provides a limited help capability. For example, if the user enters  
440    
441      TransactFeatures -h      Trace($message);
442    
443  he would see the following output.  Write a trace message to the target location specified in L</TSetup>. If there has not been
444    any prior call to B<TSetup>.
445    
446      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  
447    
448  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,  
449    
450      { trace => [0, "tracing level (default 0)"],  Message to write.
        ...  
451    
452  would set the default trace level to 0 instead of 2, while  =back
453    
454      { trace => ["2-", "tracing level (default 2)"],  =cut
        ...  
455    
456  would leave the default at 2, but trace only to the log file, not to the  sub Trace {
457  standard output.      # Get the parameters.
458        my ($message) = @_;
459        # Strip off any line terminators at the end of the message. We will add
460        # new-line stuff ourselves.
461        my $stripped = Strip($message);
462        # Compute the caller information.
463        my ($callPackage, $callFile, $callLine) = caller();
464        my $callFileTitle = basename($callFile);
465        # Check the caller.
466        my $callerInfo = ($callFileTitle ne "Tracer.pm" ? " [$callFileTitle $callLine]" : "");
467        # Get the timestamp.
468        my $timeStamp = Now();
469        # Build the prefix.
470        my $level = $LevelNames[$LastLevel] || "($LastLevel)";
471        my $prefix = "[$timeStamp] [$level] [$LastCategory]$callerInfo";
472        # Format the message.
473        my $formatted = "$prefix $stripped";
474        # Process according to the destination.
475        if ($Destination eq "TEXT") {
476            # Write the message to the standard output.
477            print "$formatted\n";
478        } elsif ($Destination eq "ERROR") {
479            # Write the message to the error output. Here, we want our prefix fields.
480            print STDERR "$formatted\n";
481        } elsif ($Destination eq "WARN") {
482            # Emit the message to the standard error output. It is presumed that the
483            # error logger will add its own prefix fields, the notable exception being
484            # the caller info.
485            print STDERR "$callerInfo$stripped\n";
486        } elsif ($Destination eq "QUEUE") {
487            # Push the message into the queue.
488            push @Queue, "$formatted";
489        } elsif ($Destination eq "HTML") {
490            # Convert the message to HTML and write it to the standard output.
491            my $escapedMessage = CGI::escapeHTML($stripped);
492            print "<p>$timeStamp $LastCategory $LastLevel: $escapedMessage</p>\n";
493        } elsif ($Destination =~ m/^>>/) {
494            # Write the trace message to an output file.
495            open(TRACING, $Destination) || die "Tracing open for \"$Destination\" failed: $!";
496            # Lock the file.
497            flock TRACING, LOCK_EX;
498            print TRACING "$formatted\n";
499            close TRACING;
500            # If the Tee flag is on, echo it to the standard output.
501            if ($TeeFlag) {
502                print "$formatted\n";
503            }
504        }
505    }
506    
507  The parameters to this method are as follows.  =head3 T
508    
509  =over 4      my $switch = T($category, $traceLevel);
510    
511  =item categories      or
512    
513  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.  
514    
515  =item options  Return TRUE if the trace level is at or above a specified value and the specified category
516    is active, else FALSE. If no category is specified, the caller's package name is used.
517    
518  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).  
519    
520  =item parmHelp  =item category
521    
522  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
523  if the user specifies the C<-h> option.  used.
524    
525  =item argv  =item traceLevel
526    
527  List of command line parameters, including the option switches, which must  Relevant tracing level.
 precede the positional parameters and be prefixed by a hyphen.  
528    
529  =item RETURN  =item RETURN
530    
531  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.  
532    
533  =back  =back
534    
535  =cut  =cut
536    
537  sub StandardSetup {  sub T {
538        # Declare the return variable.
539        my $retVal = 0;
540        # Only proceed if tracing is turned on.
541        if ($Destination ne "NONE") {
542      # Get the parameters.      # Get the parameters.
543      my ($categories, $options, $parmHelp, @argv) = @_;          my ($category, $traceLevel) = @_;
544      # Add the tracing options.          if (!defined $traceLevel) {
545      if (! exists $options->{trace}) {              # Here we have no category, so we need to get the calling package.
546          $options->{trace} = [2, "tracing level"];              # The calling package is normally the first parameter. If it is
547      }              # omitted, the first parameter will be the tracelevel. So, the
548      $options->{sql} = [0, "turn on SQL tracing"];              # first thing we do is shift the so-called category into the
549      $options->{h} = [0, "display command-line options"];              # $traceLevel variable where it belongs.
550      $options->{user} = [$$, "trace log file name suffix"];              $traceLevel = $category;
551      $options->{background} = [0, "spool standard and error output"];              my ($package, $fileName, $line) = caller;
552      # Create a parsing hash from the options hash. The parsing hash              # If there is no calling package, we default to "main".
553      # contains the default values rather than the default value              if (!$package) {
554      # and the description. While we're at it, we'll memorize the                  $category = "main";
555      # length of the longest option name.              } else {
556      my $longestName = 0;                  my @cats = split /::/, $package;
557      my %parseOptions = ();                  $category = $cats[$#cats];
     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";  
558      }      }
     # 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;  
559      }      }
560      # Now we set up the trace mode.          # Save the category name and level.
561      my $traceMode;          $LastCategory = $category;
562      # Verify that we can open a file in the FIG temporary directory.          $LastLevel = $traceLevel;
563      my $traceFileName = "$FIG_Config::temp/trace$suffix.log";          # Convert it to lower case before we hash it.
564      if (open TESTTRACE, ">$traceFileName") {          $category = lc $category;
565          # Here we can trace to a file.          # Validate the trace level.
566          $traceMode = ">$traceFileName";          if (ref $traceLevel) {
567          if ($textOKFlag) {              Confess("Bad trace level.");
568              # Echo to standard output if the text-OK flag is set.          } elsif (ref $TraceLevel) {
569              $traceMode = "+$traceMode";              Confess("Bad trace config.");
570          }          }
571          # Close the test file.          # Make the check. Note that level 0 shows even if the category is turned off.
572          close TESTTRACE;          $retVal = ($traceLevel <= $TraceLevel && ($traceLevel == 0 || $AllTrace || exists $Categories{$category}));
     } 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";  
         } else {  
             $traceMode = "WARN";  
573          }          }
574        # Return the computed result.
575        return $retVal;
576      }      }
577      # Now set up the tracing.  
578      TSetup("$traceLevel $cats", $traceMode);  =head3 QTrace
579      # Check for the "h" option. If it is specified, dump the command-line  
580      # options and exit the program.      my $data = QTrace($format);
581      if ($retOptions->{h}) {  
582          $0 =~ m#[/\\](\w+)(\.pl)?$#i;  Return the queued trace data in the specified format.
583          Trace("$1 [options] $parmHelp") if T(0);  
584          for my $key (sort keys %{$options}) {  =over 4
585              my $name = Pad($key, $longestName, 0, ' ');  
586              my $desc = $options->{$key}->[1];  =item format
587              if ($options->{$key}->[0]) {  
588                  $desc .= " (default " . $options->{$key}->[0] . ")";  C<html> to format the data as an HTML list, C<text> to format it as straight text.
589    
590    =back
591    
592    =cut
593    
594    sub QTrace {
595        # Get the parameter.
596        my ($format) = @_;
597        # Create the return variable.
598        my $retVal = "";
599        # Only proceed if there is an actual queue.
600        if (@Queue) {
601            # Process according to the format.
602            if ($format =~ m/^HTML$/i) {
603                # Convert the queue into an HTML list.
604                $retVal = "<ul>\n";
605                for my $line (@Queue) {
606                    my $escapedLine = CGI::escapeHTML($line);
607                    $retVal .= "<li>$escapedLine</li>\n";
608              }              }
609              Trace("  $name $desc") if T(0);              $retVal .= "</ul>\n";
610            } elsif ($format =~ m/^TEXT$/i) {
611                # Convert the queue into a list of text lines.
612                $retVal = join("\n", @Queue) . "\n";
613          }          }
614          exit(0);          # Clear the queue.
615            @Queue = ();
616      }      }
617      # Return the parsed parameters.      # Return the formatted list.
618      return ($retOptions, @retParameters);      return $retVal;
619  }  }
620    
621  =head3 Setups  =head3 Confess
622    
623  C<< my $count = Tracer::Setups(); >>      Confess($message);
624    
625  Return the number of times L</TSetup> has been called.  Trace the call stack and abort the program with the specified message. When used with
626    the OR operator and the L</Assert> method, B<Confess> can function as a debugging assert.
627    So, for example
628    
629  This method allows for the creation of conditional tracing setups where, for example, we      Assert($recNum >= 0) || Confess("Invalid record number $recNum.");
630  may want to set up tracing if nobody else has done it before us.  
631    Will abort the program with a stack trace if the value of C<$recNum> is negative.
632    
633    =over 4
634    
635    =item message
636    
637    Message to include in the trace.
638    
639    =back
640    
641  =cut  =cut
642    
643  sub Setups {  sub Confess {
644      return $SetupCount;      # Get the parameters.
645        my ($message) = @_;
646        # Set up the category and level.
647        $LastCategory = "(confess)";
648        $LastLevel = 0;
649        if (! defined($FIG_Config::no_tool_hdr)) {
650            # Here we have a tool header. Display its length so that the user can adjust the line numbers.
651            my $toolHeaderFile = "$FIG_Config::fig_disk/dist/releases/current/$FIG_Config::arch/tool_hdr";
652            # Only proceed if the tool header file is actually present.
653            if (-f $toolHeaderFile) {
654                my $fh;
655                if (open $fh, "<$toolHeaderFile") {
656                    my @lines = <$fh>;
657                    Trace("Tool header has " . scalar(@lines) . " lines.");
658                }
659            }
660        }
661        # Trace the call stack.
662        Cluck($message);
663        # Abort the program.
664        croak(">>> $message");
665  }  }
666    
667  =head3 Open  =head3 SaveCGI
   
 C<< my $handle = Open($fileHandle, $fileSpec, $message); >>  
668    
669  Open a file.      Tracer::SaveCGI($cgi);
670    
671  The I<$fileSpec> is essentially the second argument of the PERL C<open>  This method saves the CGI object but does not activate emergency tracing.
672  function. The mode is specified using Unix-like shell information. So, for  It is used to allow L</Warn> to work in situations where emergency
673  example,  tracing is contra-indicated (e.g. the wiki).
674    
675      Open(\*LOGFILE, '>>/usr/spool/news/twitlog', "Could not open twit log.");  =over 4
676    
677  would open for output appended to the specified file, and  =item cgi
678    
679      Open(\*DATASTREAM, "| sort -u >$outputFile", "Could not open $outputFile.");  Active CGI query object.
680    
681  would open a pipe that sorts the records written and removes duplicates. Note  =back
 the use of file handle syntax in the Open call. To use anonymous file handles,  
 code as follows.  
682    
683      my $logFile = Open(undef, '>>/usr/spool/news/twitlog', "Could not open twit log.");  =cut
684    
685  The I<$message> parameter is used if the open fails. If it is set to C<0>, then  sub SaveCGI {
686  the open returns TRUE if successful and FALSE if an error occurred. Otherwise, a      $SavedCGI = $_[0];
687  failed open will throw an exception and the third parameter will be used to construct  }
 an error message. If the parameter is omitted, a standard message is constructed  
 using the file spec.  
688    
689      Could not open "/usr/spool/news/twitlog"  =head3 Warn
690    
691  Note that the mode characters are automatically cleaned from the file name.      Warn($message, @options);
 The actual error message from the file system will be captured and appended to the  
 message in any case.  
692    
693      Could not open "/usr/spool/news/twitlog": file not found.  This method traces an important message. If an RSS feed is configured
694    (via I<FIG_Config::error_feed>) and the tracing destination is C<WARN>,
695    then the message will be echoed to the feed. In general, a tracing
696    destination of C<WARN> indicates that the caller is running as a web
697    service in a production environment; however, this is not a requirement.
698    
699  In some versions of PERL the only error message we get is a number, which  To force warnings into the RSS feed even when the tracing destination
700  corresponds to the C++ C<errno> value.  is not C<WARN>, simply specify the C<Feed> tracing module. This can be
701    configured automatically when L</StandardSetup> is used.
702    
703      Could not open "/usr/spool/news/twitlog": 6.  The L</Cluck> method calls this one for its final message. Since
704    L</Confess> calls L</Cluck>, this means that any error which is caught
705    and confessed will put something in the feed. This insures that someone
706    will be alerted relatively quickly when a failure occurs.
707    
708  =over 4  =over 4
709    
710  =item fileHandle  =item message
711    
712  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.  
713    
714  =item fileSpec  =item options
715    
716  File name and mode, as per the PERL C<open> function.  A list containing zero or more options.
717    
718  =item message (optional)  =back
719    
720  Error message to use if the open fails. If omitted, a standard error message  The permissible options are as follows.
 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>.  
721    
722  =item RETURN  =over 4
723    
724  Returns the name of the file handle assigned to the file, or C<undef> if the  =item noStack
725  open failed.  
726    If specified, then the stack trace is not included in the output.
727    
728  =back  =back
729    
730  =cut  =cut
731    
732  sub Open {  sub Warn {
733      # Get the parameters.      # Get the parameters.
734      my ($fileHandle, $fileSpec, $message) = @_;      my $message = shift @_;
735      # Attempt to open the file.      my %options = map { $_ => 1 } @_;
736      my $rv = open $fileHandle, $fileSpec;      # Save $@;
737      # If the open failed, generate an error message.      my $savedError = $@;
738      if (! $rv) {      # Trace the message.
739          # Save the system error message.      Trace($message);
740          my $sysMessage = $!;      # This will contain the lock handle. If it's defined, it means we need to unlock.
741          # See if we need a default message.      my $lock;
742          if (!$message) {      # Check for feed forcing.
743              # Clean any obvious mode characters and leading spaces from the      my $forceFeed = exists $Categories{feed};
744              # filename.      # An error here would be disastrous. Note that if debug mode is specified,
745              my ($fileName) = FindNamePart($fileSpec);      # we do this stuff even in a test environment.
746              $message = "Could not open \"$fileName\"";      eval {
747            # Do we need to put this in the RSS feed?
748            if ($FIG_Config::error_feed && ($Destination eq 'WARN' || $forceFeed)) {
749                # Probably. We need to check first, however, to see if it's from an
750                # ignored IP. For non-CGI situations, we default the IP to the self-referent.
751                my $key = "127.0.0.1";
752                if (defined $SavedCGI) {
753                    # Get the IP address.
754                    $key = $ENV{HTTP_X_FORWARDED_FOR} || $ENV{REMOTE_ADDR};
755                }
756                # Is the IP address in the ignore list?
757                my $found = scalar(grep { $_ eq $key } @FIG_Config::error_ignore_ips);
758                if (! $found) {
759                    # No. We're good. We now need to compute the date, the link, and the title.
760                    # First, the date, in a very specific format.
761                    my $date = strftime("%a, %02e %b %H:%M:%S %Y ", localtime) .
762                        (tz_local_offset() / 30);
763                    # Environment data goes in here. We start with the date.
764                    my $environment = "$date.  ";
765                    # If we need to recap the message (because it's too long to be a title), we'll
766                    # put it in here.
767                    my $recap;
768                    # Copy the message and remove excess space.
769                    my $title = $message;
770                    $title =~ s/\s+/ /gs;
771                    # If it's too long, we have to split it up.
772                    if (length $title > 60) {
773                        # Put the full message in the environment string.
774                        $recap = $title;
775                        # Excerpt it as the title.
776                        $title = substr($title, 0, 50) . "...";
777                    }
778                    # If we have a CGI object, then this is a web error. Otherwise, it's
779                    # command-line.
780                    if (defined $SavedCGI) {
781                        # We're in a web service. The environment is the user's IP, and the link
782                        # is the URL that got us here.
783                        $environment .= "Event Reported at IP address $key process $$.";
784                        my $url = $SavedCGI->self_url();
785                        # We need the user agent string and (if available) the referrer.
786                        # The referrer will be the link.
787                        $environment .= " User Agent $ENV{HTTP_USER_AGENT}";
788                        if ($ENV{HTTP_REFERER}) {
789                            my $link = $ENV{HTTP_REFERER};
790                            $environment .= " referred from <a href=\"$link\">$link</a>.";
791                        } else {
792                            $environment .= " referrer unknown.";
793                        }
794                        # Close off the sentence with the original link.
795                        $environment .= " URL of event is <a href=\"$url\">$url</a>.";
796                    } else {
797                        # No CGI object, so we're a command-line tool. Use the tracing
798                        # key and the PID as the user identifier, and add the command.
799                        my $key = EmergencyKey();
800                        $environment .= "Event Reported by $key process $$.";
801                        if ($CommandLine) {
802                            # We're in a StandardSetup script, so we have the real command line.
803                            $environment .= "\n<pre>" . CGI::escapeHTML($CommandLine) . "</pre>\n";
804                        } elsif ($ENV{_}) {
805                            # We're in a BASH script, so the command has been stored in the _ variable.
806                            $environment .= "  Command = " . CGI::escapeHTML($ENV{_}) . "\n";
807                        }
808                    }
809                    # Build a GUID. We use the current time, the title, and the process ID,
810                    # then digest the result.
811                    my $guid = Digest::MD5::md5_base64(gettimeofday(), $title, $$);
812                    # Finally, the description. This is a stack trace plus various environmental stuff.
813                    # The trace is optional.
814                    my $stackTrace;
815                    if ($options{noStack}) {
816                        $stackTrace = "";
817                    } else {
818                        my @trace = LongMess();
819                        # Only proceed if we got something back.
820                        if (scalar(@trace) > 0) {
821                            $trace[0] =~ s/Tracer::Warn.+?called/Event occurred/;
822                            $stackTrace = "Stack trace:<pre>" . join("\n", @trace, "</pre>");
823                        }
824                    }
825                    # We got the stack trace. Now it's time to put it all together.
826                    # We have a goofy thing here in that we need to HTML-escape some sections of the description
827                    # twice. They will be escaped once here, and then once when written by XML::Simple. They are
828                    # unescaped once when processed by the RSS reader, and stuff in the description is treated as
829                    # HTML. So, anything escaped here is treated as a literal when viewed in the RSS reader, but
830                    # our <br>s and <pre>s are used to format the description.
831                    $recap = (defined $recap ? "<em>" . CGI::escapeHTML($recap) . "</em><br /><br />" : "");
832                    my $description = "$recap$environment  $stackTrace";
833                    # Okay, we have all the pieces. Create a hash of the new event.
834                    my $newItem = { title => $title,
835                                    description => $description,
836                                    category => $LastCategory,
837                                    pubDate => $date,
838                                    guid => $guid,
839                                  };
840                    # We need XML capability for this.
841                    require XML::Simple;
842                    # The RSS document goes in here.
843                    my $rss;
844                    # Get the name of the RSS file. It's in the FIG temporary directory.
845                    my $fileName = "$FIG_Config::temp/$FIG_Config::error_feed";
846                    # Open the config file and lock it.
847                    $lock = Open(undef, "<$FIG_Config::fig_disk/config/FIG_Config.pm");
848                    flock $lock, LOCK_EX;
849                    # Does it exist?
850                    if (-s $fileName) {
851                        # Slurp it in.
852                        $rss = XML::Simple::XMLin($fileName, ForceArray => ['item']);
853                    } else {
854                        my $size = -s $fileName;
855                        # Create an empty channel.
856                        $rss = {
857                            channel => {
858                                title => 'NMPDR Warning Feed',
859                                link => "$FIG_Config::temp_url/$FIG_Config::error_feed",
860                                description => "Important messages regarding the status of the NMPDR.",
861                                generator => "NMPDR Trace Facility",
862                                docs => "http://blogs.law.harvard.edu/tech/rss",
863                                item => []
864                            },
865                        };
866          }          }
867          # Terminate with an error using the supplied message and the                  # Get the channel object.
868          # error message from the file system.                  my $channel = $rss->{channel};
869          Confess("$message: $!");                  # Update the last-build date.
870                    $channel->{lastBuildDate} = $date;
871                    # Get the item array.
872                    my $items = $channel->{item};
873                    # Insure it has only 100 entries.
874                    while (scalar @{$items} > 100) {
875                        pop @{$items};
876                    }
877                    # Add our new item at the front.
878                    unshift @{$items}, $newItem;
879                    # Create the XML. Note we do not include the root or the declaration. XML Simple can't handle
880                    # the requirements for those.
881                    my $xml = XML::Simple::XMLout($channel, NoAttr => 1, RootName => 'channel', XmlDecl => '');
882                    # Here we put in the root and declaration. The problem is that the root has to have the version attribute
883                    # in it. So, we suppress the root and do it by hand, and that requires suppressing the declaration, too.
884                    $xml = "<?xml version=\"1.0\" encoding=\"utf-8\"?>\n<rss version=\"2.0\">$xml\n</rss>";
885                    # We don't use Open here because we can't afford an error.
886                    if (open XMLOUT, ">$fileName") {
887                        print XMLOUT $xml;
888                        close XMLOUT;
889      }      }
890      # Return the file handle.              }
891      return $fileHandle;          }
892        };
893        if ($@) {
894            # If the feed failed, we need to know why. The error will be traced, but this method will not be involved
895            # (which is a good thing).
896            my $error = $@;
897            Trace("Feed Error: $error") if T(Feed => 0);
898        }
899        # Be sure to unlock.
900        if ($lock) {
901            flock $lock, LOCK_UN;
902            undef $lock;
903        }
904        # Restore the error message.
905        $@ = $savedError;
906  }  }
907    
 =head3 FindNamePart  
908    
 C<< my ($fileName, $start, $len) = Tracer::FindNamePart($fileSpec); >>  
909    
 Extract the portion of a file specification that contains the file name.  
910    
911  A file specification is the string passed to an C<open> call. It specifies the file  =head3 Assert
 mode and name. In a truly complex situation, it can specify a pipe sequence. This  
 method assumes that the file name is whatever follows the first angle bracket  
 sequence.  So, for example, in the following strings the file name is  
 C</usr/fig/myfile.txt>.  
912    
913      >>/usr/fig/myfile.txt      Assert($condition1, $condition2, ... $conditionN);
     </usr/fig/myfile.txt  
     | sort -u > /usr/fig/myfile.txt  
914    
915  If the method cannot find a file name using its normal methods, it will return the  Return TRUE if all the conditions are true. This method can be used in conjunction with
916  whole incoming string.  the OR operator and the L</Confess> method as a debugging assert.
917    So, for example
918    
919  =over 4      Assert($recNum >= 0) || Confess("Invalid record number $recNum.");
920    
921  =item fileSpec  Will abort the program with a stack trace if the value of C<$recNum> is negative.
922    
923  File specification string from which the file name is to be extracted.  =cut
924    sub Assert {
925        my $retVal = 1;
926        LOOP: for my $condition (@_) {
927            if (! $condition) {
928                $retVal = 0;
929                last LOOP;
930            }
931        }
932        return $retVal;
933    }
934    
935  =item RETURN  =head3 Cluck
936    
937  Returns a three-element list. The first element contains the file name portion of      Cluck($message);
 the specified string, or the whole string if a file name cannot be found via normal  
 methods. The second element contains the start position of the file name portion and  
 the third element contains the length.  
   
 =back  
   
 =cut  
 #: Return Type $;  
 sub FindNamePart {  
     # Get the parameters.  
     my ($fileSpec) = @_;  
     # Default to the whole input string.  
     my ($retVal, $pos, $len) = ($fileSpec, 0, length $fileSpec);  
     # Parse out the file name if we can.  
     if ($fileSpec =~ m/(<|>>?)(.+?)(\s*)$/) {  
         $retVal = $2;  
         $len = length $retVal;  
         $pos = (length $fileSpec) - (length $3) - $len;  
     }  
     # Return the result.  
     return ($retVal, $pos, $len);  
 }  
   
 =head3 OpenDir  
   
 C<< my @files = OpenDir($dirName, $filtered, $flag); >>  
   
 Open a directory and return all the file names. This function essentially performs  
 the functions of an C<opendir> and C<readdir>. If the I<$filtered> parameter is  
 set to TRUE, all filenames beginning with a period (C<.>), dollar sign (C<$>),  
 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,  
   
     my @files = OpenDir("/Volumes/fig/contigs", 1);  
   
 is effectively the same as  
   
     opendir(TMP, "/Volumes/fig/contigs") || Confess("Could not open /Volumes/fig/contigs.");  
     my @files = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir(TMP);  
938    
939  Similarly, the following code  Trace the call stack. Note that for best results, you should qualify the call with a
940    trace condition. For example,
941    
942      my @files = grep { $_ =~ /^\d/ } OpenDir("/Volumes/fig/orgs", 0, 1);      Cluck("Starting record parse.") if T(3);
943    
944  Returns the names of all files in C</Volumes/fig/orgs> that begin with digits and  will only trace the stack if the trace level for the package is 3 or more.
 automatically returns an empty list if the directory fails to open.  
945    
946  =over 4  =over 4
947    
948  =item dirName  =item message
949    
950  Name of the directory to open.  Message to include in the trace.
951    
952  =item filtered  =back
953    
954  TRUE if files whose names begin with a period (C<.>) should be automatically removed  =cut
 from the list, else FALSE.  
955    
956  =item flag  sub Cluck {
957        # Get the parameters.
958        my ($message) = @_;
959        # Trace what's happening.
960        Trace("Stack trace for event: $message");
961        # Get the stack trace.
962        my @trace = LongMess();
963        # Convert the trace to a series of messages.
964        for my $line (@trace) {
965            # Replace the tab at the beginning with spaces.
966            $line =~ s/^\t/    /;
967            # Trace the line.
968            Trace($line);
969        }
970        # Issue a warning. This displays the event message and inserts it into the RSS error feed.
971        Warn($message);
972    }
973    
974  TRUE if a failure to open is okay, else FALSE  =head3 LongMess
975    
976  =back      my @lines = Tracer::LongMess();
977    
978    Return a stack trace with all tracing methods removed. The return will be in the form of a list
979    of message strings.
980    
981  =cut  =cut
982  #: Return Type @;  
983  sub OpenDir {  sub LongMess {
     # Get the parameters.  
     my ($dirName, $filtered, $flag) = @_;  
984      # Declare the return variable.      # Declare the return variable.
985      my @retVal = ();      my @retVal = ();
986      # Open the directory.      my $confession = longmess("");
987      if (opendir(my $dirHandle, $dirName)) {      for my $line (split /\s*\n/, $confession) {
988          # The directory opened successfully. Get the appropriate list according to the          unless ($line =~ /Tracer\.pm/) {
989          # strictures of the filter parameter.              # Here we have a line worth keeping. Push it onto the result list.
990          if ($filtered) {              push @retVal, $line;
             @retVal = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir $dirHandle;  
         } else {  
             @retVal = readdir $dirHandle;  
991          }          }
     } elsif (! $flag) {  
         # Here the directory would not open and it's considered an error.  
         Confess("Could not open directory $dirName.");  
992      }      }
993      # Return the result.      # Return the result.
994      return @retVal;      return @retVal;
995  }  }
996    
997  =head3 SetLevel  =head3 ETracing
998    
999  C<< Tracer::SetLevel($newLevel); >>      ETracing($parameter);
1000    
1001  Modify the trace level. A higher trace level will cause more messages to appear.  Set up emergency tracing. Emergency tracing is tracing that is turned
1002    on automatically for any program that calls this method. The emergency
1003    tracing parameters are stored in a a file identified by a tracing key.
1004    If this method is called with a CGI object, then the tracing key is
1005    taken from a cookie. If it is called with no parameters, then the tracing
1006    key is taken from an environment variable. If it is called with a string,
1007    the tracing key is that string.
1008    
1009  =over 4  =over 4
1010    
1011  =item newLevel  =item parameter
1012    
1013  Proposed new trace level.  A parameter from which the tracing key is computed. If it is a scalar,
1014    that scalar is used as the tracing key. If it is a CGI object, the
1015    tracing key is taken from the C<IP> cookie. If it is omitted, the
1016    tracing key is taken from the C<TRACING> environment variable. If it
1017    is a CGI object and emergency tracing is not on, the C<Trace> and
1018    C<TF> parameters will be used to determine the type of tracing.
1019    
1020  =back  =back
1021    
1022  =cut  =cut
1023    
1024  sub SetLevel {  sub ETracing {
1025      $TraceLevel = $_[0];      # Get the parameter.
1026        my ($parameter) = @_;
1027        # Check for CGI mode.
1028        if (defined $parameter && ref $parameter eq 'CGI') {
1029            $SavedCGI = $parameter;
1030        } else {
1031            $SavedCGI = undef;
1032        }
1033        # Default to no tracing except errors.
1034        my ($tracing, $dest) = ("0", "WARN");
1035        # Check for emergency tracing.
1036        my $tkey = EmergencyKey($parameter);
1037        my $emergencyFile = EmergencyFileName($tkey);
1038        if (-e $emergencyFile) {
1039            # We have the file. Read in the data.
1040            my @tracing = GetFile($emergencyFile);
1041            # Pull off the time limit.
1042            my $expire = shift @tracing;
1043            # Convert it to seconds.
1044            $expire *= 3600;
1045            # Check the file data.
1046            my $stat = stat($emergencyFile);
1047            my ($now) = gettimeofday;
1048            if ($now - $stat->mtime > $expire) {
1049                # Delete the expired file.
1050                unlink $emergencyFile;
1051            } else {
1052                # Emergency tracing is on. Pull off the destination and
1053                # the trace level;
1054                $dest = shift @tracing;
1055                my $level = shift @tracing;
1056                # Convert the destination to a real tracing destination.
1057                # temp directory.
1058                $dest = EmergencyTracingDest($tkey, $dest);
1059                # Insure Tracer is specified.
1060                my %moduleHash = map { $_ => 1 } @tracing;
1061                $moduleHash{Tracer} = 1;
1062                # Set the trace parameter.
1063                $tracing = join(" ", $level, sort keys %moduleHash);
1064            }
1065        } elsif (defined $SavedCGI) {
1066            # There's no emergency tracing, but we have a CGI object, so check
1067            # for tracing from the form parameters.
1068            if ($SavedCGI->param('Trace')) {
1069                # Here the user has requested tracing via a form.
1070                $dest = ($SavedCGI->param('TF') ? ">$FIG_Config::temp/Trace$$.log" : "QUEUE");
1071                $tracing = $SavedCGI->param('Trace') . " Tracer";
1072            }
1073        }
1074        # Setup the tracing we've determined from all the stuff above.
1075        TSetup($tracing, $dest);
1076        # Check to see if we're a web script.
1077        if (defined $SavedCGI) {
1078            # Yes we are. Trace the form and environment data.
1079            TraceParms($SavedCGI);
1080            # Check for RAW mode. In raw mode, we print a fake header so that we see everything
1081            # emitted by the script in its raw form.
1082            if (T(Raw => 3)) {
1083                print CGI::header(-type => 'text/plain', -tracing => 'Raw');
1084            }
1085        }
1086  }  }
1087    
1088  =head3 Now  =head3 EmergencyFileName
1089    
1090  C<< my $string = Tracer::Now(); >>      my $fileName = Tracer::EmergencyFileName($tkey);
1091    
1092  Return a displayable time stamp containing the local time.  Return the emergency tracing file name. This is the file that specifies
1093    the tracing information.
1094    
1095  =cut  =over 4
1096    
1097  sub Now {  =item tkey
     my ($sec,$min,$hour,$mday,$mon,$year,$wday,$yday,$isdst) = localtime(time);  
     my $retVal = _p2($mon+1) . "/" . _p2($mday) . "/" . ($year + 1900) . " " .  
                  _p2($hour) . ":" . _p2($min) . ":" . _p2($sec);  
     return $retVal;  
 }  
1098    
1099  # Pad a number to 2 digits.  Tracing key for the current program.
1100  sub _p2 {  
1101      my ($value) = @_;  =item RETURN
1102      $value = "0$value" if ($value < 10);  
1103      return $value;  Returns the name of the file to contain the emergency tracing information.
1104    
1105    =back
1106    
1107    =cut
1108    
1109    sub EmergencyFileName {
1110        # Get the parameters.
1111        my ($tkey) = @_;
1112        # Compute the emergency tracing file name.
1113        return "$FIG_Config::temp/Emergency$tkey.txt";
1114  }  }
1115    
1116  =head3 LogErrors  =head3 EmergencyFileTarget
1117    
1118  C<< Tracer::LogErrors($fileName); >>      my $fileName = Tracer::EmergencyFileTarget($tkey);
1119    
1120  Route the standard error output to a log file.  Return the emergency tracing target file name. This is the file that receives
1121    the tracing output for file-based tracing.
1122    
1123  =over 4  =over 4
1124    
1125  =item fileName  =item tkey
1126    
1127  Name of the file to receive the error output.  Tracing key for the current program.
1128    
1129    =item RETURN
1130    
1131    Returns the name of the file to contain the trace output.
1132    
1133  =back  =back
1134    
1135  =cut  =cut
1136    
1137  sub LogErrors {  sub EmergencyFileTarget {
1138      # Get the file name.      # Get the parameters.
1139      my ($fileName) = @_;      my ($tkey) = @_;
1140      # Open the file as the standard error output.      # Compute the emergency tracing file name.
1141      open STDERR, '>', $fileName;      return "$FIG_Config::temp/trace$tkey.log";
1142  }  }
1143    
1144  =head3 ReadOptions  =head3 EmergencyTracingDest
1145    
1146  C<< my %options = Tracer::ReadOptions($fileName); >>      my $dest = Tracer::EmergencyTracingDest($tkey, $myDest);
1147    
1148  Read a set of options from a file. Each option is encoded in a line of text that has the  This method converts an emergency tracing destination to a real
1149  format  tracing destination. The main difference is that if the
1150    destination is C<FILE> or C<APPEND>, we convert it to file
1151    output. If the destination is C<DUAL>, we convert it to file
1152    and standard output.
1153    
1154  I<optionName>C<=>I<optionValue>C<; >I<comment>  =over 4
1155    
1156  The option name must consist entirely of letters, digits, and the punctuation characters  =item tkey
 C<.> and C<_>, and is case sensitive. Blank lines and lines in which the first nonblank  
 character is a semi-colon will be ignored. The return hash will map each option name to  
 the corresponding option value.  
1157    
1158  =over 4  Tracing key for this environment.
1159    
1160  =item fileName  =item myDest
1161    
1162  Name of the file containing the option data.  Destination from the emergency tracing file.
1163    
1164  =item RETURN  =item RETURN
1165    
1166  Returns a hash mapping the option names specified in the file to their corresponding option  Returns a destination that can be passed into L</TSetup>.
 value.  
1167    
1168  =back  =back
1169    
1170  =cut  =cut
1171    
1172  sub ReadOptions {  sub EmergencyTracingDest {
1173      # Get the parameters.      # Get the parameters.
1174      my ($fileName) = @_;      my ($tkey, $myDest) = @_;
1175      # Open the file.      # Declare the return variable.
1176      (open CONFIGFILE, "<$fileName") || Confess("Could not open option file $fileName.");      my $retVal = $myDest;
1177      # Count the number of records read.      # Process according to the destination value.
1178      my ($records, $comments) = 0;      if ($myDest eq 'FILE') {
1179      # Create the return hash.          $retVal = ">" . EmergencyFileTarget($tkey);
1180      my %retVal = ();      } elsif ($myDest eq 'APPEND') {
1181      # Loop through the file, accumulating key-value pairs.          $retVal = ">>" . EmergencyFileTarget($tkey);
1182      while (my $line = <CONFIGFILE>) {      } elsif ($myDest eq 'DUAL') {
1183          # Denote we've read a line.          $retVal = "+>" . EmergencyFileTarget($tkey);
1184          $records++;      } elsif ($myDest eq 'WARN') {
1185          # Determine the line type.          $retVal = "WARN";
         if ($line =~ /^\s*[\n\r]/) {  
             # A blank line is a comment.  
             $comments++;  
         } elsif ($line =~ /^\s*([A-Za-z0-9_\.]+)=([^;]*);/) {  
             # Here we have an option assignment.  
             retVal{$1} = $2;  
         } elsif ($line =~ /^\s*;/) {  
             # Here we have a text comment.  
             $comments++;  
         } else {  
             # Here we have an invalid line.  
             Trace("Invalid option statement in record $records.") if T(0);  
         }  
1186      }      }
1187      # Return the hash created.      # Return the result.
1188      return %retVal;      return $retVal;
1189  }  }
1190    
1191  =head3 GetOptions  =head3 Emergency
   
 C<< Tracer::GetOptions(\%defaults, \%options); >>  
1192    
1193  Merge a specified set of options into a table of defaults. This method takes two hash references      Emergency($key, $hours, $dest, $level, @modules);
 as input and uses the data from the second to update the first. If the second does not exist,  
 there will be no effect. An error will be thrown if one of the entries in the second hash does not  
 exist in the first.  
1194    
1195  Consider the following example.  Turn on emergency tracing. This method is normally invoked over the web from
1196    a debugging console, but it can also be called by the C<trace.pl> script.
1197    The caller specifies the duration of the emergency in hours, the desired tracing
1198    destination, the trace level, and a list of the trace modules to activate.
1199    For the length of the duration, when a program in an environment with the
1200    specified tracing key active invokes a Sprout CGI script, tracing will be
1201    turned on automatically. See L</TSetup> for more about tracing setup and
1202    L</ETracing> for more about emergency tracing.
1203    
1204  C<< my $optionTable = GetOptions({ dbType => 'mySQL', trace => 0 }, $options); >>  =over 4
1205    
1206  In this example, the variable B<$options> is expected to contain at most two options-- B<dbType> and  =item tkey
 B<trace>. The default database type is C<mySQL> and the default trace level is C<0>. If the value of  
 B<$options> is C<< {dbType => 'Oracle'} >>, then the database type will be changed to C<Oracle> and  
 the trace level will remain at 0. If B<$options> is undefined, then the database type and trace level  
 will remain C<mySQL> and C<0>. If, on the other hand, B<$options> is defined as  
1207    
1208  C<< {databaseType => 'Oracle'} >>  The tracing key. This is used to identify the control file and the trace file.
1209    
1210  an error will occur because the B<databaseType> option does not exist.  =item hours
1211    
1212  =over 4  Number of hours to keep emergency tracing alive.
1213    
1214  =item defaults  =item dest
1215    
1216  Table of default option values.  Tracing destination. If no path information is specified for a file
1217    destination, it is put in the FIG temporary directory.
1218    
1219  =item options  =item level
1220    
1221  Table of overrides, if any.  Tracing level. A higher level means more trace messages.
1222    
1223  =item RETURN  =item modules
1224    
1225  Returns a reference to the default table passed in as the first parameter.  A list of the tracing modules to activate.
1226    
1227  =back  =back
1228    
1229  =cut  =cut
1230    
1231  sub GetOptions {  sub Emergency {
1232      # Get the parameters.      # Get the parameters.
1233      my ($defaults, $options) = @_;      my ($tkey, $hours, $dest, $level, @modules) = @_;
1234      # Check for overrides.      # Create the emergency file.
1235      if ($options) {      my $specFile = EmergencyFileName($tkey);
1236          # Loop through the overrides.      my $outHandle = Open(undef, ">$specFile");
1237          while (my ($option, $setting) = each %{$options}) {      print $outHandle join("\n", $hours, $dest, $level, @modules, "");
             # Insure this override exists.  
             if (!exists $defaults->{$option}) {  
                 croak "Unrecognized option $option encountered.";  
             } else {  
                 # Apply the override.  
                 $defaults->{$option} = $setting;  
             }  
         }  
     }  
     # Return the merged table.  
     return $defaults;  
1238  }  }
1239    
1240  =head3 MergeOptions  =head3 EmergencyKey
1241    
1242  C<< Tracer::MergeOptions(\%table, \%defaults); >>      my $tkey = EmergencyKey($parameter);
1243    
1244  Merge default values into a hash table. This method looks at the key-value pairs in the  Return the Key to be used for emergency tracing. This could be an IP address,
1245  second (default) hash, and if a matching key is not found in the first hash, the default   a session ID, or a user name, depending on the environment.
 pair is copied in. The process is similar to L</GetOptions>, but there is no error-  
 checking and no return value.  
1246    
1247  =over 4  =over 4
1248    
1249  =item table  =item parameter
1250    
1251  Hash table to be updated with the default values.  Parameter defining the method for finding the tracing key. If it is a scalar,
1252    then it is presumed to be the tracing key itself. If it is a CGI object, then
1253    the tracing key is taken from the C<IP> cookie. Otherwise, the tracing key is
1254    taken from the C<TRACING> environment variable.
1255    
1256  =item defaults  =item RETURN
1257    
1258  Default values to be merged into the first hash table if they are not already present.  Returns the key to be used for labels in emergency tracing.
1259    
1260  =back  =back
1261    
1262  =cut  =cut
1263    
1264  sub MergeOptions {  sub EmergencyKey {
1265      # Get the parameters.      # Get the parameters.
1266      my ($table, $defaults) = @_;      my ($parameter) = @_;
1267      # Loop through the defaults.      # Declare the return variable.
1268      while (my ($key, $value) = each %{$defaults}) {      my $retVal;
1269          if (!exists $table->{$key}) {      # Determine the parameter type.
1270              $table->{$key} = $value;      if (! defined $parameter || defined($ENV{TRACING})) {
1271          }          # Here we're supposed to check the environment. If that fails, we
1272            # get the effective login ID.
1273            $retVal = $ENV{TRACING} || scalar getpwuid($<);
1274        } else {
1275            my $ptype = ref $parameter;
1276            if ($ptype eq 'CGI') {
1277                # Here we were invoked from a web page. Look for a cookie.
1278                $retVal = $parameter->cookie('IP');
1279            } elsif (! $ptype) {
1280                # Here the key was passed in.
1281                $retVal = $parameter;
1282            }
1283        }
1284        # If no luck finding a key, use the PID.
1285        if (! defined $retVal) {
1286            $retVal = $$;
1287      }      }
1288        # Return the result.
1289        return $retVal;
1290  }  }
1291    
 =head3 Trace  
1292    
1293  C<< Trace($message); >>  =head3 TraceParms
1294    
1295  Write a trace message to the target location specified in L</TSetup>. If there has not been      Tracer::TraceParms($cgi);
1296  any prior call to B<TSetup>.  
1297    Trace the CGI parameters at trace level CGI => 3 and the environment variables
1298    at level CGI => 4. A self-referencing URL is traced at level CGI => 2.
1299    
1300  =over 4  =over 4
1301    
1302  =item message  =item cgi
1303    
1304  Message to write.  CGI query object containing the parameters to trace.
1305    
1306  =back  =back
1307    
1308  =cut  =cut
1309    
1310  sub Trace {  sub TraceParms {
1311      # Get the parameters.      # Get the parameters.
1312      my ($message) = @_;      my ($cgi) = @_;
1313      # Get the timestamp.      if (T(CGI => 2)) {
1314      my $timeStamp = Now();          # Here we trace the GET-style URL for the script.
1315      # Format the message. Note we strip off any line terminators at the end.          Trace("[URL] " . $cgi->url(-relative => 1, -query => 1));
1316      my $formatted = "$timeStamp <$LastCategory>: " . Strip($message);      }
1317      # Process according to the destination.      if (T(CGI => 3)) {
1318      if ($Destination eq "TEXT") {          # Here we want to trace the parameter data.
1319          # Write the message to the standard output.          my @names = $cgi->param;
1320          print "$formatted\n";          for my $parmName (sort @names) {
1321      } elsif ($Destination eq "ERROR") {              # Note we skip the Trace parameters, which are for our use only.
1322          # Write the message to the error output.              if ($parmName ne 'Trace' && $parmName ne 'TF') {
1323          print STDERR "$formatted\n";                  my @values = $cgi->param($parmName);
1324      } elsif ($Destination eq "QUEUE") {                  Trace("[CGI] $parmName = " . join(", ", @values));
1325          # Push the message into the queue.              }
1326          push @Queue, "$formatted";          }
1327      } elsif ($Destination eq "HTML") {          # Display the request method.
1328          # Convert the message to HTML and write it to the standard output.          my $method = $cgi->request_method();
1329          my $escapedMessage = CGI::escapeHTML($message);          Trace("Method: $method");
1330          print "<p>$formatted</p>\n";      }
1331      } elsif ($Destination eq "WARN") {      if (T(CGI => 4)) {
1332         # Emit the message as a warning.          # Here we want the environment data too.
1333         warn $message;          for my $envName (sort keys %ENV) {
1334      } elsif ($Destination =~ m/^>>/) {              Trace("[ENV] $envName = $ENV{$envName}");
         # 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";  
1335          }          }
1336      }      }
1337  }  }
1338    
1339  =head3 T  =head3 TraceImages
   
 C<< my $switch = T($category, $traceLevel); >>  
   
     or  
1340    
1341  C<< my $switch = T($traceLevel); >>      Tracer::TraceImages($htmlString);
1342    
1343  Return TRUE if the trace level is at or above a specified value and the specified category  Trace information about all of an html document's images. The tracing
1344  is active, else FALSE. If no category is specified, the caller's package name is used.  will be for type "IMG" at level 3. The image's source string
1345    will be displayed. This is generally either the URL of the image or
1346    raw data for the image itself. If the source is too long, only the first 300
1347    characters will be shown at trace level 3. The entire source will be shown,
1348    however, at trace level 4. This method is not very smart, and might catch
1349    Javascript code, but it is still useful when debugging the arcane
1350    behavior of images in multiple browser environments.
1351    
1352  =over 4  =over 4
1353    
1354  =item category  =item htmlString
   
 Category to which the message belongs. If not specified, the caller's package name is  
 used.  
   
 =item traceLevel  
   
 Relevant tracing level.  
   
 =item RETURN  
1355    
1356  TRUE if a message at the specified trace level would appear in the trace, else FALSE.  HTML text for an outgoing web page.
1357    
1358  =back  =back
1359    
1360  =cut  =cut
1361    
1362  sub T {  sub TraceImages {
1363      # Declare the return variable.      # Only proceed if we're at the proper trace level.
1364      my $retVal = 0;      if (T(IMG => 3)) {
1365      # Only proceed if tracing is turned on.          # For performance reasons we're manipulating $_[0] instead of retrieving the string
1366      if ($Destination ne "NONE") {          # into a variable called "$htmlString". This is because we expect html strings to be
1367          # Get the parameters.          # long, and don't want to copy them any more than we have to.
1368          my ($category, $traceLevel) = @_;          Trace(length($_[0]) . " characters in web page.");
1369          if (!defined $traceLevel) {          # Loop through the HTML, culling image tags.
1370              # Here we have no category, so we need to get the calling package.          while ($_[0] =~ /<img\s+[^>]+?src="([^"]+)"/sgi) {
1371              # The calling package is normally the first parameter. If it is              # Extract the source string and determine whether or not it's too long.
1372              # omitted, the first parameter will be the tracelevel. So, the              my $srcString = $1;
1373              # first thing we do is shift the so-called category into the              my $pos = pos($_[0]) - length($srcString);
1374              # $traceLevel variable where it belongs.              my $excess = length($srcString) - 300;
1375              $traceLevel = $category;              # We'll put the display string in here.
1376              my ($package, $fileName, $line) = caller;              my $srcDisplay = $srcString;
1377              # If there is no calling package, we default to "main".              # If it's a data string, split it at the comma.
1378              if (!$package) {              $srcDisplay =~ s/^(data[^,]+,)/$1\n/;
1379                  $category = "main";              # If there's no excess or we're at trace level 4, we're done. At level 3 with
1380              } else {              # a long string, however, we only show the first 300 characters.
1381                  $category = $package;              if ($excess > 0 && ! T(IMG => 4)) {
1382                    $srcDisplay = substr($srcDisplay,0,300) . "\nplus $excess characters.";
1383              }              }
1384                # Output the trace message.
1385                Trace("Image tag at position $pos:\n$srcDisplay");
1386          }          }
         # Save the category name.  
         $LastCategory = $category;  
         # Convert it to lower case before we hash it.  
         $category = lc $category;  
         # Use the category and tracelevel to compute the result.  
         if (ref $traceLevel) {  
             Confess("Bad trace level.");  
         } elsif (ref $TraceLevel) {  
             Confess("Bad trace config.");  
         }  
         $retVal = ($traceLevel <= $TraceLevel && ($AllTrace || exists $Categories{$category}));  
1387      }      }
     # Return the computed result.  
     return $retVal;  
1388  }  }
1389    
1390  =head3 ParseCommand  =head2 Command-Line Utility Methods
   
 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  
1391    
1392  C<< -logFile=error.log apple orange rutabaga >>  =head3 SendSMS
1393    
1394  then at the end of the invocation, C<$options> will be      my $msgID = Tracer::SendSMS($phoneNumber, $msg);
1395    
1396  C<< { errors => 0, logFile => 'error.log' } >>  Send a text message to a phone number using Clickatell. The FIG_Config file must contain the
1397    user name, password, and API ID for the relevant account in the hash reference variable
1398    I<$FIG_Config::phone>, using the keys C<user>, C<password>, and C<api_id>. For
1399    example, if the user name is C<BruceTheHumanPet>, the password is C<silly>, and the API ID
1400    is C<2561022>, then the FIG_Config file must contain
1401    
1402  and C<@arguments> will contain      $phone =  { user => 'BruceTheHumanPet',
1403                    password => 'silly',
1404                    api_id => '2561022' };
1405    
1406  C<< apple orange rutabaga >>  The original purpose of this method was to insure Bruce would be notified immediately when the
1407    Sprout Load terminates. Care should be taken if you do not wish Bruce to be notified immediately
1408    when you call this method.
1409    
1410  The parser allows for some escape sequences. See L</UnEscape> for a description. There is no  The message ID will be returned if successful, and C<undef> if an error occurs.
 support for quote characters.  
1411    
1412  =over 4  =over 4
1413    
1414  =item optionTable  =item phoneNumber
1415    
1416  Table of default options.  Phone number to receive the message, in international format. A United States phone number
1417    would be prefixed by "1". A British phone number would be prefixed by "44".
1418    
1419  =item inputList  =item msg
1420    
1421  List of words on the command line.  Message to send to the specified phone.
1422    
1423  =item RETURN  =item RETURN
1424    
1425  Returns a reference to the option table and a list of the positional arguments.  Returns the message ID if successful, and C<undef> if the message could not be sent.
1426    
1427  =back  =back
1428    
1429  =cut  =cut
1430    
1431  sub ParseCommand {  sub SendSMS {
1432      # Get the parameters.      # Get the parameters.
1433      my ($optionTable, @inputList) = @_;      my ($phoneNumber, $msg) = @_;
1434      # Process any options in the input list.      # Declare the return variable. If we do not change it, C<undef> will be returned.
1435      my %overrides = ();      my $retVal;
1436      while ((@inputList > 0) && ($inputList[0] =~ /^-/)) {      # Only proceed if we have phone support.
1437          # Get the current option.      if (! defined $FIG_Config::phone) {
1438          my $arg = shift @inputList;          Trace("Phone support not present in FIG_Config.") if T(1);
         # Pull out the option name.  
         $arg =~ /^-([^=]*)/g;  
         my $name = $1;  
         # Check for an option value.  
         if ($arg =~ /\G=(.*)$/g) {  
             # Here we have a value for the option.  
             $overrides{$name} = UnEscape($1);  
1439          } else {          } else {
1440              # Here there is no value, so we use 1.          # Get the phone data.
1441              $overrides{$name} = 1;          my $parms = $FIG_Config::phone;
1442            # Get the Clickatell URL.
1443            my $url = "http://api.clickatell.com/http/";
1444            # Create the user agent.
1445            my $ua = LWP::UserAgent->new;
1446            # Request a Clickatell session.
1447            my $resp = $ua->post("$url/sendmsg", { user => $parms->{user},
1448                                         password => $parms->{password},
1449                                         api_id => $parms->{api_id},
1450                                         to => $phoneNumber,
1451                                         text => $msg});
1452            # Check for an error.
1453            if (! $resp->is_success) {
1454                Trace("Alert failed.") if T(1);
1455            } else {
1456                # Get the message ID.
1457                my $rstring = $resp->content;
1458                if ($rstring =~ /^ID:\s+(.*)$/) {
1459                    $retVal = $1;
1460                } else {
1461                    Trace("Phone attempt failed with $rstring") if T(1);
1462          }          }
1463      }      }
     # Merge the options into the defaults.  
     GetOptions($optionTable, \%overrides);  
     # Translate the remaining parameters.  
     my @retVal = ();  
     for my $inputParm (@inputList) {  
         push @retVal, UnEscape($inputParm);  
1464      }      }
1465      # Return the results.      # Return the result.
1466      return ($optionTable, @retVal);      return $retVal;
1467  }  }
1468    
1469  =head3 Escape  =head3 StandardSetup
   
 C<< my $codedString = Tracer::Escape($realString); >>  
   
 Escape a string for use in a command length. Tabs will be replaced by C<\t>, new-lines  
 replaced by C<\n>, carriage returns will be deleted, and backslashes will be doubled. The  
 result is to reverse the effect of L</UnEscape>.  
1470    
1471  =over 4      my ($options, @parameters) = StandardSetup(\@categories, \%options, $parmHelp, @ARGV);
1472    
1473  =item realString  This method performs standard command-line parsing and tracing setup. The return
1474    values are a hash of the command-line options and a list of the positional
1475    parameters. Tracing is automatically set up and the command-line options are
1476    validated.
1477    
1478  String to escape.  This is a complex method that does a lot of grunt work. The parameters can
1479    be more easily understood, however, once they are examined individually.
1480    
1481  =item RETURN  The I<categories> parameter is the most obtuse. It is a reference to a list of
1482    special-purpose tracing categories. Most tracing categories are PERL package
1483    names. So, for example, if you wanted to turn on tracing inside the B<Sprout>,
1484    B<ERDB>, and B<SproutLoad> packages, you would specify the categories
1485    
1486  Escaped equivalent of the real string.      ["Sprout", "SproutLoad", "ERDB"]
1487    
1488  =back  This would cause trace messages in the specified three packages to appear in
1489    the output. There are two special tracing categories that are automatically
1490    handled by this method. In other words, if you used L</TSetup> you would need
1491    to include these categories manually, but if you use this method they are turned
1492    on automatically.
1493    
1494  =cut  =over 4
1495    
1496  sub Escape {  =item SQL
     # Get the parameter.  
     my ($realString) = @_;  
     # Initialize the return variable.  
     my $retVal = "";  
     # Loop through the parameter string, looking for sequences to escape.  
     while (length $realString > 0) {  
         # Look for the first sequence to escape.  
         if ($realString =~ /^(.*?)([\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;  
             # 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;  
             }  
         } else {  
             # Here there are no more escape sequences. The rest of the string is  
             # transferred unmodified.  
             $retVal .= $realString;  
             $realString = "";  
         }  
     }  
     # Return the result.  
     return $retVal;  
 }  
1497    
1498  =head3 UnEscape  Traces SQL commands and activity.
1499    
1500  C<< my $realString = Tracer::UnEscape($codedString); >>  =item Tracer
1501    
1502  Replace escape sequences with their actual equivalents. C<\t> will be replaced by  Traces error messages and call stacks.
 a tab, C<\n> by a new-line character, and C<\\> by a backslash. C<\r> codes will  
 be deleted.  
1503    
1504  =over 4  =back
1505    
1506  =item codedString  C<SQL> is only turned on if the C<-sql> option is specified in the command line.
1507    The trace level is specified using the C<-trace> command-line option. For example,
1508    the following command line for C<TransactFeatures> turns on SQL tracing and runs
1509    all tracing at level 3.
1510    
1511  String to un-escape.      TransactFeatures -trace=3 -sql register ../xacts IDs.tbl
1512    
1513  =item RETURN  Standard tracing is output to the standard output and echoed to the file
1514    C<trace>I<$$>C<.log> in the FIG temporary directory, where I<$$> is the
1515    process ID. You can also specify the C<user> parameter to put a user ID
1516    instead of a process ID in the trace file name. So, for example
1517    
1518  Returns a copy of the original string with the escape sequences converted to their actual  The default trace level is 2. To get all messages, specify a trace level of 4.
1519  values.  For a genome-by-genome update, use 3.
1520    
1521  =back      TransactFeatures -trace=3 -sql -user=Bruce register ../xacts IDs.tbl
1522    
1523  =cut  would send the trace output to C<traceBruce.log> in the temporary directory.
1524    
1525  sub UnEscape {  The I<options> parameter is a reference to a hash containing the command-line
1526      # Get the parameter.  options, their default values, and an explanation of what they mean. Command-line
1527      my ($codedString) = @_;  options may be in the form of switches or keywords. In the case of a switch, the
1528      # Initialize the return variable.  option value is 1 if it is specified and 0 if it is not specified. In the case
1529      my $retVal = "";  of a keyword, the value is separated from the option name by an equal sign. You
1530      # Only proceed if the incoming string is nonempty.  can see this last in the command-line example above.
1531      if (defined $codedString) {  
1532          # Loop through the parameter string, looking for escape sequences. We can't do  You can specify a different default trace level by setting C<$options->{trace}>
1533          # translating because it causes problems with the escaped slash. ("\\t" becomes  prior to calling this method.
1534          # "\<tab>" no matter what we do.)  
1535          while (length $codedString > 0) {  An example at this point would help. Consider, for example, the command-line utility
1536              # Look for the first escape sequence.  C<TransactFeatures>. It accepts a list of positional parameters plus the options
1537              if ($codedString =~ /^(.*?)\\(\\|n|t|r)/) {  C<safe>, C<noAlias>, C<start>, and C<tblFiles>. To start up this command, we execute
1538                  # Here we found it. The text preceding the sequence is in $1. The sequence  the following code.
1539                  # itself is in $2. First, move the clear text to the return variable.  
1540                  $retVal .= $1;      my ($options, @parameters) = Tracer::StandardSetup(["DocUtils"],
1541                  $codedString = substr $codedString, (2 + length $1);                          { safe => [0, "use database transactions"],
1542                  # Get the escape value.                            noAlias => [0, "do not expect aliases in CHANGE transactions"],
1543                  my $char = $2;                            start => [' ', "start with this genome"],
1544                  # If we have a "\r", we are done.                            tblFiles => [0, "output TBL files containing the corrected IDs"] },
1545                  if ($char ne 'r') {                          "<command> <transactionDirectory> <IDfile>",
1546                      # Here it's not an 'r', so we convert it.                        @ARGV);
1547                      $char =~ tr/\\tn/\\\t\n/;  
1548                      $retVal .= $char;  
1549    The call to C<ParseCommand> specifies the default values for the options and
1550    stores the actual options in a hash that is returned as C<$options>. The
1551    positional parameters are returned in C<@parameters>.
1552    
1553    The following is a sample command line for C<TransactFeatures>.
1554    
1555        TransactFeatures -trace=2 -noAlias register ../xacts IDs.tbl
1556    
1557    Single and double hyphens are equivalent. So, you could also code the
1558    above command as
1559    
1560        TransactFeatures --trace=2 --noAlias register ../xacts IDs.tbl
1561    
1562    In this case, C<register>, C<../xacts>, and C<IDs.tbl> are the positional
1563    parameters, and would find themselves in I<@parameters> after executing the
1564    above code fragment. The tracing would be set to level 2, and the categories
1565    would be C<Tracer>, and <DocUtils>. C<Tracer> is standard,
1566    and C<DocUtils> was included because it came in within the first parameter
1567    to this method. The I<$options> hash would be
1568    
1569        { trace => 2, sql => 0, safe => 0,
1570          noAlias => 1, start => ' ', tblFiles => 0 }
1571    
1572    Use of C<StandardSetup> in this way provides a simple way of performing
1573    standard tracing setup and command-line parsing. Note that the caller is
1574    not even aware of the command-line switches C<-trace> and C<-sql>, which
1575    are used by this method to control the tracing. If additional tracing features
1576    need to be added in the future, they can be processed by this method without
1577    upsetting the command-line utilities.
1578    
1579    If the C<background> option is specified on the command line, then the
1580    standard and error outputs will be directed to files in the temporary
1581    directory, using the same suffix as the trace file. So, if the command
1582    line specified
1583    
1584        -user=Bruce -background
1585    
1586    then the trace output would go to C<traceBruce.log>, the standard output to
1587    C<outBruce.log>, and the error output to C<errBruce.log>. This is designed to
1588    simplify starting a command in the background.
1589    
1590    The user name is also used as the tracing key for L</Emergency Tracing>.
1591    Specifying a value of C<E> for the trace level causes emergency tracing to
1592    be used instead of custom tracing. If the user name is not specified,
1593    the tracing key is taken from the C<Tracing> environment variable. If there
1594    is no value for that variable, the tracing key will be computed from the active
1595    login ID.
1596    
1597    Since the default situation in StandardSetup is to trace to the standard
1598    output, errors that occur in command-line scripts will not generate
1599    RSS events. To force the events, use the C<warn> option.
1600    
1601        TransactFeatures -background -warn register ../xacts IDs.tbl
1602    
1603    Finally, if the special option C<-help> is specified, the option
1604    names will be traced at level 0 and the program will exit without processing.
1605    This provides a limited help capability. For example, if the user enters
1606    
1607        TransactFeatures -help
1608    
1609    he would see the following output.
1610    
1611        TransactFeatures [options] <command> <transactionDirectory> <IDfile>
1612            -trace    tracing level (default E)
1613            -sql      trace SQL commands
1614            -safe     use database transactions
1615            -noAlias  do not expect aliases in CHANGE transactions
1616            -start    start with this genome
1617            -tblFiles output TBL files containing the corrected IDs
1618            -forked   do not erase the trace file before tracing
1619    
1620    The caller has the option of modifying the tracing scheme by placing a value
1621    for C<trace> in the incoming options hash. The default value can be overridden,
1622    or the tracing to the standard output can be turned off by suffixing a minus
1623    sign to the trace level. So, for example,
1624    
1625        { trace => [0, "tracing level (default 0)"],
1626           ...
1627    
1628    would set the default trace level to 0 instead of E, while
1629    
1630        { trace => ["2-", "tracing level (default 2)"],
1631           ...
1632    
1633    would set the default to 2, but trace only to the log file, not to the
1634    standard output.
1635    
1636    The parameters to this method are as follows.
1637    
1638    =over 4
1639    
1640    =item categories
1641    
1642    Reference to a list of tracing category names. These should be names of
1643    packages whose internal workings will need to be debugged to get the
1644    command working.
1645    
1646    =item options
1647    
1648    Reference to a hash containing the legal options for the current command mapped
1649    to their default values and descriptions. The user can override the defaults
1650    by specifying the options as command-line switches prefixed by a hyphen.
1651    Tracing-related options may be added to this hash. If the C<-h> option is
1652    specified on the command line, the option descriptions will be used to
1653    explain the options. To turn off tracing to the standard output, add a
1654    minus sign to the value for C<trace> (see above).
1655    
1656    =item parmHelp
1657    
1658    A string that vaguely describes the positional parameters. This is used
1659    if the user specifies the C<-h> option.
1660    
1661    =item argv
1662    
1663    List of command line parameters, including the option switches, which must
1664    precede the positional parameters and be prefixed by a hyphen.
1665    
1666    =item RETURN
1667    
1668    Returns a list. The first element of the list is the reference to a hash that
1669    maps the command-line option switches to their values. These will either be the
1670    default values or overrides specified on the command line. The remaining
1671    elements of the list are the position parameters, in order.
1672    
1673    =back
1674    
1675    =cut
1676    
1677    sub StandardSetup {
1678        # Get the parameters.
1679        my ($categories, $options, $parmHelp, @argv) = @_;
1680        # Get the default tracing key.
1681        my $tkey = EmergencyKey();
1682        # Save the command line.
1683        $CommandLine = join(" ", $0, map { $_ =~ /\s/ ? "\"$_\"" : $_ } @argv);
1684        # Add the tracing options.
1685        if (! exists $options->{trace}) {
1686            $options->{trace} = ['2', "tracing level (E for emergency tracing)"];
1687        }
1688        if (! exists $options->{forked}) {
1689            $options->{forked} = [0, "keep old trace file"];
1690        }
1691        $options->{sql} = [0, "turn on SQL tracing"];
1692        $options->{help} = [0, "display command-line options"];
1693        $options->{user} = [$tkey, "tracing key"];
1694        $options->{background} = [0, "spool standard and error output"];
1695        $options->{warn} = [0, "send errors to RSS feed"];
1696        $options->{moreTracing} = ["", "comma-delimited list of additional trace modules for debugging"];
1697        # Create a parsing hash from the options hash. The parsing hash
1698        # contains the default values rather than the default value
1699        # and the description. While we're at it, we'll memorize the
1700        # length of the longest option name.
1701        my $longestName = 0;
1702        my %parseOptions = ();
1703        for my $key (keys %{$options}) {
1704            if (length $key > $longestName) {
1705                $longestName = length $key;
1706            }
1707            $parseOptions{$key} = $options->{$key}->[0];
1708        }
1709        # Parse the command line.
1710        my ($retOptions, @retParameters) = ParseCommand(\%parseOptions, @argv);
1711        # Get the logfile suffix.
1712        my $suffix = $retOptions->{user};
1713        # We'll put the trace file name in here. We need it later if background
1714        # mode is on.
1715        my $traceFileName;
1716        # Now we want to set up tracing. First, we need to know if the user
1717        # wants emergency tracing.
1718        if ($retOptions->{trace} eq 'E') {
1719            ETracing($retOptions->{user});
1720        } else {
1721            # Here the tracing is controlled from the command line.
1722            my @cats = @{$categories};
1723            if ($retOptions->{sql}) {
1724                push @cats, "SQL";
1725            }
1726            if ($retOptions->{warn}) {
1727                push @cats, "Feed";
1728            }
1729            # Add the default categories.
1730            push @cats, "Tracer";
1731            # Check for more tracing groups.
1732            if ($retOptions->{moreTracing}) {
1733                push @cats, split /,/, $retOptions->{moreTracing};
1734            }
1735            # Next, we create the category string by joining the categories.
1736            my $cats = join(" ", @cats);
1737            # Check to determine whether or not the caller wants to turn off tracing
1738            # to the standard output.
1739            my $traceLevel = $retOptions->{trace};
1740            my $textOKFlag = 1;
1741            if ($traceLevel =~ /^(.)-/) {
1742                $traceLevel = $1;
1743                $textOKFlag = 0;
1744            }
1745            # Now we set up the trace mode.
1746            my $traceMode;
1747            # Verify that we can open a file in the FIG temporary directory.
1748            my $traceFileName = "$FIG_Config::temp/trace$suffix.log";
1749            my $traceFileSpec = ($retOptions->{forked} ? ">>$traceFileName" : ">$traceFileName");
1750            if (open TESTTRACE, "$traceFileSpec") {
1751                # Here we can trace to a file.
1752                $traceMode = ">>$traceFileName";
1753                if ($textOKFlag) {
1754                    # Echo to standard output if the text-OK flag is set.
1755                    $traceMode = "+$traceMode";
1756                }
1757                # Close the test file.
1758                close TESTTRACE;
1759            } else {
1760                # Here we can't trace to a file. Complain about this.
1761                warn "Could not open trace file $traceFileName: $!\n";
1762                # We trace to the standard output if it's
1763                # okay, and the error log otherwise.
1764                if ($textOKFlag) {
1765                    $traceMode = "TEXT";
1766                } else {
1767                    $traceMode = "WARN";
1768                }
1769            }
1770            # Now set up the tracing.
1771            TSetup("$traceLevel $cats", $traceMode);
1772        }
1773        # Check for background mode.
1774        if ($retOptions->{background}) {
1775            my $outFileName = "$FIG_Config::temp/out$suffix$$.log";
1776            my $errFileName = "$FIG_Config::temp/err$suffix$$.log";
1777            # Spool the output.
1778            open STDOUT, ">$outFileName";
1779            # If we have a trace file, trace the errors to the log. Otherwise,
1780            # spool the errors.
1781            if (defined $traceFileName) {
1782                open STDERR, "| Tracer $traceFileName";
1783            } else {
1784                open STDERR, ">$errFileName";
1785            }
1786            # Check for phone support. If we have phone support and a phone number,
1787            # we want to turn it on.
1788            if ($ENV{PHONE} && defined($FIG_Config::phone)) {
1789                $retOptions->{phone} = $ENV{PHONE};
1790            }
1791        }
1792        # Check for the "help" option. If it is specified, dump the command-line
1793        # options and exit the program.
1794        if ($retOptions->{help}) {
1795            $0 =~ m#[/\\](\w+)(\.pl)?$#i;
1796            print "$1 [options] $parmHelp\n";
1797            for my $key (sort keys %{$options}) {
1798                my $name = Pad($key, $longestName, 0, ' ');
1799                my $desc = $options->{$key}->[1];
1800                if ($options->{$key}->[0]) {
1801                    $desc .= " (default " . $options->{$key}->[0] . ")";
1802                }
1803                print "  $name $desc\n";
1804            }
1805            exit(0);
1806        }
1807        # Trace the options, if applicable.
1808        if (T(3)) {
1809            my @parms = grep { $retOptions->{$_} } keys %{$retOptions};
1810            Trace("Selected options: " . join(", ", sort @parms) . ".");
1811        }
1812        # Return the parsed parameters.
1813        return ($retOptions, @retParameters);
1814    }
1815    
1816    =head3 ReadOptions
1817    
1818        my %options = Tracer::ReadOptions($fileName);
1819    
1820    Read a set of options from a file. Each option is encoded in a line of text that has the
1821    format
1822    
1823    I<optionName>C<=>I<optionValue>C<; >I<comment>
1824    
1825    The option name must consist entirely of letters, digits, and the punctuation characters
1826    C<.> and C<_>, and is case sensitive. Blank lines and lines in which the first nonblank
1827    character is a semi-colon will be ignored. The return hash will map each option name to
1828    the corresponding option value.
1829    
1830    =over 4
1831    
1832    =item fileName
1833    
1834    Name of the file containing the option data.
1835    
1836    =item RETURN
1837    
1838    Returns a hash mapping the option names specified in the file to their corresponding option
1839    value.
1840    
1841    =back
1842    
1843    =cut
1844    
1845    sub ReadOptions {
1846        # Get the parameters.
1847        my ($fileName) = @_;
1848        # Open the file.
1849        (open CONFIGFILE, "<$fileName") || Confess("Could not open option file $fileName.");
1850        # Count the number of records read.
1851        my ($records, $comments) = 0;
1852        # Create the return hash.
1853        my %retVal = ();
1854        # Loop through the file, accumulating key-value pairs.
1855        while (my $line = <CONFIGFILE>) {
1856            # Denote we've read a line.
1857            $records++;
1858            # Determine the line type.
1859            if ($line =~ /^\s*[\n\r]/) {
1860                # A blank line is a comment.
1861                $comments++;
1862            } elsif ($line =~ /^\s*([A-Za-z0-9_\.]+)=([^;]*);/) {
1863                # Here we have an option assignment.
1864                retVal{$1} = $2;
1865            } elsif ($line =~ /^\s*;/) {
1866                # Here we have a text comment.
1867                $comments++;
1868            } else {
1869                # Here we have an invalid line.
1870                Trace("Invalid option statement in record $records.") if T(0);
1871            }
1872        }
1873        # Return the hash created.
1874        return %retVal;
1875    }
1876    
1877    =head3 GetOptions
1878    
1879        Tracer::GetOptions(\%defaults, \%options);
1880    
1881    Merge a specified set of options into a table of defaults. This method takes two hash references
1882    as input and uses the data from the second to update the first. If the second does not exist,
1883    there will be no effect. An error will be thrown if one of the entries in the second hash does not
1884    exist in the first.
1885    
1886    Consider the following example.
1887    
1888        my $optionTable = GetOptions({ dbType => 'mySQL', trace => 0 }, $options);
1889    
1890    In this example, the variable B<$options> is expected to contain at most two options-- B<dbType> and
1891    B<trace>. The default database type is C<mySQL> and the default trace level is C<0>. If the value of
1892    B<$options> is C<< {dbType => 'Oracle'} >>, then the database type will be changed to C<Oracle> and
1893    the trace level will remain at 0. If B<$options> is undefined, then the database type and trace level
1894    will remain C<mySQL> and C<0>. If, on the other hand, B<$options> is defined as
1895    
1896        {databaseType => 'Oracle'}
1897    
1898    an error will occur because the B<databaseType> option does not exist.
1899    
1900    =over 4
1901    
1902    =item defaults
1903    
1904    Table of default option values.
1905    
1906    =item options
1907    
1908    Table of overrides, if any.
1909    
1910    =item RETURN
1911    
1912    Returns a reference to the default table passed in as the first parameter.
1913    
1914    =back
1915    
1916    =cut
1917    
1918    sub GetOptions {
1919        # Get the parameters.
1920        my ($defaults, $options) = @_;
1921        # Check for overrides.
1922        if ($options) {
1923            # Loop through the overrides.
1924            while (my ($option, $setting) = each %{$options}) {
1925                # Insure this override exists.
1926                if (!exists $defaults->{$option}) {
1927                    croak "Unrecognized option $option encountered.";
1928                } else {
1929                    # Apply the override.
1930                    $defaults->{$option} = $setting;
1931                }
1932            }
1933        }
1934        # Return the merged table.
1935        return $defaults;
1936    }
1937    
1938    =head3 MergeOptions
1939    
1940        Tracer::MergeOptions(\%table, \%defaults);
1941    
1942    Merge default values into a hash table. This method looks at the key-value pairs in the
1943    second (default) hash, and if a matching key is not found in the first hash, the default
1944    pair is copied in. The process is similar to L</GetOptions>, but there is no error-
1945    checking and no return value.
1946    
1947    =over 4
1948    
1949    =item table
1950    
1951    Hash table to be updated with the default values.
1952    
1953    =item defaults
1954    
1955    Default values to be merged into the first hash table if they are not already present.
1956    
1957    =back
1958    
1959    =cut
1960    
1961    sub MergeOptions {
1962        # Get the parameters.
1963        my ($table, $defaults) = @_;
1964        # Loop through the defaults.
1965        while (my ($key, $value) = each %{$defaults}) {
1966            if (!exists $table->{$key}) {
1967                $table->{$key} = $value;
1968            }
1969        }
1970    }
1971    
1972    =head3 UnparseOptions
1973    
1974        my $optionString = Tracer::UnparseOptions(\%options);
1975    
1976    Convert an option hash into a command-line string. This will not
1977    necessarily be the same text that came in, but it will nonetheless
1978    produce the same ultimate result when parsed by L</StandardSetup>.
1979    
1980    =over 4
1981    
1982    =item options
1983    
1984    Reference to a hash of options to convert into an option string.
1985    
1986    =item RETURN
1987    
1988    Returns a string that will parse to the same set of options when
1989    parsed by L</StandardSetup>.
1990    
1991    =back
1992    
1993    =cut
1994    
1995    sub UnparseOptions {
1996        # Get the parameters.
1997        my ($options) = @_;
1998        # The option segments will be put in here.
1999        my @retVal = ();
2000        # Loop through the options.
2001        for my $key (keys %$options) {
2002            # Get the option value.
2003            my $value = $options->{$key};
2004            # Only use it if it's nonempty.
2005            if (defined $value && $value ne "") {
2006                my $segment = "--$key=$value";
2007                # Quote it if necessary.
2008                if ($segment =~ /[ |<>*]/) {
2009                    $segment = '"' . $segment . '"';
2010                }
2011                # Add it to the return list.
2012                push @retVal, $segment;
2013            }
2014        }
2015        # Return the result.
2016        return join(" ", @retVal);
2017    }
2018    
2019    =head3 ParseCommand
2020    
2021        my ($options, @arguments) = Tracer::ParseCommand(\%optionTable, @inputList);
2022    
2023    Parse a command line consisting of a list of parameters. The initial parameters may be option
2024    specifiers of the form C<->I<option> or C<->I<option>C<=>I<value>. The options are stripped
2025    off and merged into a table of default options. The remainder of the command line is
2026    returned as a list of positional arguments. For example, consider the following invocation.
2027    
2028        my ($options, @arguments) = ParseCommand({ errors => 0, logFile => 'trace.log'}, @words);
2029    
2030    In this case, the list @words will be treated as a command line and there are two options available,
2031    B<errors> and B<logFile>. If @words has the following format
2032    
2033        -logFile=error.log apple orange rutabaga
2034    
2035    then at the end of the invocation, C<$options> will be
2036    
2037        { errors => 0, logFile => 'error.log' }
2038    
2039    and C<@arguments> will contain
2040    
2041        apple orange rutabaga
2042    
2043    The parser allows for some escape sequences. See L</UnEscape> for a description. There is no
2044    support for quote characters. Options can be specified with single or double hyphens.
2045    
2046    =over 4
2047    
2048    =item optionTable
2049    
2050    Table of default options.
2051    
2052    =item inputList
2053    
2054    List of words on the command line.
2055    
2056    =item RETURN
2057    
2058    Returns a reference to the option table and a list of the positional arguments.
2059    
2060    =back
2061    
2062    =cut
2063    
2064    sub ParseCommand {
2065        # Get the parameters.
2066        my ($optionTable, @inputList) = @_;
2067        # Process any options in the input list.
2068        my %overrides = ();
2069        while ((@inputList > 0) && ($inputList[0] =~ /^--?/)) {
2070            # Get the current option.
2071            my $arg = shift @inputList;
2072            # Pull out the option name.
2073            $arg =~ /^--?([^=]*)/g;
2074            my $name = $1;
2075            # Check for an option value.
2076            if ($arg =~ /\G=(.*)$/g) {
2077                # Here we have a value for the option.
2078                $overrides{$name} = UnEscape($1);
2079            } else {
2080                # Here there is no value, so we use 1.
2081                $overrides{$name} = 1;
2082                  }                  }
2083        }
2084        # Merge the options into the defaults.
2085        GetOptions($optionTable, \%overrides);
2086        # Translate the remaining parameters.
2087        my @retVal = ();
2088        for my $inputParm (@inputList) {
2089            push @retVal, UnEscape($inputParm);
2090        }
2091        # Return the results.
2092        return ($optionTable, @retVal);
2093    }
2094    
2095    
2096    =head2 File Utility Methods
2097    
2098    =head3 GetFile
2099    
2100        my @fileContents = Tracer::GetFile($fileName);
2101    
2102        or
2103    
2104        my $fileContents = Tracer::GetFile($fileName);
2105    
2106    Return the entire contents of a file. In list context, line-ends are removed and
2107    each line is a list element. In scalar context, line-ends are replaced by C<\n>.
2108    
2109    =over 4
2110    
2111    =item fileName
2112    
2113    Name of the file to read.
2114    
2115    =item RETURN
2116    
2117    In a list context, returns the entire file as a list with the line terminators removed.
2118    In a scalar context, returns the entire file as a string. If an error occurs opening
2119    the file, an empty list will be returned.
2120    
2121    =back
2122    
2123    =cut
2124    
2125    sub GetFile {
2126        # Get the parameters.
2127        my ($fileName) = @_;
2128        # Declare the return variable.
2129        my @retVal = ();
2130        # Open the file for input.
2131        my $handle = Open(undef, "<$fileName");
2132        # Read the whole file into the return variable, stripping off any terminator
2133        # characters.
2134        my $lineCount = 0;
2135        while (my $line = <$handle>) {
2136            $lineCount++;
2137            $line = Strip($line);
2138            push @retVal, $line;
2139        }
2140        # Close it.
2141        close $handle;
2142        my $actualLines = @retVal;
2143        Trace("$actualLines lines read from file $fileName.") if T(File => 2);
2144        # Return the file's contents in the desired format.
2145        if (wantarray) {
2146            return @retVal;
2147              } else {              } else {
2148                  # Here there are no more escape sequences. The rest of the string is          return join "\n", @retVal;
2149                  # transferred unmodified.      }
                 $retVal .= $codedString;  
                 $codedString = "";  
2150              }              }
2151    
2152    =head3 PutFile
2153    
2154        Tracer::PutFile($fileName, \@lines);
2155    
2156    Write out a file from a list of lines of text.
2157    
2158    =over 4
2159    
2160    =item fileName
2161    
2162    Name of the output file.
2163    
2164    =item lines
2165    
2166    Reference to a list of text lines. The lines will be written to the file in order, with trailing
2167    new-line characters. Alternatively, may be a string, in which case the string will be written without
2168    modification.
2169    
2170    =back
2171    
2172    =cut
2173    
2174    sub PutFile {
2175        # Get the parameters.
2176        my ($fileName, $lines) = @_;
2177        # Open the output file.
2178        my $handle = Open(undef, ">$fileName");
2179        # Count the lines written.
2180        if (ref $lines ne 'ARRAY') {
2181            # Here we have a scalar, so we write it raw.
2182            print $handle $lines;
2183            Trace("Scalar put to file $fileName.") if T(File => 3);
2184        } else {
2185            # Write the lines one at a time.
2186            my $count = 0;
2187            for my $line (@{$lines}) {
2188                print $handle "$line\n";
2189                $count++;
2190          }          }
2191            Trace("$count lines put to file $fileName.") if T(File => 3);
2192      }      }
2193      # Return the result.      # Close the output file.
2194      return $retVal;      close $handle;
2195  }  }
2196    
2197  =head3 ParseRecord  =head3 ParseRecord
2198    
2199  C<< my @fields = Tracer::ParseRecord($line); >>      my @fields = Tracer::ParseRecord($line);
2200    
2201  Parse a tab-delimited data line. The data line is split into field values. Embedded tab  Parse a tab-delimited data line. The data line is split into field values. Embedded tab
2202  and new-line characters in the data line must be represented as C<\t> and C<\n>, respectively.  and new-line characters in the data line must be represented as C<\t> and C<\n>, respectively.
# Line 1305  Line 2241 
2241    
2242  =head3 Merge  =head3 Merge
2243    
2244  C<< my @mergedList = Tracer::Merge(@inputList); >>      my @mergedList = Tracer::Merge(@inputList);
2245    
2246  Sort a list of strings and remove duplicates.  Sort a list of strings and remove duplicates.
2247    
# Line 1351  Line 2287 
2287      return @inputList;      return @inputList;
2288  }  }
2289    
2290  =head3 Percent  =head3 Open
2291    
2292        my $handle = Open($fileHandle, $fileSpec, $message);
2293    
2294    Open a file.
2295    
2296    The I<$fileSpec> is essentially the second argument of the PERL C<open>
2297    function. The mode is specified using Unix-like shell information. So, for
2298    example,
2299    
2300        Open(\*LOGFILE, '>>/usr/spool/news/twitlog', "Could not open twit log.");
2301    
2302    would open for output appended to the specified file, and
2303    
2304        Open(\*DATASTREAM, "| sort -u >$outputFile", "Could not open $outputFile.");
2305    
2306    would open a pipe that sorts the records written and removes duplicates. Note
2307    the use of file handle syntax in the Open call. To use anonymous file handles,
2308    code as follows.
2309    
2310        my $logFile = Open(undef, '>>/usr/spool/news/twitlog', "Could not open twit log.");
2311    
2312    The I<$message> parameter is used if the open fails. If it is set to C<0>, then
2313    the open returns TRUE if successful and FALSE if an error occurred. Otherwise, a
2314    failed open will throw an exception and the third parameter will be used to construct
2315    an error message. If the parameter is omitted, a standard message is constructed
2316    using the file spec.
2317    
2318        Could not open "/usr/spool/news/twitlog"
2319    
2320    Note that the mode characters are automatically cleaned from the file name.
2321    The actual error message from the file system will be captured and appended to the
2322    message in any case.
2323    
2324        Could not open "/usr/spool/news/twitlog": file not found.
2325    
2326    In some versions of PERL the only error message we get is a number, which
2327    corresponds to the C++ C<errno> value.
2328    
2329        Could not open "/usr/spool/news/twitlog": 6.
2330    
2331    =over 4
2332    
2333    =item fileHandle
2334    
2335    File handle. If this parameter is C<undef>, a file handle will be generated
2336    and returned as the value of this method.
2337    
2338    =item fileSpec
2339    
2340    File name and mode, as per the PERL C<open> function.
2341    
2342    =item message (optional)
2343    
2344    Error message to use if the open fails. If omitted, a standard error message
2345    will be generated. In either case, the error information from the file system
2346    is appended to the message. To specify a conditional open that does not throw
2347    an error if it fails, use C<0>.
2348    
2349    =item RETURN
2350    
2351    Returns the name of the file handle assigned to the file, or C<undef> if the
2352    open failed.
2353    
2354    =back
2355    
2356    =cut
2357    
2358    sub Open {
2359        # Get the parameters.
2360        my ($fileHandle, $fileSpec, $message) = @_;
2361        # Attempt to open the file.
2362        my $rv = open $fileHandle, $fileSpec;
2363        # If the open failed, generate an error message.
2364        if (! $rv) {
2365            # Save the system error message.
2366            my $sysMessage = $!;
2367            # See if we need a default message.
2368            if (!$message) {
2369                # Clean any obvious mode characters and leading spaces from the
2370                # filename.
2371                my ($fileName) = FindNamePart($fileSpec);
2372                $message = "Could not open \"$fileName\"";
2373            }
2374            # Terminate with an error using the supplied message and the
2375            # error message from the file system.
2376            Confess("$message: $!");
2377        }
2378        # Return the file handle.
2379        return $fileHandle;
2380    }
2381    
2382    =head3 FindNamePart
2383    
2384        my ($fileName, $start, $len) = Tracer::FindNamePart($fileSpec);
2385    
2386    Extract the portion of a file specification that contains the file name.
2387    
2388    A file specification is the string passed to an C<open> call. It specifies the file
2389    mode and name. In a truly complex situation, it can specify a pipe sequence. This
2390    method assumes that the file name is whatever follows the first angle bracket
2391    sequence.  So, for example, in the following strings the file name is
2392    C</usr/fig/myfile.txt>.
2393    
2394        >>/usr/fig/myfile.txt
2395        </usr/fig/myfile.txt
2396        | sort -u > /usr/fig/myfile.txt
2397    
2398    If the method cannot find a file name using its normal methods, it will return the
2399    whole incoming string.
2400    
2401    =over 4
2402    
2403    =item fileSpec
2404    
2405    File specification string from which the file name is to be extracted.
2406    
2407    =item RETURN
2408    
2409    Returns a three-element list. The first element contains the file name portion of
2410    the specified string, or the whole string if a file name cannot be found via normal
2411    methods. The second element contains the start position of the file name portion and
2412    the third element contains the length.
2413    
2414    =back
2415    
2416    =cut
2417    #: Return Type $;
2418    sub FindNamePart {
2419        # Get the parameters.
2420        my ($fileSpec) = @_;
2421        # Default to the whole input string.
2422        my ($retVal, $pos, $len) = ($fileSpec, 0, length $fileSpec);
2423        # Parse out the file name if we can.
2424        if ($fileSpec =~ m/(<|>>?)(.+?)(\s*)$/) {
2425            $retVal = $2;
2426            $len = length $retVal;
2427            $pos = (length $fileSpec) - (length $3) - $len;
2428        }
2429        # Return the result.
2430        return ($retVal, $pos, $len);
2431    }
2432    
2433    =head3 OpenDir
2434    
2435        my @files = OpenDir($dirName, $filtered, $flag);
2436    
2437    Open a directory and return all the file names. This function essentially performs
2438    the functions of an C<opendir> and C<readdir>. If the I<$filtered> parameter is
2439    set to TRUE, all filenames beginning with a period (C<.>), dollar sign (C<$>),
2440    or pound sign (C<#>) and all filenames ending with a tilde C<~>) will be
2441    filtered out of the return list. If the directory does not open and I<$flag> is not
2442    set, an exception is thrown. So, for example,
2443    
2444        my @files = OpenDir("/Volumes/fig/contigs", 1);
2445    
2446    is effectively the same as
2447    
2448  C<< my $percent = Tracer::Percent($number, $base); >>      opendir(TMP, "/Volumes/fig/contigs") || Confess("Could not open /Volumes/fig/contigs.");
2449        my @files = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir(TMP);
2450    
2451  Returns the percent of the base represented by the given number. If the base  Similarly, the following code
2452  is zero, returns zero.  
2453        my @files = grep { $_ =~ /^\d/ } OpenDir("/Volumes/fig/orgs", 0, 1);
2454    
2455    Returns the names of all files in C</Volumes/fig/orgs> that begin with digits and
2456    automatically returns an empty list if the directory fails to open.
2457    
2458  =over 4  =over 4
2459    
2460  =item number  =item dirName
2461    
2462  Percent numerator.  Name of the directory to open.
2463    
2464  =item base  =item filtered
2465    
2466  Percent base.  TRUE if files whose names begin with a period (C<.>) should be automatically removed
2467    from the list, else FALSE.
2468    
2469  =item RETURN  =item flag
2470    
2471  Returns the percentage of the base represented by the numerator.  TRUE if a failure to open is okay, else FALSE
2472    
2473  =back  =back
2474    
2475  =cut  =cut
2476    #: Return Type @;
2477  sub Percent {  sub OpenDir {
2478      # Get the parameters.      # Get the parameters.
2479      my ($number, $base) = @_;      my ($dirName, $filtered, $flag) = @_;
2480      # Declare the return variable.      # Declare the return variable.
2481      my $retVal = 0;      my @retVal = ();
2482      # Compute the percent.      # Open the directory.
2483      if ($base != 0) {      if (opendir(my $dirHandle, $dirName)) {
2484          $retVal = $number * 100 / $base;          # The directory opened successfully. Get the appropriate list according to the
2485            # strictures of the filter parameter.
2486            if ($filtered) {
2487                @retVal = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir $dirHandle;
2488            } else {
2489                @retVal = readdir $dirHandle;
2490            }
2491        } elsif (! $flag) {
2492            # Here the directory would not open and it's considered an error.
2493            Confess("Could not open directory $dirName.");
2494      }      }
2495      # Return the result.      # Return the result.
2496      return $retVal;      return @retVal;
2497  }  }
2498    
 =head3 GetFile  
   
 C<< my @fileContents = Tracer::GetFile($fileName); >>  
2499    
2500      or  =head3 Insure
2501    
2502  C<< my $fileContents = Tracer::GetFile($fileName); >>      Insure($dirName, $chmod);
2503    
2504  Return the entire contents of a file. In list context, line-ends are removed and  Insure a directory is present.
 each line is a list element. In scalar context, line-ends are replaced by C<\n>.  
2505    
2506  =over 4  =over 4
2507    
2508  =item fileName  =item dirName
2509    
2510  Name of the file to read.  Name of the directory to check. If it does not exist, it will be created.
2511    
2512  =item RETURN  =item chmod (optional)
2513    
2514  In a list context, returns the entire file as a list with the line terminators removed.  Security privileges to be given to the directory if it is created.
 In a scalar context, returns the entire file as a string. If an error occurs opening  
 the file, an empty list will be returned.  
2515    
2516  =back  =back
2517    
2518  =cut  =cut
2519    
2520  sub GetFile {  sub Insure {
2521      # Get the parameters.      my ($dirName, $chmod) = @_;
2522      my ($fileName) = @_;      if (! -d $dirName) {
2523      # Declare the return variable.          Trace("Creating $dirName directory.") if T(2);
2524      my @retVal = ();          eval {
2525      # Open the file for input.              mkpath $dirName;
2526      my $handle = Open(undef, "<$fileName");              # If we have permissions specified, set them here.
2527      # Read the whole file into the return variable, stripping off any terminator              if (defined($chmod)) {
2528      # characters.                  chmod $chmod, $dirName;
2529      my $lineCount = 0;              }
2530      while (my $line = <$handle>) {          };
2531          $lineCount++;          if ($@) {
2532          $line = Strip($line);              Confess("Error creating $dirName: $@");
         push @retVal, $line;  
2533      }      }
     # Close it.  
     close $handle;  
     my $actualLines = @retVal;  
     # Return the file's contents in the desired format.  
     if (wantarray) {  
         return @retVal;  
     } else {  
         return join "\n", @retVal;  
2534      }      }
2535  }  }
2536    
2537  =head3 PutFile  =head3 ChDir
2538    
2539  C<< Tracer::PutFile($fileName, \@lines); >>      ChDir($dirName);
2540    
2541  Write out a file from a list of lines of text.  Change to the specified directory.
2542    
2543  =over 4  =over 4
2544    
2545  =item fileName  =item dirName
   
 Name of the output file.  
   
 =item lines  
2546    
2547  Reference to a list of text lines. The lines will be written to the file in order, with trailing  Name of the directory to which we want to change.
 new-line characters. Alternatively, may be a string, in which case the string will be written without  
 modification.  
2548    
2549  =back  =back
2550    
2551  =cut  =cut
2552    
2553  sub PutFile {  sub ChDir {
2554      # Get the parameters.      my ($dirName) = @_;
2555      my ($fileName, $lines) = @_;      if (! -d $dirName) {
2556      # Open the output file.          Confess("Cannot change to directory $dirName: no such directory.");
     my $handle = Open(undef, ">$fileName");  
     if (ref $lines ne 'ARRAY') {  
         # Here we have a scalar, so we write it raw.  
         print $handle $lines;  
2557      } else {      } else {
2558          # Write the lines one at a time.          Trace("Changing to directory $dirName.") if T(File => 4);
2559          for my $line (@{$lines}) {          my $okFlag = chdir $dirName;
2560              print $handle "$line\n";          if (! $okFlag) {
2561                Confess("Error switching to directory $dirName.");
2562          }          }
2563      }      }
     # Close the output file.  
     close $handle;  
2564  }  }
2565    
2566  =head3 QTrace  =head3 SetPermissions
2567    
2568  C<< my $data = QTrace($format); >>      Tracer::SetPermissions($dirName, $group, $mask, %otherMasks);
2569    
2570  Return the queued trace data in the specified format.  Set the permissions for a directory and all the files and folders inside it.
2571    In addition, the group ownership will be changed to the specified value.
2572    
2573  =over 4  This method is more vulnerable than most to permission and compatability
2574    problems, so it does internal error recovery.
2575    
2576  =item format  =over 4
2577    
2578  C<html> to format the data as an HTML list, C<text> to format it as straight text.  =item dirName
2579    
2580  =back  Name of the directory to process.
2581    
2582  =cut  =item group
2583    
2584  sub QTrace {  Name of the group to be assigned.
     # Get the parameter.  
     my ($format) = @_;  
     # Create the return variable.  
     my $retVal = "";  
     # Only proceed if there is an actual queue.  
     if (@Queue) {  
         # Process according to the format.  
         if ($format =~ m/^HTML$/i) {  
             # Convert the queue into an HTML list.  
             $retVal = "<ul>\n";  
             for my $line (@Queue) {  
                 my $escapedLine = CGI::escapeHTML($line);  
                 $retVal .= "<li>$escapedLine</li>\n";  
             }  
             $retVal .= "</ul>\n";  
         } elsif ($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 $retVal;  
 }  
2585    
2586  =head3 Confess  =item mask
2587    
2588  C<< Confess($message); >>  Permission mask. Bits that are C<1> in this mask will be ORed into the
2589    permission bits of any file or directory that does not already have them
2590    set to 1.
2591    
2592  Trace the call stack and abort the program with the specified message. When used with  =item otherMasks
 the OR operator and the L</Assert> method, B<Confess> can function as a debugging assert.  
 So, for example  
2593    
2594  C<< Assert($recNum >= 0) || Confess("Invalid record number $recNum."); >>  Map of search patterns to permission masks. If a directory name matches
2595    one of the patterns, that directory and all its members and subdirectories
2596    will be assigned the new pattern. For example, the following would
2597    assign 0664 to most files, but would use 0777 for directories named C<tmp>.
2598    
2599  Will abort the program with a stack trace if the value of C<$recNum> is negative.      Tracer::SetPermissions($dirName, 'fig', 01664, '^tmp$' => 01777);
2600    
2601  =over 4  The list is ordered, so the following would use 0777 for C<tmp1> and
2602    0666 for C<tmp>, C<tmp2>, or C<tmp3>.
2603    
2604  =item message      Tracer::SetPermissions($dirName, 'fig', 01664, '^tmp1' => 0777,
2605                                                       '^tmp' => 0666);
2606    
2607  Message to include in the trace.  Note that the pattern matches are all case-insensitive, and only directory
2608    names are matched, not file names.
2609    
2610  =back  =back
2611    
2612  =cut  =cut
2613    
2614  sub Confess {  sub SetPermissions {
2615      # Get the parameters.      # Get the parameters.
2616      my ($message) = @_;      my ($dirName, $group, $mask, @otherMasks) = @_;
2617      # Trace the call stack.      # Set up for error recovery.
2618      Cluck($message);      eval {
2619      # Abort the program.          # Switch to the specified directory.
2620      croak(">>> $message");          ChDir($dirName);
2621            # Get the group ID.
2622            my $gid = getgrnam($group);
2623            # Get the mask for tracing.
2624            my $traceMask = sprintf("%04o", $mask) . "($mask)";
2625            Trace("Fixing permissions for directory $dirName using group $group($gid) and mask $traceMask.") if T(File => 2);
2626            my $fixCount = 0;
2627            my $lookCount = 0;
2628            # @dirs will be a stack of directories to be processed.
2629            my @dirs = (getcwd());
2630            while (scalar(@dirs) > 0) {
2631                # Get the current directory.
2632                my $dir = pop @dirs;
2633                # Check for a match to one of the specified directory names. To do
2634                # that, we need to pull the individual part of the name off of the
2635                # whole path.
2636                my $simpleName = $dir;
2637                if ($dir =~ m!/([^/]+)$!) {
2638                    $simpleName = $1;
2639                }
2640                Trace("Simple directory name for $dir is $simpleName.") if T(File => 4);
2641                # Search for a match.
2642                my $match = 0;
2643                my $i;
2644                for ($i = 0; $i < $#otherMasks && ! $match; $i += 2) {
2645                    my $pattern = $otherMasks[$i];
2646                    if ($simpleName =~ /$pattern/i) {
2647                        $match = 1;
2648                    }
2649                }
2650                # Find out if we have a match. Note we use $i-1 because the loop added 2
2651                # before terminating due to the match.
2652                if ($match && $otherMasks[$i-1] != $mask) {
2653                    # This directory matches one of the incoming patterns, and it's
2654                    # a different mask, so we process it recursively with that mask.
2655                    SetPermissions($dir, $group, $otherMasks[$i-1], @otherMasks);
2656                } else {
2657                    # Here we can process normally. Get all of the non-hidden members.
2658                    my @submems = OpenDir($dir, 1);
2659                    for my $submem (@submems) {
2660                        # Get the full name.
2661                        my $thisMem = "$dir/$submem";
2662                        Trace("Checking member $thisMem.") if T(4);
2663                        $lookCount++;
2664                        if ($lookCount % 1000 == 0) {
2665                            Trace("$lookCount members examined. Current is $thisMem. Mask is $traceMask") if T(File => 3);
2666                        }
2667                        # Fix the group.
2668                        chown -1, $gid, $thisMem;
2669                        # Insure this member is not a symlink.
2670                        if (! -l $thisMem) {
2671                            # Get its info.
2672                            my $fileInfo = stat $thisMem;
2673                            # Only proceed if we got the info. Otherwise, it's a hard link
2674                            # and we want to skip it anyway.
2675                            if ($fileInfo) {
2676                                my $fileMode = $fileInfo->mode;
2677                                if (($fileMode & $mask) != $mask) {
2678                                    # Fix this member.
2679                                    $fileMode |= $mask;
2680                                    chmod $fileMode, $thisMem;
2681                                    $fixCount++;
2682  }  }
2683                                # If it's a subdirectory, stack it.
2684  =head3 Assert                              if (-d $thisMem) {
2685                                    push @dirs, $thisMem;
 C<< Assert($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;  
2686          }          }
2687      }      }
2688      return $retVal;                      }
2689                    }
2690                }
2691            }
2692            Trace("$lookCount files and directories processed, $fixCount fixed.") if T(File => 2);
2693        };
2694        # Check for an error.
2695        if ($@) {
2696            Confess("SetPermissions error: $@");
2697        }
2698  }  }
2699    
2700  =head3 Cluck  =head3 GetLine
2701    
2702  C<< Cluck($message); >>      my @data = Tracer::GetLine($handle);
2703    
2704  Trace the call stack. Note that for best results, you should qualify the call with a  Read a line of data from a tab-delimited file.
 trace condition. For example,  
2705    
2706  C<< Cluck("Starting record parse.") if T(3); >>  =over 4
2707    
2708  will only trace the stack if the trace level for the package is 3 or more.  =item handle
2709    
2710  =over 4  Open file handle from which to read.
2711    
2712  =item message  =item RETURN
2713    
2714  Message to include in the trace.  Returns a list of the fields in the record read. The fields are presumed to be
2715    tab-delimited. If we are at the end of the file, then an empty list will be
2716    returned. If an empty line is read, a single list item consisting of a null
2717    string will be returned.
2718    
2719  =back  =back
2720    
2721  =cut  =cut
2722    
2723  sub Cluck {  sub GetLine {
2724      # Get the parameters.      # Get the parameters.
2725      my ($message) = @_;      my ($handle) = @_;
2726      # Trace what's happening.      # Declare the return variable.
2727      Trace("Stack trace for event: $message");      my @retVal = ();
2728      my $confession = longmess($message);      Trace("File position is " . tell($handle) . ". EOF flag is " . eof($handle) . ".") if T(File => 4);
2729      # Convert the confession to a series of trace messages. Note we skip any      # Read from the file.
2730      # messages relating to calls into Tracer.      my $line = <$handle>;
2731      for my $line (split /\s*\n/, $confession) {      # Only proceed if we found something.
2732          Trace($line) if ($line !~ /Tracer\.pm/);      if (defined $line) {
2733            # Remove the new-line. We are a bit over-cautious here because the file may be coming in via an
2734            # upload control and have a nonstandard EOL combination.
2735            $line =~ s/(\r|\n)+$//;
2736            # Here we do some fancy tracing to help in debugging complicated EOL marks.
2737            if (T(File => 4)) {
2738                my $escapedLine = $line;
2739                $escapedLine =~ s/\n/\\n/g;
2740                $escapedLine =~ s/\r/\\r/g;
2741                $escapedLine =~ s/\t/\\t/g;
2742                Trace("Line read: -->$escapedLine<--");
2743            }
2744            # If the line is empty, return a single empty string; otherwise, parse
2745            # it into fields.
2746            if ($line eq "") {
2747                push @retVal, "";
2748            } else {
2749                push @retVal, split /\t/,$line;
2750            }
2751        } else {
2752            # Trace the reason the read failed.
2753            Trace("End of file: $!") if T(File => 3);
2754      }      }
2755        # Return the result.
2756        return @retVal;
2757  }  }
2758    
2759  =head3 Min  =head3 PutLine
2760    
2761  C<< my $min = Min($value1, $value2, ... $valueN); >>      Tracer::PutLine($handle, \@fields, $eol);
2762    
2763  Return the minimum argument. The arguments are treated as numbers.  Write a line of data to a tab-delimited file. The specified field values will be
2764    output in tab-separated form, with a trailing new-line.
2765    
2766  =over 4  =over 4
2767    
2768  =item $value1, $value2, ... $valueN  =item handle
2769    
2770  List of numbers to compare.  Output file handle.
2771    
2772  =item RETURN  =item fields
2773    
2774  Returns the lowest number in the list.  List of field values.
2775    
2776    =item eol (optional)
2777    
2778    End-of-line character (default is "\n").
2779    
2780  =back  =back
2781    
2782  =cut  =cut
2783    
2784  sub Min {  sub PutLine {
2785      # Get the parameters. Note that we prime the return value with the first parameter.      # Get the parameters.
2786      my ($retVal, @values) = @_;      my ($handle, $fields, $eol) = @_;
2787      # Loop through the remaining parameters, looking for the lowest.      # Write the data.
2788      for my $value (@values) {      print $handle join("\t", @{$fields}) . ($eol || "\n");
         if ($value < $retVal) {  
             $retVal = $value;  
         }  
     }  
     # Return the minimum found.  
     return $retVal;  
2789  }  }
2790    
 =head3 Max  
   
 C<< my $max = Max($value1, $value2, ... $valueN); >>  
2791    
2792  Return the maximum argument. The arguments are treated as numbers.  =head3 PrintLine
2793    
2794  =over 4      Tracer::PrintLine($line);
2795    
2796  =item $value1, $value2, ... $valueN  Print a line of text with a trailing new-line.
2797    
2798  List of numbers to compare.  =over 4
2799    
2800  =item RETURN  =item line
2801    
2802  Returns the highest number in the list.  Line of text to print.
2803    
2804  =back  =back
2805    
2806  =cut  =cut
2807    
2808  sub Max {  sub PrintLine {
2809      # Get the parameters. Note that we prime the return value with the first parameter.      # Get the parameters.
2810      my ($retVal, @values) = @_;      my ($line) = @_;
2811      # Loop through the remaining parameters, looking for the highest.      # Print the line.
2812      for my $value (@values) {      print "$line\n";
         if ($value > $retVal) {  
             $retVal = $value;  
         }  
     }  
     # Return the maximum found.  
     return $retVal;  
2813  }  }
2814    
 =head3 AddToListMap  
2815    
2816  C<< Tracer::AddToListMap(\%hash, $key, $value1, $value2, ... valueN); >>  =head2 Other Useful Methods
2817    
2818  Add a key-value pair to a hash of lists. If no value exists for the key, a singleton list  =head3 ParseParm
 is created for the key. Otherwise, the new value is pushed onto the list.  
2819    
2820  =over 4      my $listValue = Tracer::ParseParm($string);
2821    
2822  =item hash  Convert a parameter into a list reference. If the parameter is undefined,
2823    an undefined value will be returned. Otherwise, it will be parsed as a
2824    comma-separated list of values.
2825    
2826  Reference to the target hash.  =over 4
2827    
2828  =item key  =item string
2829    
2830  Key for which the value is to be added.  Incoming string.
2831    
2832  =item value1, value2, ... valueN  =item RETURN
2833    
2834  List of values to add to the key's value list.  Returns a reference to a list of values, or C<undef> if the incoming value
2835    was undefined.
2836    
2837  =back  =back
2838    
2839  =cut  =cut
2840    
2841  sub AddToListMap {  sub ParseParm {
2842      # Get the parameters.      # Get the parameters.
2843      my ($hash, $key, @values) = @_;      my ($string) = @_;
2844      # Process according to whether or not the key already has a value.      # Declare the return variable.
2845      if (! exists $hash->{$key}) {      my $retVal;
2846          $hash->{$key} = [@values];      # Check for data.
2847      } else {      if (defined $string) {
2848          push @{$hash->{$key}}, @values;          # We have some, so split it into a list.
2849            $retVal = [ split /\s*,\s*/, $string];
2850      }      }
2851        # Return the result.
2852        return $retVal;
2853  }  }
2854    
2855  =head3 DebugMode  =head3 Now
   
 C<< if (Tracer::DebugMode) { ...code... } >>  
2856    
2857  Return TRUE if debug mode has been turned on, else output an error      my $string = Tracer::Now();
 page and return FALSE.  
2858    
2859  Certain CGI scripts are too dangerous to exist in the production  Return a displayable time stamp containing the local time. Whatever format this
2860  environment. This method provides a simple way to prevent them  method produces must be parseable by L</ParseDate>.
 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.  
2861    
2862  =cut  =cut
2863    
2864  sub DebugMode {  sub Now {
2865      # Declare the return variable.      return DisplayTime(time);
     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;  
     }  
     # Return the determination indicator.  
     return $retVal;  
2866  }  }
2867    
2868  =head3 Strip  =head3 DisplayTime
2869    
2870  C<< my $string = Tracer::Strip($line); >>      my $string = Tracer::DisplayTime($time);
2871    
2872  Strip all line terminators off a string. This is necessary when dealing with files  Convert a time value to a displayable time stamp. Whatever format this
2873  that may have been transferred back and forth several times among different  method produces must be parseable by L</ParseDate>.
 operating environments.  
2874    
2875  =over 4  =over 4
2876    
2877  =item line  =item time
2878    
2879  Line of text to be stripped.  Time to display, in seconds since the epoch, or C<undef> if the time is unknown.
2880    
2881  =item RETURN  =item RETURN
2882    
2883  The same line of text with all the line-ending characters chopped from the end.  Returns a displayable time, or C<(n/a)> if the incoming time is undefined.
2884    
2885  =back  =back
2886    
2887  =cut  =cut
2888    
2889  sub Strip {  sub DisplayTime {
2890      # Get a copy of the parameter string.      my ($time) = @_;
2891      my ($string) = @_;      my $retVal = "(n/a)";
2892      my $retVal = (defined $string ? $string : "");      if (defined $time) {
2893      # Strip the line terminator characters.          my ($sec,$min,$hour,$mday,$mon,$year,$wday,$yday,$isdst) = localtime($time);
2894      $retVal =~ s/(\r|\n)+$//g;          $retVal = _p2($mon+1) . "/" . _p2($mday) . "/" . ($year + 1900) . " " .
2895      # Return the result.                    _p2($hour) . ":" . _p2($min) . ":" . _p2($sec);
2896        }
2897      return $retVal;      return $retVal;
2898  }  }
2899    
2900  =head3 Pad  # Pad a number to 2 digits.
2901    sub _p2 {
2902  C<< my $paddedString = Tracer::Pad($string, $len, $left, $padChar); >>      my ($value) = @_;
2903        $value = "0$value" if ($value < 10);
2904  Pad a string to a specified length. The pad character will be a      return $value;
2905  space, and the padding will be on the right side unless specified  }
 in the third parameter.  
   
 =over 4  
   
 =item string  
   
 String to be padded.  
2906    
2907  =item len  =head3 Escape
2908    
2909  Desired length of the padded string.      my $codedString = Tracer::Escape($realString);
2910    
2911  =item left (optional)  Escape a string for use in a command. Tabs will be replaced by C<\t>, new-lines
2912    replaced by C<\n>, carriage returns will be deleted, and backslashes will be doubled. The
2913    result is to reverse the effect of L</UnEscape>.
2914    
2915  TRUE if the string is to be left-padded; otherwise it will be padded on the right.  =over 4
2916    
2917  =item padChar (optional)  =item realString
2918    
2919  Character to use for padding. The default is a space.  String to escape.
2920    
2921  =item RETURN  =item RETURN
2922    
2923  Returns a copy of the original string with the pad character added to the  Escaped equivalent of the real string.
 specified end so that it achieves the desired length.  
2924    
2925  =back  =back
2926    
2927  =cut  =cut
2928    
2929  sub Pad {  sub Escape {
2930      # Get the parameters.      # Get the parameter.
2931      my ($string, $len, $left, $padChar) = @_;      my ($realString) = @_;
2932      # Compute the padding character.      # Initialize the return variable.
2933      if (! defined $padChar) {      my $retVal = "";
2934          $padChar = " ";      # Loop through the parameter string, looking for sequences to escape.
2935        while (length $realString > 0) {
2936            # Look for the first sequence to escape.
2937            if ($realString =~ /^(.*?)([\n\t\r\\])/) {
2938                # Here we found it. The text preceding the sequence is in $1. The sequence
2939                # itself is in $2. First, move the clear text to the return variable.
2940                $retVal .= $1;
2941                # Strip the processed section off the real string.
2942                $realString = substr $realString, (length $2) + (length $1);
2943                # Get the matched character.
2944                my $char = $2;
2945                # If we have a CR, we are done.
2946                if ($char ne "\r") {
2947                    # It's not a CR, so encode the escape sequence.
2948                    $char =~ tr/\t\n/tn/;
2949                    $retVal .= "\\" . $char;
2950      }      }
     # Compute the number of spaces needed.  
     my $needed = $len - length $string;  
     # Copy the string into the return variable.  
     my $retVal = $string;  
     # Only proceed if padding is needed.  
     if ($needed > 0) {  
         # Create the pad string.  
         my $pad = $padChar x $needed;  
         # Affix it to the return value.  
         if ($left) {  
             $retVal = $pad . $retVal;  
2951          } else {          } else {
2952              $retVal .= $pad;              # Here there are no more escape sequences. The rest of the string is
2953                # transferred unmodified.
2954                $retVal .= $realString;
2955                $realString = "";
2956          }          }
2957      }      }
2958      # Return the result.      # Return the result.
2959      return $retVal;      return $retVal;
 }  
   
 =head3 EOF  
   
 This is a constant that is lexically greater than any useful string.  
   
 =cut  
   
 sub EOF {  
     return "\xFF\xFF\xFF\xFF\xFF";  
2960  }  }
2961    
2962  =head3 TICK  =head3 UnEscape
   
 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  
2963    
2964      TICK("./protein.cgi")      my $realString = Tracer::UnEscape($codedString);
2965    
2966  it will work correctly in both environments.  Replace escape sequences with their actual equivalents. C<\t> will be replaced by
2967    a tab, C<\n> by a new-line character, and C<\\> by a backslash. C<\r> codes will
2968    be deleted.
2969    
2970  =over 4  =over 4
2971    
2972  =item commandString  =item codedString
2973    
2974  The command string to pass to the system.  String to un-escape.
2975    
2976  =item RETURN  =item RETURN
2977    
2978  Returns the standard output from the specified command, as a list.  Returns a copy of the original string with the escape sequences converted to their actual
2979    values.
2980    
2981  =back  =back
2982    
2983  =cut  =cut
2984  #: Return Type @;  
2985  sub TICK {  sub UnEscape {
2986      # Get the parameters.      # Get the parameter.
2987      my ($commandString) = @_;      my ($codedString) = @_;
2988      # Chop off the dot-slash if this is Windows.      # Initialize the return variable.
2989      if ($FIG_Config::win_mode) {      my $retVal = "";
2990          $commandString =~ s!^\./!!;      # Only proceed if the incoming string is nonempty.
2991        if (defined $codedString) {
2992            # Loop through the parameter string, looking for escape sequences. We can't do
2993            # translating because it causes problems with the escaped slash. ("\\t" becomes
2994            # "\<tab>" no matter what we do.)
2995            while (length $codedString > 0) {
2996                # Look for the first escape sequence.
2997                if ($codedString =~ /^(.*?)\\(\\|n|t|r)/) {
2998                    # Here we found it. The text preceding the sequence is in $1. The sequence
2999                    # itself is in $2. First, move the clear text to the return variable.
3000                    $retVal .= $1;
3001                    $codedString = substr $codedString, (2 + length $1);
3002                    # Get the escape value.
3003                    my $char = $2;
3004                    # If we have a "\r", we are done.
3005                    if ($char ne 'r') {
3006                        # Here it's not an 'r', so we convert it.
3007                        $char =~ tr/\\tn/\\\t\n/;
3008                        $retVal .= $char;
3009      }      }
3010      # Activate the command and return the result.              } else {
3011      return `$commandString`;                  # Here there are no more escape sequences. The rest of the string is
3012                    # transferred unmodified.
3013                    $retVal .= $codedString;
3014                    $codedString = "";
3015                }
3016            }
3017        }
3018        # Return the result.
3019        return $retVal;
3020  }  }
3021    
3022  =head3 ScriptSetup  =head3 Percent
   
 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.  
3023    
3024  The C<Trace> query parameter is used to determine whether or not tracing is active and      my $percent = Tracer::Percent($number, $base);
 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.  
3025    
3026  =cut  Returns the percent of the base represented by the given number. If the base
3027    is zero, returns zero.
3028    
3029  sub ScriptSetup {  =over 4
     # 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, $varHash);  
 }  
3030    
3031  =head3 TraceParms  =item number
3032    
3033  C<< Tracer::TraceParms($query); >>  Percent numerator.
3034    
3035  Trace the CGI parameters at trace level CGI => 3 and the environment variables  =item base
 at level CGI => 4.  
3036    
3037  =over 4  Percent base.
3038    
3039  =item query  =item RETURN
3040    
3041  CGI query object containing the parameters to trace.  Returns the percentage of the base represented by the numerator.
3042    
3043  =back  =back
3044    
3045  =cut  =cut
3046    
3047  sub TraceParms {  sub Percent {
3048      # Get the parameters.      # Get the parameters.
3049      my ($query) = @_;      my ($number, $base) = @_;
3050      if (T(CGI => 3)) {      # Declare the return variable.
3051          # Here we want to trace the parameter data.      my $retVal = 0;
3052          my @names = $query->param;      # Compute the percent.
3053          for my $parmName (sort @names) {      if ($base != 0) {
3054              # Note we skip "Trace", which is for our use only.          $retVal = $number * 100 / $base;
             if ($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}");  
         }  
3055      }      }
3056        # Return the result.
3057        return $retVal;
3058  }  }
3059    
3060  =head3 ScriptFinish  =head3 Constrain
3061    
3062  C<< ScriptFinish($webData, $varHash); >>      my $constrained = Constrain($value, $min, $max);
3063    
3064  Output a web page at the end of a script. Either the string to be output or the  Modify a numeric value to bring it to a point in between a maximum and a minimum.
 name of a template file can be specified. If the second parameter is omitted,  
 it is assumed we have a string to be output; otherwise, it is assumed we have the  
 name of a template file. The template should have the variable C<DebugData>  
 specified in any form that invokes a standard script. If debugging mode is turned  
 on, a form field will be put in that allows the user to enter tracing data.  
 Trace messages will be placed immediately before the terminal C<BODY> tag in  
 the output, formatted as a list.  
3065    
3066  A typical standard script would loook like the following.  =over 4
3067    
3068      BEGIN {  =item value
         # Print the HTML header.  
         print "CONTENT-TYPE: text/html\n\n";  
     }  
     use Tracer;  
     use CGI;  
     use FIG;  
     # ... more uses ...  
3069    
3070      my ($query, $varHash) = ScriptSetup();  Value to constrain.
     eval {  
         # ... get data from $query, put it in $varHash ...  
     };  
     if ($@) {  
         Trace("Script Error: $@") if T(0);  
     }  
     ScriptFinish("Html/MyTemplate.html", $varHash);  
3071    
3072  The idea here is that even if the script fails, you'll see trace messages and  =item min (optional)
 useful output.  
3073    
3074  =over 4  Minimum permissible value. If this parameter is undefined, no minimum constraint will be applied.
3075    
3076  =item webData  =item max (optional)
3077    
3078  A string containing either the full web page to be written to the output or the  Maximum permissible value. If this parameter is undefined, no maximum constraint will be applied.
 name of a template file from which the page is to be constructed. If the name  
 of a template file is specified, then the second parameter must be present;  
 otherwise, it must be absent.  
3079    
3080  =item varHash (optional)  =item RETURN
3081    
3082  If specified, then a reference to a hash mapping variable names for a template  Returns the incoming value, constrained according to the other parameters.
 to their values. The template file will be read into memory, and variable markers  
 will be replaced by data in this hash reference.  
3083    
3084  =back  =back
3085    
3086  =cut  =cut
3087    
3088  sub ScriptFinish {  sub Constrain {
3089      # Get the parameters.      # Get the parameters.
3090      my ($webData, $varHash) = @_;      my ($value, $min, $max) = @_;
3091      # Check for a template file situation.      # Declare the return variable.
3092      my $outputString;      my $retVal = $value;
3093      if (defined $varHash) {      # Apply the minimum constraint.
3094          # Here we have a template file. We need to determine the template type.      if (defined $min && $retVal < $min) {
3095          my $template;          $retVal = $min;
3096          if ($FIG_Config::template_url && $webData =~ /\.php$/) {      }
3097              $template = "$FIG_Config::template_url/$webData";      # Apply the maximum constraint.
3098          } else {      if (defined $max && $retVal > $max) {
3099              $template = "<<$webData";          $retVal = $max;
         }  
         $outputString = PageBuilder::Build($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');  
3100      }      }
3101      # Write the output string.      # Return the result.
3102      print $outputString;      return $retVal;
3103  }  }
3104    
3105  =head3 Insure  =head3 Min
3106    
3107  C<< Insure($dirName); >>      my $min = Min($value1, $value2, ... $valueN);
3108    
3109  Insure a directory is present.  Return the minimum argument. The arguments are treated as numbers.
3110    
3111  =over 4  =over 4
3112    
3113  =item dirName  =item $value1, $value2, ... $valueN
3114    
3115  Name of the directory to check. If it does not exist, it will be created.  List of numbers to compare.
3116    
3117    =item RETURN
3118    
3119    Returns the lowest number in the list.
3120    
3121  =back  =back
3122    
3123  =cut  =cut
3124    
3125  sub Insure {  sub Min {
3126      my ($dirName) = @_;      # Get the parameters. Note that we prime the return value with the first parameter.
3127      if (! -d $dirName) {      my ($retVal, @values) = @_;
3128          Trace("Creating $dirName directory.") if T(2);      # Loop through the remaining parameters, looking for the lowest.
3129          eval { mkpath $dirName; };      for my $value (@values) {
3130          if ($@) {          if ($value < $retVal) {
3131              Confess("Error creating $dirName: $@");              $retVal = $value;
3132          }          }
3133      }      }
3134        # Return the minimum found.
3135        return $retVal;
3136  }  }
3137    
3138  =head3 ChDir  =head3 Max
3139    
3140  C<< ChDir($dirName); >>      my $max = Max($value1, $value2, ... $valueN);
3141    
3142  Change to the specified directory.  Return the maximum argument. The arguments are treated as numbers.
3143    
3144  =over 4  =over 4
3145    
3146  =item dirName  =item $value1, $value2, ... $valueN
3147    
3148  Name of the directory to which we want to change.  List of numbers to compare.
3149    
3150    =item RETURN
3151    
3152    Returns the highest number in the list.
3153    
3154  =back  =back
3155    
3156  =cut  =cut
3157    
3158  sub ChDir {  sub Max {
3159      my ($dirName) = @_;      # Get the parameters. Note that we prime the return value with the first parameter.
3160      if (! -d $dirName) {      my ($retVal, @values) = @_;
3161          Confess("Cannot change to directory $dirName: no such directory.");      # Loop through the remaining parameters, looking for the highest.
3162      } else {      for my $value (@values) {
3163          Trace("Changing to directory $dirName.") if T(4);          if ($value > $retVal) {
3164          my $okFlag = chdir $dirName;              $retVal = $value;
         if (! $okFlag) {  
             Confess("Error switching to directory $dirName.");  
3165          }          }
3166      }      }
3167        # Return the maximum found.
3168        return $retVal;
3169  }  }
3170    
3171  =head3 SendSMS  =head3 Strip
   
 C<< my $msgID = Tracer::SendSMS($phoneNumber, $msg); >>  
   
 Send a text message to a phone number using Clickatell. The FIG_Config file must contain the  
 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  
   
     $phone =  { user => 'BruceTheHumanPet',  
                 password => 'silly',  
                 api_id => '2561022' };  
   
 The original purpose of this method was to insure Bruce would be notified immediately when the  
 Sprout Load terminates. Care should be taken if you do not wish Bruce to be notified immediately  
 when you call this method.  
   
 The message ID will be returned if successful, and C<undef> if an error occurs.  
3172    
3173  =over 4      my $string = Tracer::Strip($line);
3174    
3175  =item phoneNumber  Strip all line terminators off a string. This is necessary when dealing with files
3176    that may have been transferred back and forth several times among different
3177    operating environments.
3178    
3179  Phone number to receive the message, in international format. A United States phone number  =over 4
 would be prefixed by "1". A British phone number would be prefixed by "44".  
3180    
3181  =item msg  =item line
3182    
3183  Message to send to the specified phone.  Line of text to be stripped.
3184    
3185  =item RETURN  =item RETURN
3186    
3187  Returns the message ID if successful, and C<undef> if the message could not be sent.  The same line of text with all the line-ending characters chopped from the end.
3188    
3189  =back  =back
3190    
3191  =cut  =cut
3192    
3193  sub SendSMS {  sub Strip {
3194      # Get the parameters.      # Get a copy of the parameter string.
3195      my ($phoneNumber, $msg) = @_;      my ($string) = @_;
3196      # Declare the return variable. If we do not change it, C<undef> will be returned.      my $retVal = (defined $string ? $string : "");
3197      my $retVal;      # Strip the line terminator characters.
3198      # Only proceed if we have phone support.      $retVal =~ s/(\r|\n)+$//g;
     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);  
             }  
         }  
     }  
3199      # Return the result.      # Return the result.
3200      return $retVal;      return $retVal;
3201  }  }
3202    
3203  =head3 CommaFormat  =head3 Pad
3204    
3205  C<< my $formatted = Tracer::CommaFormat($number); >>      my $paddedString = Tracer::Pad($string, $len, $left, $padChar);
3206    
3207  Insert commas into a number.  Pad a string to a specified length. The pad character will be a
3208    space, and the padding will be on the right side unless specified
3209    in the third parameter.
3210    
3211  =over 4  =over 4
3212    
3213  =item number  =item string
3214    
3215  A sequence of digits.  String to be padded.
3216    
3217    =item len
3218    
3219    Desired length of the padded string.
3220    
3221    =item left (optional)
3222    
3223    TRUE if the string is to be left-padded; otherwise it will be padded on the right.
3224    
3225    =item padChar (optional)
3226    
3227    Character to use for padding. The default is a space.
3228    
3229  =item RETURN  =item RETURN
3230    
3231  Returns the same digits with commas strategically inserted.  Returns a copy of the original string with the pad character added to the
3232    specified end so that it achieves the desired length.
3233    
3234  =back  =back
3235    
3236  =cut  =cut
3237    
3238  sub CommaFormat {  sub Pad {
3239      # Get the parameters.      # Get the parameters.
3240      my ($number) = @_;      my ($string, $len, $left, $padChar) = @_;
3241      # Pad the length up to a multiple of three.      # Compute the padding character.
3242      my $padded = "$number";      if (! defined $padChar) {
3243      $padded = " " . $padded while length($padded) % 3 != 0;          $padChar = " ";
3244      # This is a fancy PERL trick. The parentheses in the SPLIT pattern      }
3245      # cause the delimiters to be included in the output stream. The      # Compute the number of spaces needed.
3246      # GREP removes the empty strings in between the delimiters.      my $needed = $len - length $string;
3247      my $retVal = join(",", grep { $_ ne '' } split(/(...)/, $padded));      # Copy the string into the return variable.
3248      # Clean out the spaces.      my $retVal = $string;
3249      $retVal =~ s/ //g;      # Only proceed if padding is needed.
3250        if ($needed > 0) {
3251            # Create the pad string.
3252            my $pad = $padChar x $needed;
3253            # Affix it to the return value.
3254            if ($left) {
3255                $retVal = $pad . $retVal;
3256            } else {
3257                $retVal .= $pad;
3258            }
3259        }
3260      # Return the result.      # Return the result.
3261      return $retVal;      return $retVal;
3262  }  }
 =head3 SetPermissions  
3263    
3264  C<< Tracer::SetPermissions($dirName, $group, $mask, %otherMasks); >>  =head3 EOF
3265    
3266  Set the permissions for a directory and all the files and folders inside it.  This is a constant that is lexically greater than any useful string.
 In addition, the group ownership will be changed to the specified value.  
3267    
3268  This method is more vulnerable than most to permission and compatability  =cut
 problems, so it does internal error recovery.  
3269    
3270  =over 4  sub EOF {
3271        return "\xFF\xFF\xFF\xFF\xFF";
3272    }
3273    
3274  =item dirName  =head3 TICK
3275    
3276  Name of the directory to process.      my @results = TICK($commandString);
3277    
3278  =item group  Perform a back-tick operation on a command. If this is a Windows environment, any leading
3279    dot-slash (C<./> will be removed. So, for example, if you were doing
3280    
3281  Name of the group to be assigned.      `./protein.cgi`
3282    
3283  =item mask  from inside a CGI script, it would work fine in Unix, but would issue an error message
3284    in Windows complaining that C<'.'> is not a valid command. If instead you code
3285    
3286  Permission mask. Bits that are C<1> in this mask will be ORed into the      TICK("./protein.cgi")
 permission bits of any file or directory that does not already have them  
 set to 1.  
3287    
3288  =item otherMasks  it will work correctly in both environments.
3289    
3290  Map of search patterns to permission masks. If a directory name matches  =over 4
 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>.  
3291    
3292      Tracer::SetPermissions($dirName, 'fig', 01664, '^tmp$' => 01777);  =item commandString
3293    
3294  The list is ordered, so the following would use 0777 for C<tmp1> and  The command string to pass to the system.
 0666 for C<tmp>, C<tmp2>, or C<tmp3>.  
3295    
3296      Tracer::SetPermissions($dirName, 'fig', 01664, '^tmp1' => 0777,  =item RETURN
                                                    '^tmp' => 0666);  
3297    
3298  Note that the pattern matches are all case-insensitive, and only directory  Returns the standard output from the specified command, as a list.
 names are matched, not file names.  
3299    
3300  =back  =back
3301    
3302  =cut  =cut
3303    #: Return Type @;
3304  sub SetPermissions {  sub TICK {
3305      # Get the parameters.      # Get the parameters.
3306      my ($dirName, $group, $mask, @otherMasks) = @_;      my ($commandString) = @_;
3307      # Set up for error recovery.      # Chop off the dot-slash if this is Windows.
3308      eval {      if ($FIG_Config::win_mode) {
3309          # Switch to the specified directory.          $commandString =~ s!^\./!!;
         ChDir($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) {