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revision 1.69, Mon Oct 2 02:59:47 2006 UTC revision 1.110, Tue Sep 23 21:48:27 2008 UTC
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1  #  # -*- perl -*-
2    ########################################################################
3  # Copyright (c) 2003-2006 University of Chicago and Fellowship  # Copyright (c) 2003-2006 University of Chicago and Fellowship
4  # for Interpretations of Genomes. All Rights Reserved.  # for Interpretations of Genomes. All Rights Reserved.
5  #  #
# Line 13  Line 14 
14  # at info@ci.uchicago.edu or the Fellowship for Interpretation of  # at info@ci.uchicago.edu or the Fellowship for Interpretation of
15  # Genomes at veronika@thefig.info or download a copy from  # Genomes at veronika@thefig.info or download a copy from
16  # http://www.theseed.org/LICENSE.TXT.  # http://www.theseed.org/LICENSE.TXT.
17  #  ########################################################################
18    
19  package Tracer;  package Tracer;
20    
21      require Exporter;      require Exporter;
22      @ISA = ('Exporter');      @ISA = ('Exporter');
23      @EXPORT = qw(Trace T TSetup QTrace Confess Cluck Min Max Assert Open OpenDir TICK StandardSetup EmergencyIP ScriptSetup ScriptFinish Insure ChDir Emergency);      @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 ':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 122  Line 151 
151  =back  =back
152    
153  The format of trace messages is important because some utilities analyze trace files.  The format of trace messages is important because some utilities analyze trace files.
154  The time stamp is between square brackets, the module name between angle brackets,  There are three fields-- the time stamp, the category name, and the text.
155  a colon (C<:>), and the message text after that. If the square brackets or angle  The time stamp is between square brackets and the category name between angle brackets.
156  brackets are missing, then the trace management utilities assume that they  After the category name there is a colon (C<:>) followed by the message text.
157  are encountering a set of pre-formatted lines.  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  =head2 Public Methods  =cut
227    
228    sub Setups {
229        return $SetupCount;
230    }
231    
232  =head3 TSetup  =head3 TSetup
233    
234  C<< TSetup($categoryList, $target); >>      TSetup($categoryList, $target);
235    
236  This method is used to specify the trace options. The options are stored as package data  This method is used to specify the trace options. The options are stored as package data
237  and interrogated by the L</Trace> and L</T> methods.  and interrogated by the L</Trace> and L</T> methods.
# Line 197  Line 281 
281          }          }
282      }      }
283      # Now we need to process the destination information. The most important special      # Now we need to process the destination information. The most important special
284      # cases are the single ">", which requires we clear the file first, and the      # case is when we're writing to a file. This is indicated by ">" (overwrite) and
285      # "+" prefix which indicates a double echo.      # ">>" (append). A leading "+" for either indicates that we are also writing to
286        # the standard output (tee mode).
287      if ($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() . "] <Tracer>: 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 219  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 two 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 SQL  sub SetLevel {
326        $TraceLevel = $_[0];
327    }
328    
329  Traces SQL commands and activity.  =head3 ParseDate
330    
331  =item Tracer      my $time = Tracer::ParseDate($dateString);
332    
333  Traces error messages and call stacks.  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  =back  If a time of day is present, it must be in military time with two digits for
340    everything but the hour.
341    
342  C<SQL> is only turned on if the C<-sql> option is specified in the command line.  The year must be exactly four digits.
 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.  
343    
344      TransactFeatures -trace=3 -sql register ../xacts IDs.tbl  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  Standard tracing is output to the standard output and echoed to the file  It should be guaranteed that this method will parse the output of the L</Now> function.
 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  
349    
350  The default trace level is 2. To get all messages, specify a trace level of 4.  The parameters are as follows.
 For a genome-by-genome update, use 3.  
351    
352      TransactFeatures -trace=3 -sql -user=Bruce register ../xacts IDs.tbl  =over 4
353    
354  would send the trace output to C<traceBruce.log> in the temporary directory.  =item dateString
355    
356  The I<options> parameter is a reference to a hash containing the command-line  The date string to convert.
 options, their default values, and an explanation of what they mean. Command-line  
 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.  
357    
358  You can specify a different default trace level by setting C<$options->{trace}>  =item RETURN
 prior to calling this method.  
359    
360  An example at this point would help. Consider, for example, the command-line utility  Returns a PERL time, that is, a number of seconds since the epoch, or C<undef> if
361  C<TransactFeatures>. It accepts a list of positional parameters plus the options  the date string is invalid. A valid date string must contain a month and day.
 C<safe>, C<noAlias>, C<start>, and C<tblFiles>. To start up this command, we execute  
 the following code.  
362    
363      my ($options, @parameters) = Tracer::StandardSetup(["DocUtils"],  =back
                         { safe => [0, "use database transactions"],  
                           noAlias => [0, "do not expect aliases in CHANGE transactions"],  
                           start => [' ', "start with this genome"],  
                           tblFiles => [0, "output TBL files containing the corrected IDs"] },  
                         "command transactionDirectory IDfile",  
                       @ARGV);  
364    
365    =cut
366    
367  The call to C<ParseCommand> specifies the default values for the options and  # Universal month conversion table.
368  stores the actual options in a hash that is returned as C<$options>. The  use constant MONTHS => {    Jan =>  0, January   =>  0, '01' =>  0,  '1' =>  0,
369  positional parameters are returned in C<@parameters>.                              Feb =>  1, February  =>  1, '02' =>  1,  '2' =>  1,
370                                Mar =>  2, March     =>  2, '03' =>  2,  '3' =>  2,
371                                Apr =>  3, April     =>  3, '04' =>  3,  '4' =>  3,
372                                May =>  4, May       =>  4, '05' =>  4,  '5' =>  4,
373                                Jun =>  5, June      =>  5, '06' =>  5,  '6' =>  5,
374                                Jul =>  6, July      =>  6, '07' =>  6,  '7' =>  6,
375                                Aug =>  7, August    =>  7, '08' =>  7,  '8' =>  7,
376                                Sep =>  8, September =>  8, '09' =>  8,  '9' =>  8,
377                                Oct =>  9, October  =>   9, '10' =>  9,
378                                Nov => 10, November =>  10, '11' => 10,
379                                Dec => 11, December =>  11, '12' => 11
380                            };
381    
382  The following is a sample command line for C<TransactFeatures>.  sub ParseDate {
383        # Get the parameters.
384        my ($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 $retVal;
414    }
415    
416      TransactFeatures -trace=2 -noAlias register ../xacts IDs.tbl  =head3 LogErrors
417    
418  In this case, C<register>, C<../xacts>, and C<IDs.tbl> are the positional      Tracer::LogErrors($fileName);
 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<Tracer>, and <DocUtils>. C<Tracer> is standard,  
 and C<DocUtils> was included because it came in within the first parameter  
 to this method. The I<$options> hash would be  
419    
420      { trace => 2, sql => 0, safe => 0,  Route the standard error output to a log file.
       noAlias => 1, start => ' ', tblFiles => 0 }  
421    
422  Use of C<StandardSetup> in this way provides a simple way of performing  =over 4
 standard tracing setup and command-line parsing. Note that the caller is  
 not even aware of the command-line switches C<-trace> and C<-sql>, which  
 are used by this method to control the tracing. If additional tracing features  
 need to be added in the future, they can be processed by this method without  
 upsetting the command-line utilities.  
423    
424  If the C<background> option is specified on the command line, then the  =item fileName
 standard and error outputs will be directed to files in the temporary  
 directory, using the same suffix as the trace file. So, if the command  
 line specified  
425    
426      -user=Bruce -background  Name of the file to receive the error output.
427    
428  then the trace output would go to C<traceBruce.log>, the standard output to  =back
 C<outBruce.log>, and the error output to C<errBruce.log>. This is designed to  
 simplify starting a command in the background.  
429    
430  Finally, if the special option C<-h> is specified, the option names will  =cut
 be traced at level 0 and the program will exit without processing.  
 This provides a limited help capability. For example, if the user enters  
431    
432      TransactFeatures -h  sub LogErrors {
433        # Get the file name.
434        my ($fileName) = @_;
435        # Open the file as the standard error output.
436        open STDERR, '>', $fileName;
437    }
438    
439  he would see the following output.  =head3 Trace
440    
441      TransactFeatures [options] command transactionDirectory IDfile      Trace($message);
         -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  
442    
443  The caller has the option of modifying the tracing scheme by placing a value  Write a trace message to the target location specified in L</TSetup>. If there has not been
444  for C<trace> in the incoming options hash. The default value can be overridden,  any prior call to B<TSetup>.
 or the tracing to the standard output can be turned off by suffixing a minus  
 sign to the trace level. So, for example,  
445    
446      { trace => [0, "tracing level (default 0)"],  =over 4
        ...  
447    
448  would set the default trace level to 0 instead of 2, while  =item message
449    
450      { trace => ["2-", "tracing level (default 2)"],  Message to write.
        ...  
451    
452  would leave the default at 2, but trace only to the log file, not to the  =back
 standard output.  
453    
454  The parameters to this method are as follows.  =cut
455    
456  =over 4  sub Trace {
457        # 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: $!";
496            print TRACING "$formatted\n";
497            close TRACING;
498            # If the Tee flag is on, echo it to the standard output.
499            if ($TeeFlag) {
500                print "$formatted\n";
501            }
502        }
503    }
504    
505  =item categories  =head3 T
506    
507  Reference to a list of tracing category names. These should be names of      my $switch = T($category, $traceLevel);
 packages whose internal workings will need to be debugged to get the  
 command working.  
508    
509  =item options      or
510    
511  Reference to a hash containing the legal options for the current command mapped      my $switch = T($traceLevel);
 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).  
512    
513  =item parmHelp  Return TRUE if the trace level is at or above a specified value and the specified category
514    is active, else FALSE. If no category is specified, the caller's package name is used.
515    
516  A string that vaguely describes the positional parameters. This is used  =over 4
 if the user specifies the C<-h> option.  
517    
518  =item argv  =item category
519    
520  List of command line parameters, including the option switches, which must  Category to which the message belongs. If not specified, the caller's package name is
521  precede the positional parameters and be prefixed by a hyphen.  used.
522    
523    =item traceLevel
524    
525    Relevant tracing level.
526    
527  =item RETURN  =item RETURN
528    
529  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.  
530    
531  =back  =back
532    
533  =cut  =cut
534    
535  sub StandardSetup {  sub T {
536        # Declare the return variable.
537        my $retVal = 0;
538        # Only proceed if tracing is turned on.
539        if ($Destination ne "NONE") {
540      # Get the parameters.      # Get the parameters.
541      my ($categories, $options, $parmHelp, @argv) = @_;          my ($category, $traceLevel) = @_;
542      # Add the tracing options.          if (!defined $traceLevel) {
543      if (! exists $options->{trace}) {              # Here we have no category, so we need to get the calling package.
544          $options->{trace} = [2, "tracing level"];              # The calling package is normally the first parameter. If it is
545      }              # omitted, the first parameter will be the tracelevel. So, the
546      $options->{sql} = [0, "turn on SQL tracing"];              # first thing we do is shift the so-called category into the
547      $options->{h} = [0, "display command-line options"];              # $traceLevel variable where it belongs.
548      $options->{user} = [$$, "trace log file name suffix"];              $traceLevel = $category;
549      $options->{background} = [0, "spool standard and error output"];              my ($package, $fileName, $line) = caller;
550      # Create a parsing hash from the options hash. The parsing hash              # If there is no calling package, we default to "main".
551      # contains the default values rather than the default value              if (!$package) {
552      # and the description. While we're at it, we'll memorize the                  $category = "main";
553      # length of the longest option name.              } else {
554      my $longestName = 0;                  my @cats = split /::/, $package;
555      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";  
556      }      }
     # Add the default categories.  
     push @cats, "Tracer";  
     # 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;  
557      }      }
558      # Now we set up the trace mode.          # Save the category name and level.
559      my $traceMode;          $LastCategory = $category;
560      # Verify that we can open a file in the FIG temporary directory.          $LastLevel = $traceLevel;
561      my $traceFileName = "$FIG_Config::temp/trace$suffix.log";          # Convert it to lower case before we hash it.
562      if (open TESTTRACE, ">$traceFileName") {          $category = lc $category;
563          # Here we can trace to a file.          # Validate the trace level.
564          $traceMode = ">$traceFileName";          if (ref $traceLevel) {
565          if ($textOKFlag) {              Confess("Bad trace level.");
566              # Echo to standard output if the text-OK flag is set.          } elsif (ref $TraceLevel) {
567              $traceMode = "+$traceMode";              Confess("Bad trace config.");
568          }          }
569          # Close the test file.          # Make the check. Note that level 0 shows even if the category is turned off.
570          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";  
571          }          }
572        # Return the computed result.
573        return $retVal;
574      }      }
575      # Now set up the tracing.  
576      TSetup("$traceLevel $cats", $traceMode);  =head3 QTrace
577      # Check for the "h" option. If it is specified, dump the command-line  
578      # options and exit the program.      my $data = QTrace($format);
579      if ($retOptions->{h}) {  
580          $0 =~ m#[/\\](\w+)(\.pl)?$#i;  Return the queued trace data in the specified format.
581          print "$1 [options] $parmHelp\n";  
582          for my $key (sort keys %{$options}) {  =over 4
583              my $name = Pad($key, $longestName, 0, ' ');  
584              my $desc = $options->{$key}->[1];  =item format
585              if ($options->{$key}->[0]) {  
586                  $desc .= " (default " . $options->{$key}->[0] . ")";  C<html> to format the data as an HTML list, C<text> to format it as straight text.
587    
588    =back
589    
590    =cut
591    
592    sub QTrace {
593        # Get the parameter.
594        my ($format) = @_;
595        # Create the return variable.
596        my $retVal = "";
597        # Only proceed if there is an actual queue.
598        if (@Queue) {
599            # Process according to the format.
600            if ($format =~ m/^HTML$/i) {
601                # Convert the queue into an HTML list.
602                $retVal = "<ul>\n";
603                for my $line (@Queue) {
604                    my $escapedLine = CGI::escapeHTML($line);
605                    $retVal .= "<li>$escapedLine</li>\n";
606              }              }
607              print "  $name $desc\n";              $retVal .= "</ul>\n";
608            } elsif ($format =~ m/^TEXT$/i) {
609                # Convert the queue into a list of text lines.
610                $retVal = join("\n", @Queue) . "\n";
611          }          }
612          exit(0);          # Clear the queue.
613            @Queue = ();
614      }      }
615      # Return the parsed parameters.      # Return the formatted list.
616      return ($retOptions, @retParameters);      return $retVal;
617  }  }
618    
619  =head3 Setups  =head3 Confess
620    
621  C<< my $count = Tracer::Setups(); >>      Confess($message);
622    
623  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
624    the OR operator and the L</Assert> method, B<Confess> can function as a debugging assert.
625    So, for example
626    
627  This method allows for the creation of conditional tracing setups where, for example, we      Assert($recNum >= 0) || Confess("Invalid record number $recNum.");
628  may want to set up tracing if nobody else has done it before us.  
629    Will abort the program with a stack trace if the value of C<$recNum> is negative.
630    
631    =over 4
632    
633    =item message
634    
635    Message to include in the trace.
636    
637    =back
638    
639  =cut  =cut
640    
641  sub Setups {  sub Confess {
642      return $SetupCount;      # Get the parameters.
643        my ($message) = @_;
644        # Set up the category and level.
645        $LastCategory = "(confess)";
646        $LastLevel = 0;
647        if (! defined($FIG_Config::no_tool_hdr)) {
648            # Here we have a tool header. Display its length so that the user can adjust the line numbers.
649            my $toolHeaderFile = "$FIG_Config::fig_disk/dist/releases/current/$FIG_Config::arch/tool_hdr";
650            # Only proceed if the tool header file is actually present.
651            if (-f $toolHeaderFile) {
652                my $fh;
653                if (open $fh, "<$toolHeaderFile") {
654                    my @lines = <$fh>;
655                    Trace("Tool header has " . scalar(@lines) . " lines.");
656                }
657            }
658        }
659        # Trace the call stack.
660        Cluck($message);
661        # Abort the program.
662        croak(">>> $message");
663  }  }
664    
665  =head3 Open  =head3 SaveCGI
   
 C<< my $handle = Open($fileHandle, $fileSpec, $message); >>  
666    
667  Open a file.      Tracer::SaveCGI($cgi);
668    
669  The I<$fileSpec> is essentially the second argument of the PERL C<open>  This method saves the CGI object but does not activate emergency tracing.
670  function. The mode is specified using Unix-like shell information. So, for  It is used to allow L</Warn> to work in situations where emergency
671  example,  tracing is contra-indicated (e.g. the wiki).
672    
673      Open(\*LOGFILE, '>>/usr/spool/news/twitlog', "Could not open twit log.");  =over 4
674    
675  would open for output appended to the specified file, and  =item cgi
676    
677      Open(\*DATASTREAM, "| sort -u >$outputFile", "Could not open $outputFile.");  Active CGI query object.
678    
679  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.  
680    
681      my $logFile = Open(undef, '>>/usr/spool/news/twitlog', "Could not open twit log.");  =cut
682    
683  The I<$message> parameter is used if the open fails. If it is set to C<0>, then  sub SaveCGI {
684  the open returns TRUE if successful and FALSE if an error occurred. Otherwise, a      $SavedCGI = $_[0];
685  failed open will throw an exception and the third parameter will be used to construct  }
 an error message. If the parameter is omitted, a standard message is constructed  
 using the file spec.  
686    
687      Could not open "/usr/spool/news/twitlog"  =head3 Warn
688    
689  Note that the mode characters are automatically cleaned from the file name.      Warn($message, @options);
 The actual error message from the file system will be captured and appended to the  
 message in any case.  
690    
691      Could not open "/usr/spool/news/twitlog": file not found.  This method traces an important message. If an RSS feed is configured
692    (via I<FIG_Config::error_feed>) and the tracing destination is C<WARN>,
693    then the message will be echoed to the feed. In general, a tracing
694    destination of C<WARN> indicates that the caller is running as a web
695    service in a production environment; however, this is not a requirement.
696    
697  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
698  corresponds to the C++ C<errno> value.  is not C<WARN>, simply specify the C<Feed> tracing module. This can be
699    configured automatically when L</StandardSetup> is used.
700    
701      Could not open "/usr/spool/news/twitlog": 6.  The L</Cluck> method calls this one for its final message. Since
702    L</Confess> calls L</Cluck>, this means that any error which is caught
703    and confessed will put something in the feed. This insures that someone
704    will be alerted relatively quickly when a failure occurs.
705    
706  =over 4  =over 4
707    
708  =item fileHandle  =item message
709    
710  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.  
711    
712  =item fileSpec  =item options
713    
714  File name and mode, as per the PERL C<open> function.  A list containing zero or more options.
715    
716  =item message (optional)  =back
717    
718  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>.  
719    
720  =item RETURN  =over 4
721    
722  Returns the name of the file handle assigned to the file, or C<undef> if the  =item noStack
723  open failed.  
724    If specified, then the stack trace is not included in the output.
725    
726  =back  =back
727    
728  =cut  =cut
729    
730  sub Open {  sub Warn {
731      # Get the parameters.      # Get the parameters.
732      my ($fileHandle, $fileSpec, $message) = @_;      my $message = shift @_;
733      # Attempt to open the file.      my %options = map { $_ => 1 } @_;
734      my $rv = open $fileHandle, $fileSpec;      # Save $@;
735      # If the open failed, generate an error message.      my $savedError = $@;
736      if (! $rv) {      # Trace the message.
737          # Save the system error message.      Trace($message);
738          my $sysMessage = $!;      # This will contain the lock handle. If it's defined, it means we need to unlock.
739          # See if we need a default message.      my $lock;
740          if (!$message) {      # Check for feed forcing.
741              # Clean any obvious mode characters and leading spaces from the      my $forceFeed = exists $Categories{feed};
742              # filename.      # An error here would be disastrous. Note that if debug mode is specified,
743              my ($fileName) = FindNamePart($fileSpec);      # we do this stuff even in a test environment.
744              $message = "Could not open \"$fileName\"";      eval {
745            # Do we need to put this in the RSS feed?
746            if ($FIG_Config::error_feed && ($Destination eq 'WARN' || $forceFeed)) {
747                # Probably. We need to check first, however, to see if it's from an
748                # ignored IP. For non-CGI situations, we default the IP to the self-referent.
749                my $key = "127.0.0.1";
750                if (defined $SavedCGI) {
751                    # Get the IP address.
752                    $key = $ENV{HTTP_X_FORWARDED_FOR} || $ENV{REMOTE_ADDR};
753                }
754                # Is the IP address in the ignore list?
755                my $found = scalar(grep { $_ eq $key } @FIG_Config::error_ignore_ips);
756                if (! $found) {
757                    # No. We're good. We now need to compute the date, the link, and the title.
758                    # First, the date, in a very specific format.
759                    my $date = strftime("%a, %02e %b %H:%M:%S %Y ", localtime) .
760                        (tz_local_offset() / 30);
761                    # Environment data goes in here. We start with the date.
762                    my $environment = "$date.  ";
763                    # If we need to recap the message (because it's too long to be a title), we'll
764                    # put it in here.
765                    my $recap;
766                    # Copy the message and remove excess space.
767                    my $title = $message;
768                    $title =~ s/\s+/ /gs;
769                    # If it's too long, we have to split it up.
770                    if (length $title > 60) {
771                        # Put the full message in the environment string.
772                        $recap = $title;
773                        # Excerpt it as the title.
774                        $title = substr($title, 0, 50) . "...";
775                    }
776                    # If we have a CGI object, then this is a web error. Otherwise, it's
777                    # command-line.
778                    if (defined $SavedCGI) {
779                        # We're in a web service. The environment is the user's IP, and the link
780                        # is the URL that got us here.
781                        $environment .= "Event Reported at IP address $key process $$.";
782                        my $url = $SavedCGI->self_url();
783                        # We need the user agent string and (if available) the referrer.
784                        # The referrer will be the link.
785                        $environment .= " User Agent $ENV{HTTP_USER_AGENT}";
786                        if ($ENV{HTTP_REFERER}) {
787                            my $link = $ENV{HTTP_REFERER};
788                            $environment .= " referred from <a href=\"$link\">$link</a>.";
789                        } else {
790                            $environment .= " referrer unknown.";
791                        }
792                        # Close off the sentence with the original link.
793                        $environment .= " URL of event is <a href=\"$url\">$url</a>.";
794                    } else {
795                        # No CGI object, so we're a command-line tool. Use the tracing
796                        # key and the PID as the user identifier, and add the command.
797                        my $key = EmergencyKey();
798                        $environment .= "Event Reported by $key process $$.";
799                        if ($CommandLine) {
800                            # We're in a StandardSetup script, so we have the real command line.
801                            $environment .= "\n<pre>" . CGI::escapeHTML($CommandLine) . "</pre>\n";
802                        } elsif ($ENV{_}) {
803                            # We're in a BASH script, so the command has been stored in the _ variable.
804                            $environment .= "  Command = " . CGI::escapeHTML($ENV{_}) . "\n";
805                        }
806                    }
807                    # Build a GUID. We use the current time, the title, and the process ID,
808                    # then digest the result.
809                    my $guid = Digest::MD5::md5_base64(gettimeofday(), $title, $$);
810                    # Finally, the description. This is a stack trace plus various environmental stuff.
811                    # The trace is optional.
812                    my $stackTrace;
813                    if ($options{noStack}) {
814                        $stackTrace = "";
815                    } else {
816                        my @trace = LongMess();
817                        # Only proceed if we got something back.
818                        if (scalar(@trace) > 0) {
819                            $trace[0] =~ s/Tracer::Warn.+?called/Event occurred/;
820                            $stackTrace = "Stack trace:<pre>" . join("\n", @trace, "</pre>");
821                        }
822                    }
823                    # We got the stack trace. Now it's time to put it all together.
824                    # We have a goofy thing here in that we need to HTML-escape some sections of the description
825                    # twice. They will be escaped once here, and then once when written by XML::Simple. They are
826                    # unescaped once when processed by the RSS reader, and stuff in the description is treated as
827                    # HTML. So, anything escaped here is treated as a literal when viewed in the RSS reader, but
828                    # our <br>s and <pre>s are used to format the description.
829                    $recap = (defined $recap ? "<em>" . CGI::escapeHTML($recap) . "</em><br /><br />" : "");
830                    my $description = "$recap$environment  $stackTrace";
831                    # Okay, we have all the pieces. Create a hash of the new event.
832                    my $newItem = { title => $title,
833                                    description => $description,
834                                    category => $LastCategory,
835                                    pubDate => $date,
836                                    guid => $guid,
837                                  };
838                    # We need XML capability for this.
839                    require XML::Simple;
840                    # The RSS document goes in here.
841                    my $rss;
842                    # Get the name of the RSS file. It's in the FIG temporary directory.
843                    my $fileName = "$FIG_Config::temp/$FIG_Config::error_feed";
844                    # Open the config file and lock it.
845                    $lock = Open(undef, "<$FIG_Config::fig_disk/config/FIG_Config.pm");
846                    flock $lock, LOCK_EX;
847                    # Does it exist?
848                    if (-s $fileName) {
849                        # Slurp it in.
850                        $rss = XML::Simple::XMLin($fileName, ForceArray => ['item']);
851                    } else {
852                        my $size = -s $fileName;
853                        # Create an empty channel.
854                        $rss = {
855                            channel => {
856                                title => 'NMPDR Warning Feed',
857                                link => "$FIG_Config::temp_url/$FIG_Config::error_feed",
858                                description => "Important messages regarding the status of the NMPDR.",
859                                generator => "NMPDR Trace Facility",
860                                docs => "http://blogs.law.harvard.edu/tech/rss",
861                                item => []
862                            },
863                        };
864                    }
865                    # Get the channel object.
866                    my $channel = $rss->{channel};
867                    # Update the last-build date.
868                    $channel->{lastBuildDate} = $date;
869                    # Get the item array.
870                    my $items = $channel->{item};
871                    # Insure it has only 100 entries.
872                    while (scalar @{$items} > 100) {
873                        pop @{$items};
874                    }
875                    # Add our new item at the front.
876                    unshift @{$items}, $newItem;
877                    # Create the XML. Note we do not include the root or the declaration. XML Simple can't handle
878                    # the requirements for those.
879                    my $xml = XML::Simple::XMLout($channel, NoAttr => 1, RootName => 'channel', XmlDecl => '');
880                    # Here we put in the root and declaration. The problem is that the root has to have the version attribute
881                    # in it. So, we suppress the root and do it by hand, and that requires suppressing the declaration, too.
882                    $xml = "<?xml version=\"1.0\" encoding=\"utf-8\"?>\n<rss version=\"2.0\">$xml\n</rss>";
883                    # We don't use Open here because we can't afford an error.
884                    if (open XMLOUT, ">$fileName") {
885                        print XMLOUT $xml;
886                        close XMLOUT;
887          }          }
         # Terminate with an error using the supplied message and the  
         # error message from the file system.  
         Confess("$message: $!");  
888      }      }
889      # Return the file handle.          }
890      return $fileHandle;      };
891        if ($@) {
892            # If the feed failed, we need to know why. The error will be traced, but this method will not be involved
893            # (which is a good thing).
894            my $error = $@;
895            Trace("Feed Error: $error") if T(Feed => 0);
896        }
897        # Be sure to unlock.
898        if ($lock) {
899            flock $lock, LOCK_UN;
900            undef $lock;
901        }
902        # Restore the error message.
903        $@ = $savedError;
904  }  }
905    
 =head3 FindNamePart  
906    
 C<< my ($fileName, $start, $len) = Tracer::FindNamePart($fileSpec); >>  
907    
 Extract the portion of a file specification that contains the file name.  
908    
909  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>.  
910    
911      >>/usr/fig/myfile.txt      Assert($condition1, $condition2, ... $conditionN);
     </usr/fig/myfile.txt  
     | sort -u > /usr/fig/myfile.txt  
912    
913  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
914  whole incoming string.  the OR operator and the L</Confess> method as a debugging assert.
915    So, for example
916    
917  =over 4      Assert($recNum >= 0) || Confess("Invalid record number $recNum.");
918    
919  =item fileSpec  Will abort the program with a stack trace if the value of C<$recNum> is negative.
920    
921  File specification string from which the file name is to be extracted.  =cut
922    sub Assert {
923        my $retVal = 1;
924        LOOP: for my $condition (@_) {
925            if (! $condition) {
926                $retVal = 0;
927                last LOOP;
928            }
929        }
930        return $retVal;
931    }
932    
933  =item RETURN  =head3 Cluck
934    
935  Returns a three-element list. The first element contains the file name portion of      Cluck($message);
936  the specified string, or the whole string if a file name cannot be found via normal  
937  methods. The second element contains the start position of the file name portion and  Trace the call stack. Note that for best results, you should qualify the call with a
938  the third element contains the length.  trace condition. For example,
939    
940        Cluck("Starting record parse.") if T(3);
941    
942    will only trace the stack if the trace level for the package is 3 or more.
943    
944    =over 4
945    
946    =item message
947    
948    Message to include in the trace.
949    
950  =back  =back
951    
952  =cut  =cut
953  #: Return Type $;  
954  sub FindNamePart {  sub Cluck {
955      # Get the parameters.      # Get the parameters.
956      my ($fileSpec) = @_;      my ($message) = @_;
957      # Default to the whole input string.      # Trace what's happening.
958      my ($retVal, $pos, $len) = ($fileSpec, 0, length $fileSpec);      Trace("Stack trace for event: $message");
959      # Parse out the file name if we can.      # Get the stack trace.
960      if ($fileSpec =~ m/(<|>>?)(.+?)(\s*)$/) {      my @trace = LongMess();
961          $retVal = $2;      # Convert the trace to a series of messages.
962          $len = length $retVal;      for my $line (@trace) {
963          $pos = (length $fileSpec) - (length $3) - $len;          # Replace the tab at the beginning with spaces.
964            $line =~ s/^\t/    /;
965            # Trace the line.
966            Trace($line);
967        }
968        # Issue a warning. This displays the event message and inserts it into the RSS error feed.
969        Warn($message);
970    }
971    
972    =head3 LongMess
973    
974        my @lines = Tracer::LongMess();
975    
976    Return a stack trace with all tracing methods removed. The return will be in the form of a list
977    of message strings.
978    
979    =cut
980    
981    sub LongMess {
982        # Declare the return variable.
983        my @retVal = ();
984        my $confession = longmess("");
985        for my $line (split /\s*\n/, $confession) {
986            unless ($line =~ /Tracer\.pm/) {
987                # Here we have a line worth keeping. Push it onto the result list.
988                push @retVal, $line;
989            }
990      }      }
991      # Return the result.      # Return the result.
992      return ($retVal, $pos, $len);      return @retVal;
993  }  }
994    
995  =head3 OpenDir  =head3 ETracing
996    
997  C<< my @files = OpenDir($dirName, $filtered, $flag); >>      ETracing($parameter);
998    
999  Open a directory and return all the file names. This function essentially performs  Set up emergency tracing. Emergency tracing is tracing that is turned
1000  the functions of an C<opendir> and C<readdir>. If the I<$filtered> parameter is  on automatically for any program that calls this method. The emergency
1001  set to TRUE, all filenames beginning with a period (C<.>), dollar sign (C<$>),  tracing parameters are stored in a a file identified by a tracing key.
1002  or pound sign (C<#>) and all filenames ending with a tilde C<~>) will be  If this method is called with a CGI object, then the tracing key is
1003  filtered out of the return list. If the directory does not open and I<$flag> is not  taken from a cookie. If it is called with no parameters, then the tracing
1004  set, an exception is thrown. So, for example,  key is taken from an environment variable. If it is called with a string,
1005    the tracing key is that string.
1006    
1007      my @files = OpenDir("/Volumes/fig/contigs", 1);  =over 4
1008    
1009  is effectively the same as  =item parameter
1010    
1011      opendir(TMP, "/Volumes/fig/contigs") || Confess("Could not open /Volumes/fig/contigs.");  A parameter from which the tracing key is computed. If it is a scalar,
1012      my @files = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir(TMP);  that scalar is used as the tracing key. If it is a CGI object, the
1013    tracing key is taken from the C<IP> cookie. If it is omitted, the
1014    tracing key is taken from the C<TRACING> environment variable. If it
1015    is a CGI object and emergency tracing is not on, the C<Trace> and
1016    C<TF> parameters will be used to determine the type of tracing.
1017    
1018  Similarly, the following code  =back
1019    
1020      my @files = grep { $_ =~ /^\d/ } OpenDir("/Volumes/fig/orgs", 0, 1);  =cut
1021    
1022  Returns the names of all files in C</Volumes/fig/orgs> that begin with digits and  sub ETracing {
1023  automatically returns an empty list if the directory fails to open.      # Get the parameter.
1024        my ($parameter) = @_;
1025        # Check for CGI mode.
1026        if (defined $parameter && ref $parameter eq 'CGI') {
1027            $SavedCGI = $parameter;
1028        } else {
1029            $SavedCGI = undef;
1030        }
1031        # Default to no tracing except errors.
1032        my ($tracing, $dest) = ("0", "WARN");
1033        # Check for emergency tracing.
1034        my $tkey = EmergencyKey($parameter);
1035        my $emergencyFile = EmergencyFileName($tkey);
1036        if (-e $emergencyFile) {
1037            # We have the file. Read in the data.
1038            my @tracing = GetFile($emergencyFile);
1039            # Pull off the time limit.
1040            my $expire = shift @tracing;
1041            # Convert it to seconds.
1042            $expire *= 3600;
1043            # Check the file data.
1044            my $stat = stat($emergencyFile);
1045            my ($now) = gettimeofday;
1046            if ($now - $stat->mtime > $expire) {
1047                # Delete the expired file.
1048                unlink $emergencyFile;
1049            } else {
1050                # Emergency tracing is on. Pull off the destination and
1051                # the trace level;
1052                $dest = shift @tracing;
1053                my $level = shift @tracing;
1054                # Convert the destination to a real tracing destination.
1055                # temp directory.
1056                $dest = EmergencyTracingDest($tkey, $dest);
1057                # Insure Tracer is specified.
1058                my %moduleHash = map { $_ => 1 } @tracing;
1059                $moduleHash{Tracer} = 1;
1060                # Set the trace parameter.
1061                $tracing = join(" ", $level, sort keys %moduleHash);
1062            }
1063        } elsif (defined $SavedCGI) {
1064            # There's no emergency tracing, but we have a CGI object, so check
1065            # for tracing from the form parameters.
1066            if ($SavedCGI->param('Trace')) {
1067                # Here the user has requested tracing via a form.
1068                $dest = ($SavedCGI->param('TF') ? ">$FIG_Config::temp/Trace$$.log" : "QUEUE");
1069                $tracing = $SavedCGI->param('Trace') . " Tracer";
1070            }
1071        }
1072        # Setup the tracing we've determined from all the stuff above.
1073        TSetup($tracing, $dest);
1074        # Check to see if we're a web script.
1075        if (defined $SavedCGI) {
1076            # Yes we are. Trace the form and environment data.
1077            TraceParms($SavedCGI);
1078            # Check for RAW mode. In raw mode, we print a fake header so that we see everything
1079            # emitted by the script in its raw form.
1080            if (T(Raw => 3)) {
1081                print CGI::header(-type => 'text/plain', -tracing => 'Raw');
1082            }
1083        }
1084    }
1085    
1086    =head3 EmergencyFileName
1087    
1088        my $fileName = Tracer::EmergencyFileName($tkey);
1089    
1090    Return the emergency tracing file name. This is the file that specifies
1091    the tracing information.
1092    
1093  =over 4  =over 4
1094    
1095  =item dirName  =item tkey
1096    
1097  Name of the directory to open.  Tracing key for the current program.
1098    
1099  =item filtered  =item RETURN
1100    
1101  TRUE if files whose names begin with a period (C<.>) should be automatically removed  Returns the name of the file to contain the emergency tracing information.
 from the list, else FALSE.  
1102    
1103  =item flag  =back
1104    
1105  TRUE if a failure to open is okay, else FALSE  =cut
1106    
1107    sub EmergencyFileName {
1108        # Get the parameters.
1109        my ($tkey) = @_;
1110        # Compute the emergency tracing file name.
1111        return "$FIG_Config::temp/Emergency$tkey.txt";
1112    }
1113    
1114    =head3 EmergencyFileTarget
1115    
1116        my $fileName = Tracer::EmergencyFileTarget($tkey);
1117    
1118    Return the emergency tracing target file name. This is the file that receives
1119    the tracing output for file-based tracing.
1120    
1121    =over 4
1122    
1123    =item tkey
1124    
1125    Tracing key for the current program.
1126    
1127    =item RETURN
1128    
1129    Returns the name of the file to contain the trace output.
1130    
1131  =back  =back
1132    
1133  =cut  =cut
1134  #: Return Type @;  
1135  sub OpenDir {  sub EmergencyFileTarget {
1136      # Get the parameters.      # Get the parameters.
1137      my ($dirName, $filtered, $flag) = @_;      my ($tkey) = @_;
1138        # Compute the emergency tracing file name.
1139        return "$FIG_Config::temp/trace$tkey.log";
1140    }
1141    
1142    =head3 EmergencyTracingDest
1143    
1144        my $dest = Tracer::EmergencyTracingDest($tkey, $myDest);
1145    
1146    This method converts an emergency tracing destination to a real
1147    tracing destination. The main difference is that if the
1148    destination is C<FILE> or C<APPEND>, we convert it to file
1149    output. If the destination is C<DUAL>, we convert it to file
1150    and standard output.
1151    
1152    =over 4
1153    
1154    =item tkey
1155    
1156    Tracing key for this environment.
1157    
1158    =item myDest
1159    
1160    Destination from the emergency tracing file.
1161    
1162    =item RETURN
1163    
1164    Returns a destination that can be passed into L</TSetup>.
1165    
1166    =back
1167    
1168    =cut
1169    
1170    sub EmergencyTracingDest {
1171        # Get the parameters.
1172        my ($tkey, $myDest) = @_;
1173      # Declare the return variable.      # Declare the return variable.
1174      my @retVal = ();      my $retVal = $myDest;
1175      # Open the directory.      # Process according to the destination value.
1176      if (opendir(my $dirHandle, $dirName)) {      if ($myDest eq 'FILE') {
1177          # The directory opened successfully. Get the appropriate list according to the          $retVal = ">" . EmergencyFileTarget($tkey);
1178          # strictures of the filter parameter.      } elsif ($myDest eq 'APPEND') {
1179          if ($filtered) {          $retVal = ">>" . EmergencyFileTarget($tkey);
1180              @retVal = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir $dirHandle;      } elsif ($myDest eq 'DUAL') {
1181            $retVal = "+>" . EmergencyFileTarget($tkey);
1182        } elsif ($myDest eq 'WARN') {
1183            $retVal = "WARN";
1184        }
1185        # Return the result.
1186        return $retVal;
1187    }
1188    
1189    =head3 Emergency
1190    
1191        Emergency($key, $hours, $dest, $level, @modules);
1192    
1193    Turn on emergency tracing. This method is normally invoked over the web from
1194    a debugging console, but it can also be called by the C<trace.pl> script.
1195    The caller specifies the duration of the emergency in hours, the desired tracing
1196    destination, the trace level, and a list of the trace modules to activate.
1197    For the length of the duration, when a program in an environment with the
1198    specified tracing key active invokes a Sprout CGI script, tracing will be
1199    turned on automatically. See L</TSetup> for more about tracing setup and
1200    L</ETracing> for more about emergency tracing.
1201    
1202    =over 4
1203    
1204    =item tkey
1205    
1206    The tracing key. This is used to identify the control file and the trace file.
1207    
1208    =item hours
1209    
1210    Number of hours to keep emergency tracing alive.
1211    
1212    =item dest
1213    
1214    Tracing destination. If no path information is specified for a file
1215    destination, it is put in the FIG temporary directory.
1216    
1217    =item level
1218    
1219    Tracing level. A higher level means more trace messages.
1220    
1221    =item modules
1222    
1223    A list of the tracing modules to activate.
1224    
1225    =back
1226    
1227    =cut
1228    
1229    sub Emergency {
1230        # Get the parameters.
1231        my ($tkey, $hours, $dest, $level, @modules) = @_;
1232        # Create the emergency file.
1233        my $specFile = EmergencyFileName($tkey);
1234        my $outHandle = Open(undef, ">$specFile");
1235        print $outHandle join("\n", $hours, $dest, $level, @modules, "");
1236    }
1237    
1238    =head3 EmergencyKey
1239    
1240        my $tkey = EmergencyKey($parameter);
1241    
1242    Return the Key to be used for emergency tracing. This could be an IP address,
1243     a session ID, or a user name, depending on the environment.
1244    
1245    =over 4
1246    
1247    =item parameter
1248    
1249    Parameter defining the method for finding the tracing key. If it is a scalar,
1250    then it is presumed to be the tracing key itself. If it is a CGI object, then
1251    the tracing key is taken from the C<IP> cookie. Otherwise, the tracing key is
1252    taken from the C<TRACING> environment variable.
1253    
1254    =item RETURN
1255    
1256    Returns the key to be used for labels in emergency tracing.
1257    
1258    =back
1259    
1260    =cut
1261    
1262    sub EmergencyKey {
1263        # Get the parameters.
1264        my ($parameter) = @_;
1265        # Declare the return variable.
1266        my $retVal;
1267        # Determine the parameter type.
1268        if (! defined $parameter) {
1269            # Here we're supposed to check the environment. If that fails, we
1270            # get the effective login ID.
1271            $retVal = $ENV{TRACING} || scalar getpwuid($<);
1272        } else {
1273            my $ptype = ref $parameter;
1274            if ($ptype eq 'CGI') {
1275                # Here we were invoked from a web page. Look for a cookie.
1276                $retVal = $parameter->cookie('IP');
1277            } elsif (! $ptype) {
1278                # Here the key was passed in.
1279                $retVal = $parameter;
1280            }
1281        }
1282        # If no luck finding a key, use the PID.
1283        if (! defined $retVal) {
1284            $retVal = $$;
1285        }
1286        # Return the result.
1287        return $retVal;
1288    }
1289    
1290    
1291    =head3 TraceParms
1292    
1293        Tracer::TraceParms($cgi);
1294    
1295    Trace the CGI parameters at trace level CGI => 3 and the environment variables
1296    at level CGI => 4. A self-referencing URL is traced at level CGI => 2.
1297    
1298    =over 4
1299    
1300    =item cgi
1301    
1302    CGI query object containing the parameters to trace.
1303    
1304    =back
1305    
1306    =cut
1307    
1308    sub TraceParms {
1309        # Get the parameters.
1310        my ($cgi) = @_;
1311        if (T(CGI => 2)) {
1312            # Here we trace the GET-style URL for the script.
1313            Trace("[URL] " . $cgi->url(-relative => 1, -query => 1));
1314        }
1315        if (T(CGI => 3)) {
1316            # Here we want to trace the parameter data.
1317            my @names = $cgi->param;
1318            for my $parmName (sort @names) {
1319                # Note we skip the Trace parameters, which are for our use only.
1320                if ($parmName ne 'Trace' && $parmName ne 'TF') {
1321                    my @values = $cgi->param($parmName);
1322                    Trace("[CGI] $parmName = " . join(", ", @values));
1323                }
1324            }
1325            # Display the request method.
1326            my $method = $cgi->request_method();
1327            Trace("Method: $method");
1328        }
1329        if (T(CGI => 4)) {
1330            # Here we want the environment data too.
1331            for my $envName (sort keys %ENV) {
1332                Trace("[ENV] $envName = $ENV{$envName}");
1333            }
1334        }
1335    }
1336    
1337    =head3 TraceImages
1338    
1339        Tracer::TraceImages($htmlString);
1340    
1341    Trace information about all of an html document's images. The tracing
1342    will be for type "IMG" at level 3. The image's source string
1343    will be displayed. This is generally either the URL of the image or
1344    raw data for the image itself. If the source is too long, only the first 300
1345    characters will be shown at trace level 3. The entire source will be shown,
1346    however, at trace level 4. This method is not very smart, and might catch
1347    Javascript code, but it is still useful when debugging the arcane
1348    behavior of images in multiple browser environments.
1349    
1350    =over 4
1351    
1352    =item htmlString
1353    
1354    HTML text for an outgoing web page.
1355    
1356    =back
1357    
1358    =cut
1359    
1360    sub TraceImages {
1361        # Only proceed if we're at the proper trace level.
1362        if (T(IMG => 3)) {
1363            # For performance reasons we're manipulating $_[0] instead of retrieving the string
1364            # into a variable called "$htmlString". This is because we expect html strings to be
1365            # long, and don't want to copy them any more than we have to.
1366            Trace(length($_[0]) . " characters in web page.");
1367            # Loop through the HTML, culling image tags.
1368            while ($_[0] =~ /<img\s+[^>]+?src="([^"]+)"/sgi) {
1369                # Extract the source string and determine whether or not it's too long.
1370                my $srcString = $1;
1371                my $pos = pos($_[0]) - length($srcString);
1372                my $excess = length($srcString) - 300;
1373                # We'll put the display string in here.
1374                my $srcDisplay = $srcString;
1375                # If it's a data string, split it at the comma.
1376                $srcDisplay =~ s/^(data[^,]+,)/$1\n/;
1377                # If there's no excess or we're at trace level 4, we're done. At level 3 with
1378                # a long string, however, we only show the first 300 characters.
1379                if ($excess > 0 && ! T(IMG => 4)) {
1380                    $srcDisplay = substr($srcDisplay,0,300) . "\nplus $excess characters.";
1381                }
1382                # Output the trace message.
1383                Trace("Image tag at position $pos:\n$srcDisplay");
1384            }
1385        }
1386    }
1387    
1388    =head2 Command-Line Utility Methods
1389    
1390    =head3 SendSMS
1391    
1392        my $msgID = Tracer::SendSMS($phoneNumber, $msg);
1393    
1394    Send a text message to a phone number using Clickatell. The FIG_Config file must contain the
1395    user name, password, and API ID for the relevant account in the hash reference variable
1396    I<$FIG_Config::phone>, using the keys C<user>, C<password>, and C<api_id>. For
1397    example, if the user name is C<BruceTheHumanPet>, the password is C<silly>, and the API ID
1398    is C<2561022>, then the FIG_Config file must contain
1399    
1400        $phone =  { user => 'BruceTheHumanPet',
1401                    password => 'silly',
1402                    api_id => '2561022' };
1403    
1404    The original purpose of this method was to insure Bruce would be notified immediately when the
1405    Sprout Load terminates. Care should be taken if you do not wish Bruce to be notified immediately
1406    when you call this method.
1407    
1408    The message ID will be returned if successful, and C<undef> if an error occurs.
1409    
1410    =over 4
1411    
1412    =item phoneNumber
1413    
1414    Phone number to receive the message, in international format. A United States phone number
1415    would be prefixed by "1". A British phone number would be prefixed by "44".
1416    
1417    =item msg
1418    
1419    Message to send to the specified phone.
1420    
1421    =item RETURN
1422    
1423    Returns the message ID if successful, and C<undef> if the message could not be sent.
1424    
1425    =back
1426    
1427    =cut
1428    
1429    sub SendSMS {
1430        # Get the parameters.
1431        my ($phoneNumber, $msg) = @_;
1432        # Declare the return variable. If we do not change it, C<undef> will be returned.
1433        my $retVal;
1434        # Only proceed if we have phone support.
1435        if (! defined $FIG_Config::phone) {
1436            Trace("Phone support not present in FIG_Config.") if T(1);
1437          } else {          } else {
1438              @retVal = readdir $dirHandle;          # Get the phone data.
1439            my $parms = $FIG_Config::phone;
1440            # Get the Clickatell URL.
1441            my $url = "http://api.clickatell.com/http/";
1442            # Create the user agent.
1443            my $ua = LWP::UserAgent->new;
1444            # Request a Clickatell session.
1445            my $resp = $ua->post("$url/sendmsg", { user => $parms->{user},
1446                                         password => $parms->{password},
1447                                         api_id => $parms->{api_id},
1448                                         to => $phoneNumber,
1449                                         text => $msg});
1450            # Check for an error.
1451            if (! $resp->is_success) {
1452                Trace("Alert failed.") if T(1);
1453            } else {
1454                # Get the message ID.
1455                my $rstring = $resp->content;
1456                if ($rstring =~ /^ID:\s+(.*)$/) {
1457                    $retVal = $1;
1458                } else {
1459                    Trace("Phone attempt failed with $rstring") if T(1);
1460                }
1461          }          }
     } elsif (! $flag) {  
         # Here the directory would not open and it's considered an error.  
         Confess("Could not open directory $dirName.");  
1462      }      }
1463      # Return the result.      # Return the result.
1464      return @retVal;      return $retVal;
1465  }  }
1466    
1467  =head3 SetLevel  =head3 StandardSetup
1468    
1469        my ($options, @parameters) = StandardSetup(\@categories, \%options, $parmHelp, @ARGV);
1470    
1471    This method performs standard command-line parsing and tracing setup. The return
1472    values are a hash of the command-line options and a list of the positional
1473    parameters. Tracing is automatically set up and the command-line options are
1474    validated.
1475    
1476    This is a complex method that does a lot of grunt work. The parameters can
1477    be more easily understood, however, once they are examined individually.
1478    
1479    The I<categories> parameter is the most obtuse. It is a reference to a list of
1480    special-purpose tracing categories. Most tracing categories are PERL package
1481    names. So, for example, if you wanted to turn on tracing inside the B<Sprout>,
1482    B<ERDB>, and B<SproutLoad> packages, you would specify the categories
1483    
1484        ["Sprout", "SproutLoad", "ERDB"]
1485    
1486    This would cause trace messages in the specified three packages to appear in
1487    the output. There are two special tracing categories that are automatically
1488    handled by this method. In other words, if you used L</TSetup> you would need
1489    to include these categories manually, but if you use this method they are turned
1490    on automatically.
1491    
1492    =over 4
1493    
1494    =item SQL
1495    
1496    Traces SQL commands and activity.
1497    
1498    =item Tracer
1499    
1500    Traces error messages and call stacks.
1501    
1502    =back
1503    
1504    C<SQL> is only turned on if the C<-sql> option is specified in the command line.
1505    The trace level is specified using the C<-trace> command-line option. For example,
1506    the following command line for C<TransactFeatures> turns on SQL tracing and runs
1507    all tracing at level 3.
1508    
1509        TransactFeatures -trace=3 -sql register ../xacts IDs.tbl
1510    
1511    Standard tracing is output to the standard output and echoed to the file
1512    C<trace>I<$$>C<.log> in the FIG temporary directory, where I<$$> is the
1513    process ID. You can also specify the C<user> parameter to put a user ID
1514    instead of a process ID in the trace file name. So, for example
1515    
1516    The default trace level is 2. To get all messages, specify a trace level of 4.
1517    For a genome-by-genome update, use 3.
1518    
1519        TransactFeatures -trace=3 -sql -user=Bruce register ../xacts IDs.tbl
1520    
1521    would send the trace output to C<traceBruce.log> in the temporary directory.
1522    
1523    The I<options> parameter is a reference to a hash containing the command-line
1524    options, their default values, and an explanation of what they mean. Command-line
1525    options may be in the form of switches or keywords. In the case of a switch, the
1526    option value is 1 if it is specified and 0 if it is not specified. In the case
1527    of a keyword, the value is separated from the option name by an equal sign. You
1528    can see this last in the command-line example above.
1529    
1530    You can specify a different default trace level by setting C<$options->{trace}>
1531    prior to calling this method.
1532    
1533    An example at this point would help. Consider, for example, the command-line utility
1534    C<TransactFeatures>. It accepts a list of positional parameters plus the options
1535    C<safe>, C<noAlias>, C<start>, and C<tblFiles>. To start up this command, we execute
1536    the following code.
1537    
1538        my ($options, @parameters) = Tracer::StandardSetup(["DocUtils"],
1539                            { safe => [0, "use database transactions"],
1540                              noAlias => [0, "do not expect aliases in CHANGE transactions"],
1541                              start => [' ', "start with this genome"],
1542                              tblFiles => [0, "output TBL files containing the corrected IDs"] },
1543                            "<command> <transactionDirectory> <IDfile>",
1544                          @ARGV);
1545    
1546    
1547    The call to C<ParseCommand> specifies the default values for the options and
1548    stores the actual options in a hash that is returned as C<$options>. The
1549    positional parameters are returned in C<@parameters>.
1550    
1551    The following is a sample command line for C<TransactFeatures>.
1552    
1553        TransactFeatures -trace=2 -noAlias register ../xacts IDs.tbl
1554    
1555    Single and double hyphens are equivalent. So, you could also code the
1556    above command as
1557    
1558        TransactFeatures --trace=2 --noAlias register ../xacts IDs.tbl
1559    
1560    In this case, C<register>, C<../xacts>, and C<IDs.tbl> are the positional
1561    parameters, and would find themselves in I<@parameters> after executing the
1562    above code fragment. The tracing would be set to level 2, and the categories
1563    would be C<Tracer>, and <DocUtils>. C<Tracer> is standard,
1564    and C<DocUtils> was included because it came in within the first parameter
1565    to this method. The I<$options> hash would be
1566    
1567        { trace => 2, sql => 0, safe => 0,
1568          noAlias => 1, start => ' ', tblFiles => 0 }
1569    
1570    Use of C<StandardSetup> in this way provides a simple way of performing
1571    standard tracing setup and command-line parsing. Note that the caller is
1572    not even aware of the command-line switches C<-trace> and C<-sql>, which
1573    are used by this method to control the tracing. If additional tracing features
1574    need to be added in the future, they can be processed by this method without
1575    upsetting the command-line utilities.
1576    
1577    If the C<background> option is specified on the command line, then the
1578    standard and error outputs will be directed to files in the temporary
1579    directory, using the same suffix as the trace file. So, if the command
1580    line specified
1581    
1582        -user=Bruce -background
1583    
1584  C<< Tracer::SetLevel($newLevel); >>  then the trace output would go to C<traceBruce.log>, the standard output to
1585    C<outBruce.log>, and the error output to C<errBruce.log>. This is designed to
1586    simplify starting a command in the background.
1587    
1588  Modify the trace level. A higher trace level will cause more messages to appear.  The user name is also used as the tracing key for L</Emergency Tracing>.
1589    Specifying a value of C<E> for the trace level causes emergency tracing to
1590    be used instead of custom tracing. If the user name is not specified,
1591    the tracing key is taken from the C<Tracing> environment variable. If there
1592    is no value for that variable, the tracing key will be computed from the active
1593    login ID.
1594    
1595    Since the default situation in StandardSetup is to trace to the standard
1596    output, errors that occur in command-line scripts will not generate
1597    RSS events. To force the events, use the C<warn> option.
1598    
1599  =over 4      TransactFeatures -background -warn register ../xacts IDs.tbl
1600    
1601  =item newLevel  Finally, if the special option C<-help> is specified, the option
1602    names will be traced at level 0 and the program will exit without processing.
1603    This provides a limited help capability. For example, if the user enters
1604    
1605  Proposed new trace level.      TransactFeatures -help
1606    
1607  =back  he would see the following output.
1608    
1609  =cut      TransactFeatures [options] <command> <transactionDirectory> <IDfile>
1610            -trace    tracing level (default E)
1611            -sql      trace SQL commands
1612            -safe     use database transactions
1613            -noAlias  do not expect aliases in CHANGE transactions
1614            -start    start with this genome
1615            -tblFiles output TBL files containing the corrected IDs
1616    
1617  sub SetLevel {  The caller has the option of modifying the tracing scheme by placing a value
1618      $TraceLevel = $_[0];  for C<trace> in the incoming options hash. The default value can be overridden,
1619  }  or the tracing to the standard output can be turned off by suffixing a minus
1620    sign to the trace level. So, for example,
1621    
1622  =head3 Now      { trace => [0, "tracing level (default 0)"],
1623           ...
1624    
1625  C<< my $string = Tracer::Now(); >>  would set the default trace level to 0 instead of E, while
1626    
1627  Return a displayable time stamp containing the local time.      { trace => ["2-", "tracing level (default 2)"],
1628           ...
1629    
1630  =cut  would set the default to 2, but trace only to the log file, not to the
1631    standard output.
1632    
1633  sub Now {  The parameters to this method are as follows.
     my ($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 $retVal;  
 }  
1634    
1635  # Pad a number to 2 digits.  =over 4
 sub _p2 {  
     my ($value) = @_;  
     $value = "0$value" if ($value < 10);  
     return $value;  
 }  
1636    
1637  =head3 LogErrors  =item categories
1638    
1639  C<< Tracer::LogErrors($fileName); >>  Reference to a list of tracing category names. These should be names of
1640    packages whose internal workings will need to be debugged to get the
1641    command working.
1642    
1643  Route the standard error output to a log file.  =item options
1644    
1645  =over 4  Reference to a hash containing the legal options for the current command mapped
1646    to their default values and descriptions. The user can override the defaults
1647    by specifying the options as command-line switches prefixed by a hyphen.
1648    Tracing-related options may be added to this hash. If the C<-h> option is
1649    specified on the command line, the option descriptions will be used to
1650    explain the options. To turn off tracing to the standard output, add a
1651    minus sign to the value for C<trace> (see above).
1652    
1653  =item fileName  =item parmHelp
1654    
1655  Name of the file to receive the error output.  A string that vaguely describes the positional parameters. This is used
1656    if the user specifies the C<-h> option.
1657    
1658    =item argv
1659    
1660    List of command line parameters, including the option switches, which must
1661    precede the positional parameters and be prefixed by a hyphen.
1662    
1663    =item RETURN
1664    
1665    Returns a list. The first element of the list is the reference to a hash that
1666    maps the command-line option switches to their values. These will either be the
1667    default values or overrides specified on the command line. The remaining
1668    elements of the list are the position parameters, in order.
1669    
1670  =back  =back
1671    
1672  =cut  =cut
1673    
1674  sub LogErrors {  sub StandardSetup {
1675      # Get the file name.      # Get the parameters.
1676      my ($fileName) = @_;      my ($categories, $options, $parmHelp, @argv) = @_;
1677      # Open the file as the standard error output.      # Get the default tracing key.
1678      open STDERR, '>', $fileName;      my $tkey = EmergencyKey();
1679        # Save the command line.
1680        $CommandLine = join(" ", $0, map { $_ =~ /\s/ ? "\"$_\"" : $_ } @argv);
1681        # Add the tracing options.
1682        if (! exists $options->{trace}) {
1683            $options->{trace} = ['2', "tracing level (E for emergency tracing)"];
1684        }
1685        $options->{sql} = [0, "turn on SQL tracing"];
1686        $options->{help} = [0, "display command-line options"];
1687        $options->{user} = [$tkey, "tracing key"];
1688        $options->{background} = [0, "spool standard and error output"];
1689        $options->{warn} = [0, "send errors to RSS feed"];
1690        # Create a parsing hash from the options hash. The parsing hash
1691        # contains the default values rather than the default value
1692        # and the description. While we're at it, we'll memorize the
1693        # length of the longest option name.
1694        my $longestName = 0;
1695        my %parseOptions = ();
1696        for my $key (keys %{$options}) {
1697            if (length $key > $longestName) {
1698                $longestName = length $key;
1699            }
1700            $parseOptions{$key} = $options->{$key}->[0];
1701        }
1702        # Parse the command line.
1703        my ($retOptions, @retParameters) = ParseCommand(\%parseOptions, @argv);
1704        # Get the logfile suffix.
1705        my $suffix = $retOptions->{user};
1706        # Check for background mode.
1707        if ($retOptions->{background}) {
1708            my $outFileName = "$FIG_Config::temp/out$suffix.log";
1709            my $errFileName = "$FIG_Config::temp/err$suffix.log";
1710            open STDOUT, ">$outFileName";
1711            open STDERR, ">$errFileName";
1712            # Check for phone support. If we have phone support and a phone number,
1713            # we want to turn it on.
1714            if ($ENV{PHONE} && defined($FIG_Config::phone)) {
1715                $retOptions->{phone} = $ENV{PHONE};
1716            }
1717        }
1718        # Now we want to set up tracing. First, we need to know if the user
1719        # wants emergency tracing.
1720        if ($retOptions->{trace} eq 'E') {
1721            ETracing($retOptions->{user});
1722        } else {
1723            # Here the tracing is controlled from the command line.
1724            my @cats = @{$categories};
1725            if ($retOptions->{sql}) {
1726                push @cats, "SQL";
1727            }
1728            if ($retOptions->{warn}) {
1729                push @cats, "Feed";
1730            }
1731            # Add the default categories.
1732            push @cats, "Tracer";
1733            # Next, we create the category string by joining the categories.
1734            my $cats = join(" ", @cats);
1735            # Check to determine whether or not the caller wants to turn off tracing
1736            # to the standard output.
1737            my $traceLevel = $retOptions->{trace};
1738            my $textOKFlag = 1;
1739            if ($traceLevel =~ /^(.)-/) {
1740                $traceLevel = $1;
1741                $textOKFlag = 0;
1742            }
1743            # Now we set up the trace mode.
1744            my $traceMode;
1745            # Verify that we can open a file in the FIG temporary directory.
1746            my $traceFileName = "$FIG_Config::temp/trace$suffix.log";
1747            if (open TESTTRACE, ">$traceFileName") {
1748                # Here we can trace to a file.
1749                $traceMode = ">$traceFileName";
1750                if ($textOKFlag) {
1751                    # Echo to standard output if the text-OK flag is set.
1752                    $traceMode = "+$traceMode";
1753                }
1754                # Close the test file.
1755                close TESTTRACE;
1756            } else {
1757                # Here we can't trace to a file. Complain about this.
1758                warn "Could not open trace file $traceFileName: $!\n";
1759                # We trace to the standard output if it's
1760                # okay, and the error log otherwise.
1761                if ($textOKFlag) {
1762                    $traceMode = "TEXT";
1763                } else {
1764                    $traceMode = "WARN";
1765                }
1766            }
1767            # Now set up the tracing.
1768            TSetup("$traceLevel $cats", $traceMode);
1769        }
1770        # Check for the "help" option. If it is specified, dump the command-line
1771        # options and exit the program.
1772        if ($retOptions->{help}) {
1773            $0 =~ m#[/\\](\w+)(\.pl)?$#i;
1774            print "$1 [options] $parmHelp\n";
1775            for my $key (sort keys %{$options}) {
1776                my $name = Pad($key, $longestName, 0, ' ');
1777                my $desc = $options->{$key}->[1];
1778                if ($options->{$key}->[0]) {
1779                    $desc .= " (default " . $options->{$key}->[0] . ")";
1780                }
1781                print "  $name $desc\n";
1782            }
1783            exit(0);
1784        }
1785        # Trace the options, if applicable.
1786        if (T(3)) {
1787            my @parms = grep { $retOptions->{$_} } keys %{$retOptions};
1788            Trace("Selected options: " . join(", ", sort @parms) . ".");
1789        }
1790        # Return the parsed parameters.
1791        return ($retOptions, @retParameters);
1792  }  }
1793    
1794  =head3 ReadOptions  =head3 ReadOptions
1795    
1796  C<< my %options = Tracer::ReadOptions($fileName); >>      my %options = Tracer::ReadOptions($fileName);
1797    
1798  Read a set of options from a file. Each option is encoded in a line of text that has the  Read a set of options from a file. Each option is encoded in a line of text that has the
1799  format  format
# Line 855  Line 1854 
1854    
1855  =head3 GetOptions  =head3 GetOptions
1856    
1857  C<< Tracer::GetOptions(\%defaults, \%options); >>      Tracer::GetOptions(\%defaults, \%options);
1858    
1859  Merge a specified set of options into a table of defaults. This method takes two hash references  Merge a specified set of options into a table of defaults. This method takes two hash references
1860  as input and uses the data from the second to update the first. If the second does not exist,  as input and uses the data from the second to update the first. If the second does not exist,
# Line 864  Line 1863 
1863    
1864  Consider the following example.  Consider the following example.
1865    
1866  C<< my $optionTable = GetOptions({ dbType => 'mySQL', trace => 0 }, $options); >>      my $optionTable = GetOptions({ dbType => 'mySQL', trace => 0 }, $options);
1867    
1868  In this example, the variable B<$options> is expected to contain at most two options-- B<dbType> and  In this example, the variable B<$options> is expected to contain at most two options-- B<dbType> and
1869  B<trace>. The default database type is C<mySQL> and the default trace level is C<0>. If the value of  B<trace>. The default database type is C<mySQL> and the default trace level is C<0>. If the value of
# Line 872  Line 1871 
1871  the trace level will remain at 0. If B<$options> is undefined, then the database type and trace level  the trace level will remain at 0. If B<$options> is undefined, then the database type and trace level
1872  will remain C<mySQL> and C<0>. If, on the other hand, B<$options> is defined as  will remain C<mySQL> and C<0>. If, on the other hand, B<$options> is defined as
1873    
1874  C<< {databaseType => 'Oracle'} >>      {databaseType => 'Oracle'}
1875    
1876  an error will occur because the B<databaseType> option does not exist.  an error will occur because the B<databaseType> option does not exist.
1877    
# Line 916  Line 1915 
1915    
1916  =head3 MergeOptions  =head3 MergeOptions
1917    
1918  C<< Tracer::MergeOptions(\%table, \%defaults); >>      Tracer::MergeOptions(\%table, \%defaults);
1919    
1920  Merge default values into a hash table. This method looks at the key-value pairs in the  Merge default values into a hash table. This method looks at the key-value pairs in the
1921  second (default) hash, and if a matching key is not found in the first hash, the default  second (default) hash, and if a matching key is not found in the first hash, the default
# Line 931  Line 1930 
1930    
1931  =item defaults  =item defaults
1932    
1933  Default values to be merged into the first hash table if they are not already present.  Default values to be merged into the first hash table if they are not already present.
   
 =back  
   
 =cut  
   
 sub MergeOptions {  
     # Get the parameters.  
     my ($table, $defaults) = @_;  
     # Loop through the defaults.  
     while (my ($key, $value) = each %{$defaults}) {  
         if (!exists $table->{$key}) {  
             $table->{$key} = $value;  
         }  
     }  
 }  
   
 =head3 Trace  
   
 C<< Trace($message); >>  
   
 Write a trace message to the target location specified in L</TSetup>. If there has not been  
 any prior call to B<TSetup>.  
   
 =over 4  
   
 =item message  
   
 Message to write.  
   
 =back  
   
 =cut  
   
 sub Trace {  
     # Get the parameters.  
     my ($message) = @_;  
     # Get the timestamp.  
     my $timeStamp = Now();  
     # Format the message. Note we strip off any line terminators at the end.  
     my $formatted = "[$timeStamp] <$LastCategory>: " . Strip($message);  
     # Process according to the destination.  
     if ($Destination eq "TEXT") {  
         # Write the message to the standard output.  
         print "$formatted\n";  
     } elsif ($Destination eq "ERROR") {  
         # Write the message to the error output.  
         print STDERR "$formatted\n";  
     } elsif ($Destination eq "QUEUE") {  
         # Push the message into the queue.  
         push @Queue, "$formatted";  
     } elsif ($Destination eq "HTML") {  
         # Convert the message to HTML and write it to the standard output.  
         my $escapedMessage = CGI::escapeHTML($message);  
         print "<p>$formatted</p>\n";  
     } elsif ($Destination eq "WARN") {  
        # Emit the message as a warning.  
        warn $message;  
     } elsif ($Destination =~ m/^>>/) {  
         # Write the trace message to an output file.  
         (open TRACING, $Destination) || die "Tracing open for \"$Destination\" failed: $!";  
         print TRACING "$formatted\n";  
         close TRACING;  
         # If the Tee flag is on, echo it to the standard output.  
         if ($TeeFlag) {  
             print "$formatted\n";  
         }  
     }  
 }  
   
 =head3 T  
   
 C<< my $switch = T($category, $traceLevel); >>  
   
     or  
   
 C<< my $switch = T($traceLevel); >>  
   
 Return TRUE if the trace level is at or above a specified value and the specified category  
 is active, else FALSE. If no category is specified, the caller's package name is used.  
   
 =over 4  
   
 =item category  
   
 Category to which the message belongs. If not specified, the caller's package name is  
 used.  
   
 =item traceLevel  
   
 Relevant tracing level.  
   
 =item RETURN  
   
 TRUE if a message at the specified trace level would appear in the trace, else FALSE.  
1934    
1935  =back  =back
1936    
1937  =cut  =cut
1938    
1939  sub T {  sub MergeOptions {
     # Declare the return variable.  
     my $retVal = 0;  
     # Only proceed if tracing is turned on.  
     if ($Destination ne "NONE") {  
1940          # Get the parameters.          # Get the parameters.
1941          my ($category, $traceLevel) = @_;      my ($table, $defaults) = @_;
1942          if (!defined $traceLevel) {      # Loop through the defaults.
1943              # Here we have no category, so we need to get the calling package.      while (my ($key, $value) = each %{$defaults}) {
1944              # The calling package is normally the first parameter. If it is          if (!exists $table->{$key}) {
1945              # omitted, the first parameter will be the tracelevel. So, the              $table->{$key} = $value;
             # first thing we do is shift the so-called category into the  
             # $traceLevel variable where it belongs.  
             $traceLevel = $category;  
             my ($package, $fileName, $line) = caller;  
             # If there is no calling package, we default to "main".  
             if (!$package) {  
                 $category = "main";  
             } else {  
                 $category = $package;  
             }  
         }  
         # Save the category name.  
         $LastCategory = $category;  
         # Convert it to lower case before we hash it.  
         $category = lc $category;  
         # Use the category and tracelevel to compute the result.  
         if (ref $traceLevel) {  
             Confess("Bad trace level.");  
         } elsif (ref $TraceLevel) {  
             Confess("Bad trace config.");  
1946          }          }
         $retVal = ($traceLevel <= $TraceLevel && ($AllTrace || exists $Categories{$category}));  
1947      }      }
     # Return the computed result.  
     return $retVal;  
1948  }  }
1949    
1950  =head3 ParseCommand  =head3 ParseCommand
1951    
1952  C<< my ($options, @arguments) = Tracer::ParseCommand(\%optionTable, @inputList); >>      my ($options, @arguments) = Tracer::ParseCommand(\%optionTable, @inputList);
1953    
1954  Parse a command line consisting of a list of parameters. The initial parameters may be option  Parse a command line consisting of a list of parameters. The initial parameters may be option
1955  specifiers of the form C<->I<option> or C<->I<option>C<=>I<value>. The options are stripped  specifiers of the form C<->I<option> or C<->I<option>C<=>I<value>. The options are stripped
1956  off and merged into a table of default options. The remainder of the command line is  off and merged into a table of default options. The remainder of the command line is
1957  returned as a list of positional arguments. For example, consider the following invocation.  returned as a list of positional arguments. For example, consider the following invocation.
1958    
1959  C<< my ($options, @arguments) = ParseCommand({ errors => 0, logFile => 'trace.log'}, @words); >>      my ($options, @arguments) = ParseCommand({ errors => 0, logFile => 'trace.log'}, @words);
1960    
1961  In this case, the list @words will be treated as a command line. There are two options available,  In this case, the list @words will be treated as a command line and there are two options available,
1962  B<errors> and B<logFile>. If @words has the following format  B<errors> and B<logFile>. If @words has the following format
1963    
1964  C<< -logFile=error.log apple orange rutabaga >>      -logFile=error.log apple orange rutabaga
1965    
1966  then at the end of the invocation, C<$options> will be  then at the end of the invocation, C<$options> will be
1967    
1968  C<< { errors => 0, logFile => 'error.log' } >>      { errors => 0, logFile => 'error.log' }
1969    
1970  and C<@arguments> will contain  and C<@arguments> will contain
1971    
1972  C<< apple orange rutabaga >>      apple orange rutabaga
1973    
1974  The parser allows for some escape sequences. See L</UnEscape> for a description. There is no  The parser allows for some escape sequences. See L</UnEscape> for a description. There is no
1975  support for quote characters.  support for quote characters. Options can be specified with single or double hyphens.
1976    
1977  =over 4  =over 4
1978    
# Line 1119  Line 1997 
1997      my ($optionTable, @inputList) = @_;      my ($optionTable, @inputList) = @_;
1998      # Process any options in the input list.      # Process any options in the input list.
1999      my %overrides = ();      my %overrides = ();
2000      while ((@inputList > 0) && ($inputList[0] =~ /^-/)) {      while ((@inputList > 0) && ($inputList[0] =~ /^--?/)) {
2001          # Get the current option.          # Get the current option.
2002          my $arg = shift @inputList;          my $arg = shift @inputList;
2003          # Pull out the option name.          # Pull out the option name.
2004          $arg =~ /^-([^=]*)/g;          $arg =~ /^--?([^=]*)/g;
2005          my $name = $1;          my $name = $1;
2006          # Check for an option value.          # Check for an option value.
2007          if ($arg =~ /\G=(.*)$/g) {          if ($arg =~ /\G=(.*)$/g) {
# Line 1145  Line 2023 
2023      return ($optionTable, @retVal);      return ($optionTable, @retVal);
2024  }  }
2025    
 =head3 Escape  
2026    
2027  C<< my $codedString = Tracer::Escape($realString); >>  =head2 File Utility Methods
2028    
2029  Escape a string for use in a command length. Tabs will be replaced by C<\t>, new-lines  =head3 GetFile
2030  replaced by C<\n>, carriage returns will be deleted, and backslashes will be doubled. The  
2031  result is to reverse the effect of L</UnEscape>.      my @fileContents = Tracer::GetFile($fileName);
2032    
2033        or
2034    
2035        my $fileContents = Tracer::GetFile($fileName);
2036    
2037    Return the entire contents of a file. In list context, line-ends are removed and
2038    each line is a list element. In scalar context, line-ends are replaced by C<\n>.
2039    
2040  =over 4  =over 4
2041    
2042  =item realString  =item fileName
2043    
2044  String to escape.  Name of the file to read.
2045    
2046  =item RETURN  =item RETURN
2047    
2048  Escaped equivalent of the real string.  In a list context, returns the entire file as a list with the line terminators removed.
2049    In a scalar context, returns the entire file as a string. If an error occurs opening
2050    the file, an empty list will be returned.
2051    
2052  =back  =back
2053    
2054  =cut  =cut
2055    
2056  sub Escape {  sub GetFile {
2057      # Get the parameter.      # Get the parameters.
2058      my ($realString) = @_;      my ($fileName) = @_;
2059      # Initialize the return variable.      # Declare the return variable.
2060      my $retVal = "";      my @retVal = ();
2061      # Loop through the parameter string, looking for sequences to escape.      # Open the file for input.
2062      while (length $realString > 0) {      my $handle = Open(undef, "<$fileName");
2063          # Look for the first sequence to escape.      # Read the whole file into the return variable, stripping off any terminator
2064          if ($realString =~ /^(.*?)([\n\t\r\\])/) {      # characters.
2065              # Here we found it. The text preceding the sequence is in $1. The sequence      my $lineCount = 0;
2066              # itself is in $2. First, move the clear text to the return variable.      while (my $line = <$handle>) {
2067              $retVal .= $1;          $lineCount++;
2068              # Strip the processed section off the real string.          $line = Strip($line);
2069              $realString = substr $realString, (length $2) + (length $1);          push @retVal, $line;
             # 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;  
2070              }              }
2071        # Close it.
2072        close $handle;
2073        my $actualLines = @retVal;
2074        Trace("$actualLines lines read from file $fileName.") if T(File => 2);
2075        # Return the file's contents in the desired format.
2076        if (wantarray) {
2077            return @retVal;
2078          } else {          } else {
2079              # Here there are no more escape sequences. The rest of the string is          return join "\n", @retVal;
             # transferred unmodified.  
             $retVal .= $realString;  
             $realString = "";  
         }  
2080      }      }
     # Return the result.  
     return $retVal;  
2081  }  }
2082    
2083  =head3 UnEscape  =head3 PutFile
2084    
2085  C<< my $realString = Tracer::UnEscape($codedString); >>      Tracer::PutFile($fileName, \@lines);
2086    
2087  Replace escape sequences with their actual equivalents. C<\t> will be replaced by  Write out a file from a list of lines of text.
 a tab, C<\n> by a new-line character, and C<\\> by a backslash. C<\r> codes will  
 be deleted.  
2088    
2089  =over 4  =over 4
2090    
2091  =item codedString  =item fileName
2092    
2093  String to un-escape.  Name of the output file.
2094    
2095  =item RETURN  =item lines
2096    
2097  Returns a copy of the original string with the escape sequences converted to their actual  Reference to a list of text lines. The lines will be written to the file in order, with trailing
2098  values.  new-line characters. Alternatively, may be a string, in which case the string will be written without
2099    modification.
2100    
2101  =back  =back
2102    
2103  =cut  =cut
2104    
2105  sub UnEscape {  sub PutFile {
2106      # Get the parameter.      # Get the parameters.
2107      my ($codedString) = @_;      my ($fileName, $lines) = @_;
2108      # Initialize the return variable.      # Open the output file.
2109      my $retVal = "";      my $handle = Open(undef, ">$fileName");
2110      # Only proceed if the incoming string is nonempty.      # Count the lines written.
2111      if (defined $codedString) {      if (ref $lines ne 'ARRAY') {
2112          # Loop through the parameter string, looking for escape sequences. We can't do          # Here we have a scalar, so we write it raw.
2113          # translating because it causes problems with the escaped slash. ("\\t" becomes          print $handle $lines;
2114          # "\<tab>" no matter what we do.)          Trace("Scalar put to file $fileName.") if T(File => 3);
         while (length $codedString > 0) {  
             # Look for the first escape sequence.  
             if ($codedString =~ /^(.*?)\\(\\|n|t|r)/) {  
                 # Here we found it. The text preceding the sequence is in $1. The sequence  
                 # itself is in $2. First, move the clear text to the return variable.  
                 $retVal .= $1;  
                 $codedString = substr $codedString, (2 + length $1);  
                 # Get the escape value.  
                 my $char = $2;  
                 # If we have a "\r", we are done.  
                 if ($char ne 'r') {  
                     # Here it's not an 'r', so we convert it.  
                     $char =~ tr/\\tn/\\\t\n/;  
                     $retVal .= $char;  
                 }  
2115              } else {              } else {
2116                  # Here there are no more escape sequences. The rest of the string is          # Write the lines one at a time.
2117                  # transferred unmodified.          my $count = 0;
2118                  $retVal .= $codedString;          for my $line (@{$lines}) {
2119                  $codedString = "";              print $handle "$line\n";
2120              }              $count++;
2121          }          }
2122            Trace("$count lines put to file $fileName.") if T(File => 3);
2123      }      }
2124      # Return the result.      # Close the output file.
2125      return $retVal;      close $handle;
2126  }  }
2127    
2128  =head3 ParseRecord  =head3 ParseRecord
2129    
2130  C<< my @fields = Tracer::ParseRecord($line); >>      my @fields = Tracer::ParseRecord($line);
2131    
2132  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
2133  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 1307  Line 2172 
2172    
2173  =head3 Merge  =head3 Merge
2174    
2175  C<< my @mergedList = Tracer::Merge(@inputList); >>      my @mergedList = Tracer::Merge(@inputList);
2176    
2177  Sort a list of strings and remove duplicates.  Sort a list of strings and remove duplicates.
2178    
# Line 1339  Line 2204 
2204              # Find out how many elements duplicate the current entry.              # Find out how many elements duplicate the current entry.
2205              my $j = $i + 1;              my $j = $i + 1;
2206              my $dup1 = $i + 1;              my $dup1 = $i + 1;
2207              while ($j < @inputList && $inputList[$j] eq $thisEntry) { $j++; };              while ($j < @inputList && $inputList[$j] eq $thisEntry) { $j++; };
2208              # If the number is nonzero, splice out the duplicates found.              # If the number is nonzero, splice out the duplicates found.
2209              if ($j > $dup1) {              if ($j > $dup1) {
2210                  splice @inputList, $dup1, $j - $dup1;                  splice @inputList, $dup1, $j - $dup1;
2211              }              }
2212              # Now the element at position $dup1 is different from the element before it              # Now the element at position $dup1 is different from the element before it
2213              # at position $i. We push $i forward one position and start again.              # at position $i. We push $i forward one position and start again.
2214              $i++;              $i++;
         }  
     }  
     # Return the merged list.  
     return @inputList;  
 }  
   
 =head3 Percent  
   
 C<< my $percent = Tracer::Percent($number, $base); >>  
   
 Returns the percent of the base represented by the given number. If the base  
 is zero, returns zero.  
   
 =over 4  
   
 =item number  
   
 Percent numerator.  
   
 =item base  
   
 Percent base.  
   
 =item RETURN  
   
 Returns the percentage of the base represented by the numerator.  
   
 =back  
   
 =cut  
   
 sub Percent {  
     # Get the parameters.  
     my ($number, $base) = @_;  
     # Declare the return variable.  
     my $retVal = 0;  
     # Compute the percent.  
     if ($base != 0) {  
         $retVal = $number * 100 / $base;  
     }  
     # Return the result.  
     return $retVal;  
 }  
   
 =head3 GetFile  
   
 C<< my @fileContents = Tracer::GetFile($fileName); >>  
   
     or  
   
 C<< my $fileContents = Tracer::GetFile($fileName); >>  
   
 Return the entire contents of a file. In list context, line-ends are removed and  
 each line is a list element. In scalar context, line-ends are replaced by C<\n>.  
   
 =over 4  
   
 =item fileName  
   
 Name of the file to read.  
   
 =item RETURN  
   
 In a list context, returns the entire file as a list with the line terminators removed.  
 In a scalar context, returns the entire file as a string. If an error occurs opening  
 the file, an empty list will be returned.  
   
 =back  
   
 =cut  
   
 sub GetFile {  
     # Get the parameters.  
     my ($fileName) = @_;  
     # Declare the return variable.  
     my @retVal = ();  
     # Open the file for input.  
     my $handle = Open(undef, "<$fileName");  
     # Read the whole file into the return variable, stripping off any terminator  
     # characters.  
     my $lineCount = 0;  
     while (my $line = <$handle>) {  
         $lineCount++;  
         $line = Strip($line);  
         push @retVal, $line;  
2215      }      }
     # Close it.  
     close $handle;  
     my $actualLines = @retVal;  
     # Return the file's contents in the desired format.  
     if (wantarray) {  
         return @retVal;  
     } else {  
         return join "\n", @retVal;  
2216      }      }
2217        # Return the merged list.
2218        return @inputList;
2219  }  }
2220    
2221  =head3 PutFile  =head3 Open
2222    
2223  C<< Tracer::PutFile($fileName, \@lines); >>      my $handle = Open($fileHandle, $fileSpec, $message);
2224    
2225  Write out a file from a list of lines of text.  Open a file.
2226    
2227  =over 4  The I<$fileSpec> is essentially the second argument of the PERL C<open>
2228    function. The mode is specified using Unix-like shell information. So, for
2229    example,
2230    
2231  =item fileName      Open(\*LOGFILE, '>>/usr/spool/news/twitlog', "Could not open twit log.");
2232    
2233  Name of the output file.  would open for output appended to the specified file, and
2234    
2235  =item lines      Open(\*DATASTREAM, "| sort -u >$outputFile", "Could not open $outputFile.");
2236    
2237  Reference to a list of text lines. The lines will be written to the file in order, with trailing  would open a pipe that sorts the records written and removes duplicates. Note
2238  new-line characters. Alternatively, may be a string, in which case the string will be written without  the use of file handle syntax in the Open call. To use anonymous file handles,
2239  modification.  code as follows.
2240    
2241  =back      my $logFile = Open(undef, '>>/usr/spool/news/twitlog', "Could not open twit log.");
2242    
2243  =cut  The I<$message> parameter is used if the open fails. If it is set to C<0>, then
2244    the open returns TRUE if successful and FALSE if an error occurred. Otherwise, a
2245    failed open will throw an exception and the third parameter will be used to construct
2246    an error message. If the parameter is omitted, a standard message is constructed
2247    using the file spec.
2248    
2249  sub PutFile {      Could not open "/usr/spool/news/twitlog"
     # Get the parameters.  
     my ($fileName, $lines) = @_;  
     # Open the output file.  
     my $handle = Open(undef, ">$fileName");  
     if (ref $lines ne 'ARRAY') {  
         # Here we have a scalar, so we write it raw.  
         print $handle $lines;  
     } else {  
         # Write the lines one at a time.  
         for my $line (@{$lines}) {  
             print $handle "$line\n";  
         }  
     }  
     # Close the output file.  
     close $handle;  
 }  
2250    
2251  =head3 QTrace  Note that the mode characters are automatically cleaned from the file name.
2252    The actual error message from the file system will be captured and appended to the
2253    message in any case.
2254    
2255  C<< my $data = QTrace($format); >>      Could not open "/usr/spool/news/twitlog": file not found.
2256    
2257  Return the queued trace data in the specified format.  In some versions of PERL the only error message we get is a number, which
2258    corresponds to the C++ C<errno> value.
2259    
2260        Could not open "/usr/spool/news/twitlog": 6.
2261    
2262  =over 4  =over 4
2263    
2264  =item format  =item fileHandle
2265    
2266  C<html> to format the data as an HTML list, C<text> to format it as straight text.  File handle. If this parameter is C<undef>, a file handle will be generated
2267    and returned as the value of this method.
2268    
2269    =item fileSpec
2270    
2271    File name and mode, as per the PERL C<open> function.
2272    
2273    =item message (optional)
2274    
2275    Error message to use if the open fails. If omitted, a standard error message
2276    will be generated. In either case, the error information from the file system
2277    is appended to the message. To specify a conditional open that does not throw
2278    an error if it fails, use C<0>.
2279    
2280    =item RETURN
2281    
2282    Returns the name of the file handle assigned to the file, or C<undef> if the
2283    open failed.
2284    
2285  =back  =back
2286    
2287  =cut  =cut
2288    
2289  sub QTrace {  sub Open {
2290      # Get the parameter.      # Get the parameters.
2291      my ($format) = @_;      my ($fileHandle, $fileSpec, $message) = @_;
2292      # Create the return variable.      # Attempt to open the file.
2293      my $retVal = "";      my $rv = open $fileHandle, $fileSpec;
2294      # Only proceed if there is an actual queue.      # If the open failed, generate an error message.
2295      if (@Queue) {      if (! $rv) {
2296          # Process according to the format.          # Save the system error message.
2297          if ($format =~ m/^HTML$/i) {          my $sysMessage = $!;
2298              # Convert the queue into an HTML list.          # See if we need a default message.
2299              $retVal = "<ul>\n";          if (!$message) {
2300              for my $line (@Queue) {              # Clean any obvious mode characters and leading spaces from the
2301                  my $escapedLine = CGI::escapeHTML($line);              # filename.
2302                  $retVal .= "<li>$escapedLine</li>\n";              my ($fileName) = FindNamePart($fileSpec);
2303              }              $message = "Could not open \"$fileName\"";
             $retVal .= "</ul>\n";  
         } elsif ($format =~ m/^TEXT$/i) {  
             # Convert the queue into a list of text lines.  
             $retVal = join("\n", @Queue) . "\n";  
2304          }          }
2305          # Clear the queue.          # Terminate with an error using the supplied message and the
2306          @Queue = ();          # error message from the file system.
2307            Confess("$message: $!");
2308      }      }
2309      # Return the formatted list.      # Return the file handle.
2310      return $retVal;      return $fileHandle;
2311  }  }
2312    
2313  =head3 Confess  =head3 FindNamePart
2314    
2315  C<< Confess($message); >>      my ($fileName, $start, $len) = Tracer::FindNamePart($fileSpec);
2316    
2317  Trace the call stack and abort the program with the specified message. When used with  Extract the portion of a file specification that contains the file name.
 the OR operator and the L</Assert> method, B<Confess> can function as a debugging assert.  
 So, for example  
2318    
2319  C<< Assert($recNum >= 0) || Confess("Invalid record number $recNum."); >>  A file specification is the string passed to an C<open> call. It specifies the file
2320    mode and name. In a truly complex situation, it can specify a pipe sequence. This
2321    method assumes that the file name is whatever follows the first angle bracket
2322    sequence.  So, for example, in the following strings the file name is
2323    C</usr/fig/myfile.txt>.
2324    
2325  Will abort the program with a stack trace if the value of C<$recNum> is negative.      >>/usr/fig/myfile.txt
2326        </usr/fig/myfile.txt
2327        | sort -u > /usr/fig/myfile.txt
2328    
2329    If the method cannot find a file name using its normal methods, it will return the
2330    whole incoming string.
2331    
2332  =over 4  =over 4
2333    
2334  =item message  =item fileSpec
2335    
2336  Message to include in the trace.  File specification string from which the file name is to be extracted.
2337    
2338    =item RETURN
2339    
2340    Returns a three-element list. The first element contains the file name portion of
2341    the specified string, or the whole string if a file name cannot be found via normal
2342    methods. The second element contains the start position of the file name portion and
2343    the third element contains the length.
2344    
2345  =back  =back
2346    
2347  =cut  =cut
2348    #: Return Type $;
2349  sub Confess {  sub FindNamePart {
2350      # Get the parameters.      # Get the parameters.
2351      my ($message) = @_;      my ($fileSpec) = @_;
2352      # Trace the call stack.      # Default to the whole input string.
2353      Cluck($message);      my ($retVal, $pos, $len) = ($fileSpec, 0, length $fileSpec);
2354      # Abort the program.      # Parse out the file name if we can.
2355      croak(">>> $message");      if ($fileSpec =~ m/(<|>>?)(.+?)(\s*)$/) {
2356            $retVal = $2;
2357            $len = length $retVal;
2358            $pos = (length $fileSpec) - (length $3) - $len;
2359        }
2360        # Return the result.
2361        return ($retVal, $pos, $len);
2362  }  }
2363    
2364  =head3 Assert  =head3 OpenDir
2365    
2366  C<< Assert($condition1, $condition2, ... $conditionN); >>      my @files = OpenDir($dirName, $filtered, $flag);
2367    
2368  Return TRUE if all the conditions are true. This method can be used in conjunction with  Open a directory and return all the file names. This function essentially performs
2369  the OR operator and the L</Confess> method as a debugging assert.  the functions of an C<opendir> and C<readdir>. If the I<$filtered> parameter is
2370  So, for example  set to TRUE, all filenames beginning with a period (C<.>), dollar sign (C<$>),
2371    or pound sign (C<#>) and all filenames ending with a tilde C<~>) will be
2372    filtered out of the return list. If the directory does not open and I<$flag> is not
2373    set, an exception is thrown. So, for example,
2374    
2375  C<< Assert($recNum >= 0) || Confess("Invalid record number $recNum."); >>      my @files = OpenDir("/Volumes/fig/contigs", 1);
2376    
2377  Will abort the program with a stack trace if the value of C<$recNum> is negative.  is effectively the same as
2378    
2379  =cut      opendir(TMP, "/Volumes/fig/contigs") || Confess("Could not open /Volumes/fig/contigs.");
2380  sub Assert {      my @files = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir(TMP);
     my $retVal = 1;  
     LOOP: for my $condition (@_) {  
         if (! $condition) {  
             $retVal = 0;  
             last LOOP;  
         }  
     }  
     return $retVal;  
 }  
2381    
2382  =head3 Cluck  Similarly, the following code
2383    
2384  C<< Cluck($message); >>      my @files = grep { $_ =~ /^\d/ } OpenDir("/Volumes/fig/orgs", 0, 1);
2385    
2386  Trace the call stack. Note that for best results, you should qualify the call with a  Returns the names of all files in C</Volumes/fig/orgs> that begin with digits and
2387  trace condition. For example,  automatically returns an empty list if the directory fails to open.
2388    
2389  C<< Cluck("Starting record parse.") if T(3); >>  =over 4
2390    
2391  will only trace the stack if the trace level for the package is 3 or more.  =item dirName
2392    
2393  =over 4  Name of the directory to open.
2394    
2395  =item message  =item filtered
2396    
2397  Message to include in the trace.  TRUE if files whose names begin with a period (C<.>) should be automatically removed
2398    from the list, else FALSE.
2399    
2400    =item flag
2401    
2402    TRUE if a failure to open is okay, else FALSE
2403    
2404  =back  =back
2405    
2406  =cut  =cut
2407    #: Return Type @;
2408  sub Cluck {  sub OpenDir {
2409      # Get the parameters.      # Get the parameters.
2410      my ($message) = @_;      my ($dirName, $filtered, $flag) = @_;
2411      # Trace what's happening.      # Declare the return variable.
2412      Trace("Stack trace for event: $message");      my @retVal = ();
2413      my $confession = longmess($message);      # Open the directory.
2414      # Convert the confession to a series of trace messages. Note we skip any      if (opendir(my $dirHandle, $dirName)) {
2415      # messages relating to calls into Tracer.          # The directory opened successfully. Get the appropriate list according to the
2416      for my $line (split /\s*\n/, $confession) {          # strictures of the filter parameter.
2417          Trace($line) if ($line !~ /Tracer\.pm/);          if ($filtered) {
2418                @retVal = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir $dirHandle;
2419            } else {
2420                @retVal = readdir $dirHandle;
2421            }
2422        } elsif (! $flag) {
2423            # Here the directory would not open and it's considered an error.
2424            Confess("Could not open directory $dirName.");
2425      }      }
2426        # Return the result.
2427        return @retVal;
2428  }  }
2429    
 =head3 Min  
2430    
2431  C<< my $min = Min($value1, $value2, ... $valueN); >>  =head3 Insure
2432    
2433        Insure($dirName, $chmod);
2434    
2435  Return the minimum argument. The arguments are treated as numbers.  Insure a directory is present.
2436    
2437  =over 4  =over 4
2438    
2439  =item $value1, $value2, ... $valueN  =item dirName
2440    
2441  List of numbers to compare.  Name of the directory to check. If it does not exist, it will be created.
2442    
2443  =item RETURN  =item chmod (optional)
2444    
2445  Returns the lowest number in the list.  Security privileges to be given to the directory if it is created.
2446    
2447  =back  =back
2448    
2449  =cut  =cut
2450    
2451  sub Min {  sub Insure {
2452      # Get the parameters. Note that we prime the return value with the first parameter.      my ($dirName, $chmod) = @_;
2453      my ($retVal, @values) = @_;      if (! -d $dirName) {
2454      # Loop through the remaining parameters, looking for the lowest.          Trace("Creating $dirName directory.") if T(2);
2455      for my $value (@values) {          eval {
2456          if ($value < $retVal) {              mkpath $dirName;
2457              $retVal = $value;              # If we have permissions specified, set them here.
2458                if (defined($chmod)) {
2459                    chmod $chmod, $dirName;
2460                }
2461            };
2462            if ($@) {
2463                Confess("Error creating $dirName: $@");
2464          }          }
2465      }      }
     # Return the minimum found.  
     return $retVal;  
2466  }  }
2467    
2468  =head3 Max  =head3 ChDir
2469    
2470  C<< my $max = Max($value1, $value2, ... $valueN); >>      ChDir($dirName);
2471    
2472  Return the maximum argument. The arguments are treated as numbers.  Change to the specified directory.
2473    
2474  =over 4  =over 4
2475    
2476  =item $value1, $value2, ... $valueN  =item dirName
   
 List of numbers to compare.  
   
 =item RETURN  
2477    
2478  Returns the highest number in the list.  Name of the directory to which we want to change.
2479    
2480  =back  =back
2481    
2482  =cut  =cut
2483    
2484  sub Max {  sub ChDir {
2485      # Get the parameters. Note that we prime the return value with the first parameter.      my ($dirName) = @_;
2486      my ($retVal, @values) = @_;      if (! -d $dirName) {
2487      # Loop through the remaining parameters, looking for the highest.          Confess("Cannot change to directory $dirName: no such directory.");
2488      for my $value (@values) {      } else {
2489          if ($value > $retVal) {          Trace("Changing to directory $dirName.") if T(File => 4);
2490              $retVal = $value;          my $okFlag = chdir $dirName;
2491            if (! $okFlag) {
2492                Confess("Error switching to directory $dirName.");
2493          }          }
2494      }      }
     # Return the maximum found.  
     return $retVal;  
2495  }  }
2496    
2497  =head3 AddToListMap  =head3 SetPermissions
2498    
2499        Tracer::SetPermissions($dirName, $group, $mask, %otherMasks);
2500    
2501  C<< Tracer::AddToListMap(\%hash, $key, $value1, $value2, ... valueN); >>  Set the permissions for a directory and all the files and folders inside it.
2502    In addition, the group ownership will be changed to the specified value.
2503    
2504  Add a key-value pair to a hash of lists. If no value exists for the key, a singleton list  This method is more vulnerable than most to permission and compatability
2505  is created for the key. Otherwise, the new value is pushed onto the list.  problems, so it does internal error recovery.
2506    
2507  =over 4  =over 4
2508    
2509  =item hash  =item dirName
2510    
2511  Reference to the target hash.  Name of the directory to process.
2512    
2513  =item key  =item group
2514    
2515  Key for which the value is to be added.  Name of the group to be assigned.
2516    
2517  =item value1, value2, ... valueN  =item mask
2518    
2519  List of values to add to the key's value list.  Permission mask. Bits that are C<1> in this mask will be ORed into the
2520    permission bits of any file or directory that does not already have them
2521    set to 1.
2522    
2523  =back  =item otherMasks
2524    
2525  =cut  Map of search patterns to permission masks. If a directory name matches
2526    one of the patterns, that directory and all its members and subdirectories
2527    will be assigned the new pattern. For example, the following would
2528    assign 0664 to most files, but would use 0777 for directories named C<tmp>.
2529    
2530  sub AddToListMap {      Tracer::SetPermissions($dirName, 'fig', 01664, '^tmp$' => 01777);
     # Get the parameters.  
     my ($hash, $key, @values) = @_;  
     # Process according to whether or not the key already has a value.  
     if (! exists $hash->{$key}) {  
         $hash->{$key} = [@values];  
     } else {  
         push @{$hash->{$key}}, @values;  
     }  
 }  
2531    
2532  =head3 DebugMode  The list is ordered, so the following would use 0777 for C<tmp1> and
2533    0666 for C<tmp>, C<tmp2>, or C<tmp3>.
2534    
2535  C<< if (Tracer::DebugMode) { ...code... } >>      Tracer::SetPermissions($dirName, 'fig', 01664, '^tmp1' => 0777,
2536                                                       '^tmp' => 0666);
2537    
2538  Return TRUE if debug mode has been turned on, else abort.  Note that the pattern matches are all case-insensitive, and only directory
2539    names are matched, not file names.
2540    
2541  Certain CGI scripts are too dangerous to exist in the production  =back
 environment. This method provides a simple way to prevent them  
 from working unless they are explicitly turned on by creating a password  
 cookie via the B<SetPassword> script.  If debugging mode  
 is not turned on, an error will occur.  
2542    
2543  =cut  =cut
2544    
2545  sub DebugMode {  sub SetPermissions {
2546      # Declare the return variable.      # Get the parameters.
2547      my $retVal = 0;      my ($dirName, $group, $mask, @otherMasks) = @_;
2548      # Check the debug configuration.      # Set up for error recovery.
2549      my $password = CGI::cookie("DebugMode");      eval {
2550      my $encrypted = Digest::MD5::md5_hex($password);          # Switch to the specified directory.
2551      if ($encrypted eq "252dec43280e0c0d6a75ffcec486e61d") {          ChDir($dirName);
2552          $retVal = 1;          # Get the group ID.
2553            my $gid = getgrnam($group);
2554            # Get the mask for tracing.
2555            my $traceMask = sprintf("%04o", $mask) . "($mask)";
2556            Trace("Fixing permissions for directory $dirName using group $group($gid) and mask $traceMask.") if T(File => 2);
2557            my $fixCount = 0;
2558            my $lookCount = 0;
2559            # @dirs will be a stack of directories to be processed.
2560            my @dirs = (getcwd());
2561            while (scalar(@dirs) > 0) {
2562                # Get the current directory.
2563                my $dir = pop @dirs;
2564                # Check for a match to one of the specified directory names. To do
2565                # that, we need to pull the individual part of the name off of the
2566                # whole path.
2567                my $simpleName = $dir;
2568                if ($dir =~ m!/([^/]+)$!) {
2569                    $simpleName = $1;
2570                }
2571                Trace("Simple directory name for $dir is $simpleName.") if T(File => 4);
2572                # Search for a match.
2573                my $match = 0;
2574                my $i;
2575                for ($i = 0; $i < $#otherMasks && ! $match; $i += 2) {
2576                    my $pattern = $otherMasks[$i];
2577                    if ($simpleName =~ /$pattern/i) {
2578                        $match = 1;
2579                    }
2580                }
2581                # Find out if we have a match. Note we use $i-1 because the loop added 2
2582                # before terminating due to the match.
2583                if ($match && $otherMasks[$i-1] != $mask) {
2584                    # This directory matches one of the incoming patterns, and it's
2585                    # a different mask, so we process it recursively with that mask.
2586                    SetPermissions($dir, $group, $otherMasks[$i-1], @otherMasks);
2587      } else {      } else {
2588          # Here debug mode is off, so we generate an error.                  # Here we can process normally. Get all of the non-hidden members.
2589          Confess("Cannot use this facility without logging in.");                  my @submems = OpenDir($dir, 1);
2590                    for my $submem (@submems) {
2591                        # Get the full name.
2592                        my $thisMem = "$dir/$submem";
2593                        Trace("Checking member $thisMem.") if T(4);
2594                        $lookCount++;
2595                        if ($lookCount % 1000 == 0) {
2596                            Trace("$lookCount members examined. Current is $thisMem. Mask is $traceMask") if T(File => 3);
2597      }      }
2598      # Return the determination indicator.                      # Fix the group.
2599      return $retVal;                      chown -1, $gid, $thisMem;
2600                        # Insure this member is not a symlink.
2601                        if (! -l $thisMem) {
2602                            # Get its info.
2603                            my $fileInfo = stat $thisMem;
2604                            # Only proceed if we got the info. Otherwise, it's a hard link
2605                            # and we want to skip it anyway.
2606                            if ($fileInfo) {
2607                                my $fileMode = $fileInfo->mode;
2608                                if (($fileMode & $mask) != $mask) {
2609                                    # Fix this member.
2610                                    $fileMode |= $mask;
2611                                    chmod $fileMode, $thisMem;
2612                                    $fixCount++;
2613                                }
2614                                # If it's a subdirectory, stack it.
2615                                if (-d $thisMem) {
2616                                    push @dirs, $thisMem;
2617                                }
2618                            }
2619                        }
2620                    }
2621                }
2622            }
2623            Trace("$lookCount files and directories processed, $fixCount fixed.") if T(File => 2);
2624        };
2625        # Check for an error.
2626        if ($@) {
2627            Confess("SetPermissions error: $@");
2628  }  }
   
 =head3 Strip  
   
 C<< my $string = Tracer::Strip($line); >>  
   
 Strip all line terminators off a string. This is necessary when dealing with files  
 that may have been transferred back and forth several times among different  
 operating environments.  
   
 =over 4  
   
 =item line  
   
 Line of text to be stripped.  
   
 =item RETURN  
   
 The same line of text with all the line-ending characters chopped from the end.  
   
 =back  
   
 =cut  
   
 sub Strip {  
     # Get a copy of the parameter string.  
     my ($string) = @_;  
     my $retVal = (defined $string ? $string : "");  
     # Strip the line terminator characters.  
     $retVal =~ s/(\r|\n)+$//g;  
     # Return the result.  
     return $retVal;  
2629  }  }
2630    
2631  =head3 Pad  =head3 GetLine
2632    
2633  C<< my $paddedString = Tracer::Pad($string, $len, $left, $padChar); >>      my @data = Tracer::GetLine($handle);
2634    
2635  Pad a string to a specified length. The pad character will be a  Read a line of data from a tab-delimited file.
 space, and the padding will be on the right side unless specified  
 in the third parameter.  
2636    
2637  =over 4  =over 4
2638    
2639  =item string  =item handle
   
 String to be padded.  
   
 =item len  
   
 Desired length of the padded string.  
   
 =item left (optional)  
   
 TRUE if the string is to be left-padded; otherwise it will be padded on the right.  
   
 =item padChar (optional)  
2640    
2641  Character to use for padding. The default is a space.  Open file handle from which to read.
2642    
2643  =item RETURN  =item RETURN
2644    
2645  Returns a copy of the original string with the pad character added to the  Returns a list of the fields in the record read. The fields are presumed to be
2646  specified end so that it achieves the desired length.  tab-delimited. If we are at the end of the file, then an empty list will be
2647    returned. If an empty line is read, a single list item consisting of a null
2648    string will be returned.
2649    
2650  =back  =back
2651    
2652  =cut  =cut
2653    
2654  sub Pad {  sub GetLine {
2655      # Get the parameters.      # Get the parameters.
2656      my ($string, $len, $left, $padChar) = @_;      my ($handle) = @_;
2657      # Compute the padding character.      # Declare the return variable.
2658      if (! defined $padChar) {      my @retVal = ();
2659          $padChar = " ";      Trace("File position is " . tell($handle) . ". EOF flag is " . eof($handle) . ".") if T(File => 4);
2660      }      # Read from the file.
2661      # Compute the number of spaces needed.      my $line = <$handle>;
2662      my $needed = $len - length $string;      # Only proceed if we found something.
2663      # Copy the string into the return variable.      if (defined $line) {
2664      my $retVal = $string;          # Remove the new-line. We are a bit over-cautious here because the file may be coming in via an
2665      # Only proceed if padding is needed.          # upload control and have a nonstandard EOL combination.
2666      if ($needed > 0) {          $line =~ s/(\r|\n)+$//;
2667          # Create the pad string.          # Here we do some fancy tracing to help in debugging complicated EOL marks.
2668          my $pad = $padChar x $needed;          if (T(File => 4)) {
2669          # Affix it to the return value.              my $escapedLine = $line;
2670          if ($left) {              $escapedLine =~ s/\n/\\n/g;
2671              $retVal = $pad . $retVal;              $escapedLine =~ s/\r/\\r/g;
2672                $escapedLine =~ s/\t/\\t/g;
2673                Trace("Line read: -->$escapedLine<--");
2674            }
2675            # If the line is empty, return a single empty string; otherwise, parse
2676            # it into fields.
2677            if ($line eq "") {
2678                push @retVal, "";
2679          } else {          } else {
2680              $retVal .= $pad;              push @retVal, split /\t/,$line;
2681          }          }
2682        } else {
2683            # Trace the reason the read failed.
2684            Trace("End of file: $!") if T(File => 3);
2685      }      }
2686      # Return the result.      # Return the result.
2687      return $retVal;      return @retVal;
2688  }  }
2689    
2690  =head3 EOF  =head3 PutLine
2691    
2692  This is a constant that is lexically greater than any useful string.      Tracer::PutLine($handle, \@fields, $eol);
2693    
2694  =cut  Write a line of data to a tab-delimited file. The specified field values will be
2695    output in tab-separated form, with a trailing new-line.
2696    
2697  sub EOF {  =over 4
     return "\xFF\xFF\xFF\xFF\xFF";  
 }  
2698    
2699  =head3 TICK  =item handle
2700    
2701  C<< my @results = TICK($commandString); >>  Output file handle.
2702    
2703  Perform a back-tick operation on a command. If this is a Windows environment, any leading  =item fields
 dot-slash (C<./> will be removed. So, for example, if you were doing  
2704    
2705      `./protein.cgi`  List of field values.
2706    
2707  from inside a CGI script, it would work fine in Unix, but would issue an error message  =item eol (optional)
 in Windows complaining that C<'.'> is not a valid command. If instead you code  
2708    
2709      TICK("./protein.cgi")  End-of-line character (default is "\n").
2710    
2711  it will work correctly in both environments.  =back
2712    
2713  =over 4  =cut
2714    
2715  =item commandString  sub PutLine {
2716        # Get the parameters.
2717        my ($handle, $fields, $eol) = @_;
2718        # Write the data.
2719        print $handle join("\t", @{$fields}) . ($eol || "\n");
2720    }
2721    
 The command string to pass to the system.  
2722    
2723  =item RETURN  =head3 PrintLine
2724    
2725  Returns the standard output from the specified command, as a list.      Tracer::PrintLine($line);
2726    
2727    Print a line of text with a trailing new-line.
2728    
2729    =over 4
2730    
2731    =item line
2732    
2733    Line of text to print.
2734    
2735  =back  =back
2736    
2737  =cut  =cut
2738  #: Return Type @;  
2739  sub TICK {  sub PrintLine {
2740      # Get the parameters.      # Get the parameters.
2741      my ($commandString) = @_;      my ($line) = @_;
2742      # Chop off the dot-slash if this is Windows.      # Print the line.
2743      if ($FIG_Config::win_mode) {      print "$line\n";
         $commandString =~ s!^\./!!;  
     }  
     # Activate the command and return the result.  
     return `$commandString`;  
2744  }  }
2745    
 =head3 ScriptSetup  
2746    
2747  C<< my ($cgi, $varHash) = ScriptSetup($noTrace); >>  =head2 Other Useful Methods
2748    
2749  Perform standard tracing and debugging setup for scripts. The value returned is  =head3 ParseParm
 the CGI object followed by a pre-built variable hash.  
2750    
2751  The C<Trace> query parameter is used to determine whether or not tracing is active and      my $listValue = Tracer::ParseParm($string);
2752  which trace modules (other than C<Tracer> itself) should be turned on. Specifying  
2753  the C<CGI> trace module will trace parameter and environment information. Parameters are  Convert a parameter into a list reference. If the parameter is undefined,
2754  traced at level 3 and environment variables at level 4. To trace to a file instead of to  an undefined value will be returned. Otherwise, it will be parsed as a
2755  the web page, set C<TF> to 1. At the end of the script, the client should call  comma-separated list of values.
 L</ScriptFinish> to output the web page.  
   
 In some situations, it is not practical to invoke tracing via form parameters. For this  
 situation, you can turn on emergency tracing by invoking the L</Emergency> method from  
 a web page. Emergency tracing is detected via a file with the name  
 C<Emergency>I<IPaddr>C<.txt> in the FIG temporary directory, where I<IPaddr> is the  
 IP address of the remote user who wants tracing turned on. The file contains a time  
 limit in hours on the first line, a tracing destination on the second line, a trace  
 level on the third line, and the tracing modules on subsequent lines.  
2756    
2757  =over 4  =over 4
2758    
2759  =item noTrace (optional)  =item string
2760    
2761  If specified, tracing will be suppressed. This is useful if the script wants to set up  Incoming string.
 tracing manually.  
2762    
2763  =item RETURN  =item RETURN
2764    
2765  Returns a two-element list consisting of a CGI query object and a variable hash for  Returns a reference to a list of values, or C<undef> if the incoming value
2766  the output page.  was undefined.
2767    
2768  =back  =back
2769    
2770  =cut  =cut
2771    
2772  sub ScriptSetup {  sub ParseParm {
2773      # Get the parameters.      # Get the parameters.
2774      my ($noTrace) = @_;      my ($string) = @_;
2775      # Get the CGI query object.      # Declare the return variable.
2776      my $cgi = CGI->new();      my $retVal;
2777      # Set up tracing if it's not suppressed.      # Check for data.
2778      CGITrace($cgi) unless $noTrace;      if (defined $string) {
2779      # Create the variable hash.          # We have some, so split it into a list.
2780      my $varHash = { results => '' };          $retVal = [ split /\s*,\s*/, $string];
2781      # Return the query object and variable hash.      }
2782      return ($cgi, $varHash);      # Return the result.
2783        return $retVal;
2784    }
2785    
2786    =head3 Now
2787    
2788        my $string = Tracer::Now();
2789    
2790    Return a displayable time stamp containing the local time. Whatever format this
2791    method produces must be parseable by L</ParseDate>.
2792    
2793    =cut
2794    
2795    sub Now {
2796        return DisplayTime(time);
2797  }  }
2798    
2799  =head3 CGITrace  =head3 DisplayTime
2800    
2801  C<< Tracer::CGITrace($cgi); >>      my $string = Tracer::DisplayTime($time);
2802    
2803  Set up tracing for a CGI script. See L</ScriptSetup> for more information.  Convert a time value to a displayable time stamp. Whatever format this
2804    method produces must be parseable by L</ParseDate>.
2805    
2806  =over 4  =over 4
2807    
2808  =item cgi  =item time
2809    
2810    Time to display, in seconds since the epoch, or C<undef> if the time is unknown.
2811    
2812    =item RETURN
2813    
2814  Ths CGI query object for this script.  Returns a displayable time, or C<(n/a)> if the incoming time is undefined.
2815    
2816  =back  =back
2817    
2818  =cut  =cut
2819    
2820  sub CGITrace {  sub DisplayTime {
2821      # Get the parameters.      my ($time) = @_;
2822      my ($cgi) = @_;      my $retVal = "(n/a)";
2823      # Default to no tracing except errors.      if (defined $time) {
2824      my ($tracing, $dest) = ("0", "WARN");          my ($sec,$min,$hour,$mday,$mon,$year,$wday,$yday,$isdst) = localtime($time);
2825      # Check for emergency tracing.          $retVal = _p2($mon+1) . "/" . _p2($mday) . "/" . ($year + 1900) . " " .
2826      my $ip = EmergencyIP($cgi);                    _p2($hour) . ":" . _p2($min) . ":" . _p2($sec);
     my $emergencyFile = EmergencyFileName($ip);  
     if (-e $emergencyFile) {  
         # We have the file. Read in the data.  
         my @tracing = GetFile($emergencyFile);  
         # Pull off the time limit.  
         my $expire = shift @tracing;  
         # Convert it to seconds.  
         $expire *= 3600;  
         # Check the file data.  
         my $stat = stat($emergencyFile);  
         my ($now) = gettimeofday;  
         if ($now - $stat->mtime > $expire) {  
             # Delete the expired file.  
             unlink $emergencyFile;  
         } else {  
             # Emergency tracing is on. Pull off the destination and  
             # the trace level;  
             $dest = shift @tracing;  
             my $level = shift @tracing;  
             # Convert the destination to a real tracing destination.  
             # temp directory.  
             $dest = EmergencyTracingDest($ip, $dest);  
             # Insure Tracer is specified.  
             my %moduleHash = map { $_ => 1 } @tracing;  
             $moduleHash{Tracer} = 1;  
             # Set the trace parameter.  
             $tracing = join(" ", $level, sort keys %moduleHash);  
             # Make sure the script knows tracing is on.  
             $cgi->param(-name => 'Trace', -value => $tracing);  
             $cgi->param(-name => 'TF', -value => (($dest =~ /^>/) ? 1 : 0));  
2827          }          }
2828      } elsif ($cgi->param('Trace')) {      return $retVal;
         # Here the user has requested tracing via a form.  
         $dest = ($cgi->param('TF') ? ">$FIG_Config::temp/Trace$$.log" : "QUEUE");  
         $tracing = $cgi->param('Trace') . " Tracer";  
2829      }      }
2830      # Setup the tracing we've determined from all the stuff above.  
2831      TSetup($tracing, $dest);  # Pad a number to 2 digits.
2832      # Trace the parameter and environment data.  sub _p2 {
2833      TraceParms($cgi);      my ($value) = @_;
2834        $value = "0$value" if ($value < 10);
2835        return $value;
2836  }  }
2837    
2838  =head3 EmergencyFileName  =head3 Escape
2839    
2840  C<< my $fileName = Tracer::EmergencyFileName($ip); >>      my $codedString = Tracer::Escape($realString);
2841    
2842  Return the emergency tracing file name. This is the file that specifies  Escape a string for use in a command. Tabs will be replaced by C<\t>, new-lines
2843  the tracing information.  replaced by C<\n>, carriage returns will be deleted, and backslashes will be doubled. The
2844    result is to reverse the effect of L</UnEscape>.
2845    
2846  =over 4  =over 4
2847    
2848  =item ip  =item realString
2849    
2850  IP address of the user who wants tracing, as taken from the C<< $cgi->remote_host() >>  String to escape.
 method.  
2851    
2852  =item RETURN  =item RETURN
2853    
2854  Returns the name of the file to contain the emergency tracing information.  Escaped equivalent of the real string.
2855    
2856  =back  =back
2857    
2858  =cut  =cut
2859    
2860  sub EmergencyFileName {  sub Escape {
2861      # Get the parameters.      # Get the parameter.
2862      my ($ip) = @_;      my ($realString) = @_;
2863      # Compute the emergency tracing file name.      # Initialize the return variable.
2864      return "$FIG_Config::temp/Emergency$ip.txt";      my $retVal = "";
2865        # Loop through the parameter string, looking for sequences to escape.
2866        while (length $realString > 0) {
2867            # Look for the first sequence to escape.
2868            if ($realString =~ /^(.*?)([\n\t\r\\])/) {
2869                # Here we found it. The text preceding the sequence is in $1. The sequence
2870                # itself is in $2. First, move the clear text to the return variable.
2871                $retVal .= $1;
2872                # Strip the processed section off the real string.
2873                $realString = substr $realString, (length $2) + (length $1);
2874                # Get the matched character.
2875                my $char = $2;
2876                # If we have a CR, we are done.
2877                if ($char ne "\r") {
2878                    # It's not a CR, so encode the escape sequence.
2879                    $char =~ tr/\t\n/tn/;
2880                    $retVal .= "\\" . $char;
2881                }
2882            } else {
2883                # Here there are no more escape sequences. The rest of the string is
2884                # transferred unmodified.
2885                $retVal .= $realString;
2886                $realString = "";
2887            }
2888        }
2889        # Return the result.
2890        return $retVal;
2891  }  }
2892    
2893  =head3 EmergencyFileTarget  =head3 UnEscape
2894    
2895  C<< my $fileName = Tracer::EmergencyFileTarget($ip); >>      my $realString = Tracer::UnEscape($codedString);
2896    
2897  Return the emergency tracing target file name. This is the file that receives  Replace escape sequences with their actual equivalents. C<\t> will be replaced by
2898  the tracing output for file-based tracing.  a tab, C<\n> by a new-line character, and C<\\> by a backslash. C<\r> codes will
2899    be deleted.
2900    
2901  =over 4  =over 4
2902    
2903  =item ip  =item codedString
2904    
2905  IP address of the user who wants tracing, as taken from the C<< $cgi->remote_host() >>  String to un-escape.
 method.  
2906    
2907  =item RETURN  =item RETURN
2908    
2909  Returns the name of the file to contain the emergency tracing information.  Returns a copy of the original string with the escape sequences converted to their actual
2910    values.
2911    
2912  =back  =back
2913    
2914  =cut  =cut
2915    
2916  sub EmergencyFileTarget {  sub UnEscape {
2917      # Get the parameters.      # Get the parameter.
2918      my ($ip) = @_;      my ($codedString) = @_;
2919      # Compute the emergency tracing file name.      # Initialize the return variable.
2920      return "$FIG_Config::temp/Emergency$ip.log";      my $retVal = "";
2921        # Only proceed if the incoming string is nonempty.
2922        if (defined $codedString) {
2923            # Loop through the parameter string, looking for escape sequences. We can't do
2924            # translating because it causes problems with the escaped slash. ("\\t" becomes
2925            # "\<tab>" no matter what we do.)
2926            while (length $codedString > 0) {
2927                # Look for the first escape sequence.
2928                if ($codedString =~ /^(.*?)\\(\\|n|t|r)/) {
2929                    # Here we found it. The text preceding the sequence is in $1. The sequence
2930                    # itself is in $2. First, move the clear text to the return variable.
2931                    $retVal .= $1;
2932                    $codedString = substr $codedString, (2 + length $1);
2933                    # Get the escape value.
2934                    my $char = $2;
2935                    # If we have a "\r", we are done.
2936                    if ($char ne 'r') {
2937                        # Here it's not an 'r', so we convert it.
2938                        $char =~ tr/\\tn/\\\t\n/;
2939                        $retVal .= $char;
2940                    }
2941                } else {
2942                    # Here there are no more escape sequences. The rest of the string is
2943                    # transferred unmodified.
2944                    $retVal .= $codedString;
2945                    $codedString = "";
2946                }
2947            }
2948        }
2949        # Return the result.
2950        return $retVal;
2951  }  }
2952    
2953  =head3 EmergencyTracingDest  =head3 Percent
2954    
2955  C<< my $dest = Tracer::EmergencyTracingDest($ip, $myDest); >>      my $percent = Tracer::Percent($number, $base);
2956    
2957  This method converts an emergency tracing destination to a real  Returns the percent of the base represented by the given number. If the base
2958  tracing destination. The main difference is that if the  is zero, returns zero.
 destination is C<FILE> or C<APPEND>, we convert it to file  
 output.  
2959    
2960  =over 4  =over 4
2961    
2962  =item ip  =item number
2963    
2964  IP address of the user who wants tracing, as taken from the C<< $cgi->remote_host() >>  Percent numerator.
 method.  
2965    
2966  =item myDest  =item base
2967    
2968  Destination from the emergency tracing file.  Percent base.
2969    
2970  =item RETURN  =item RETURN
2971    
2972  Returns a destination that can be passed into L</TSetup>.  Returns the percentage of the base represented by the numerator.
2973    
2974  =back  =back
2975    
2976  =cut  =cut
2977    
2978  sub EmergencyTracingDest {  sub Percent {
2979      # Get the parameters.      # Get the parameters.
2980      my ($ip, $myDest) = @_;      my ($number, $base) = @_;
2981      # Declare the return variable.      # Declare the return variable.
2982      my $retVal;      my $retVal = 0;
2983      # Process according to the destination value.      # Compute the percent.
2984      if ($myDest eq 'FILE') {      if ($base != 0) {
2985          $retVal = ">" . EmergencyFileTarget($ip);          $retVal = $number * 100 / $base;
     } elsif ($myDest eq 'APPEND') {  
         $retVal = ">>" . EmergencyFileTarget($ip);  
     } else {  
         $retVal = $myDest;  
2986      }      }
2987      # Return the result.      # Return the result.
2988      return $retVal;      return $retVal;
2989  }  }
2990    
2991  =head3 Emergency  =head3 Constrain
2992    
2993  C<< Emergency($cgi, $hours, $dest, $level, @modules); >>      my $constrained = Constrain($value, $min, $max);
2994    
2995  Turn on emergency tracing. This method can only be invoked over the web and is  Modify a numeric value to bring it to a point in between a maximum and a minimum.
 should not be called if debug mode is off. The caller specifies the duration of the  
 emergency in hours, the desired tracing destination, the trace level,  
 and a list of the trace modules to activate. For the duration, when a user  
 from the specified remote web location invokes a Sprout CGI script, tracing  
 will be turned on automatically. See L</TSetup> for more about tracing  
 setup and L</ScriptSetup> for more about emergency tracing.  
2996    
2997  =over 4  =over 4
2998    
2999  =item cgi  =item value
   
 A CGI query object.  
3000    
3001  =item hours  Value to constrain.
   
 Number of hours to keep emergency tracing alive.  
3002    
3003  =item dest  =item min (optional)
3004    
3005  Tracing destination. If no path information is specified for a file  Minimum permissible value. If this parameter is undefined, no minimum constraint will be applied.
 destination, it is put in the FIG temporary directory.  
3006    
3007  =item level  =item max (optional)
3008    
3009  Tracing level. A higher level means more trace messages.  Maximum permissible value. If this parameter is undefined, no maximum constraint will be applied.
3010    
3011  =item modules  =item RETURN
3012    
3013  A list of the tracing modules to activate.  Returns the incoming value, constrained according to the other parameters.
3014    
3015  =back  =back
3016    
3017  =cut  =cut
3018    
3019  sub Emergency {  sub Constrain {
3020      # Get the parameters.      # Get the parameters.
3021      my ($cgi, $hours, $dest, $level, @modules) = @_;      my ($value, $min, $max) = @_;
3022      # Get the IP address.      # Declare the return variable.
3023      my $ip = EmergencyIP($cgi);      my $retVal = $value;
3024      # Create the emergency file.      # Apply the minimum constraint.
3025      my $specFile = EmergencyFileName($ip);      if (defined $min && $retVal < $min) {
3026      my $outHandle = Open(undef, ">$specFile");          $retVal = $min;
3027      print $outHandle join("\n",$hours, $dest, $level, @modules, "");      }
3028        # Apply the maximum constraint.
3029        if (defined $max && $retVal > $max) {
3030            $retVal = $max;
3031        }
3032        # Return the result.
3033        return $retVal;
3034  }  }
3035    
3036  =head3 EmergencyIP  =head3 Min
3037    
3038  C<< my $ip = EmergencyIP($cgi); >>      my $min = Min($value1, $value2, ... $valueN);
3039    
3040  Return the IP address to be used for emergency tracing. If at smoe point we need  Return the minimum argument. The arguments are treated as numbers.
 to change the way we compute the IP address, or we decide to use something else,  
 all we need to do is change this method.  
3041    
3042  =over 4  =over 4
3043    
3044  =item cgi  =item $value1, $value2, ... $valueN
3045    
3046  CGI query object.  List of numbers to compare.
3047    
3048  =item RETURN  =item RETURN
3049    
3050  Returns the IP address to be used for labelling emergency tracing.  Returns the lowest number in the list.
3051    
3052  =back  =back
3053    
3054  =cut  =cut
3055    
3056  sub EmergencyIP {  sub Min {
3057      # Get the parameters.      # Get the parameters. Note that we prime the return value with the first parameter.
3058      my ($cgi) = @_;      my ($retVal, @values) = @_;
3059      # Return the result.      # Loop through the remaining parameters, looking for the lowest.
3060      return $cgi->remote_addr();      for my $value (@values) {
3061            if ($value < $retVal) {
3062                $retVal = $value;
3063            }
3064        }
3065        # Return the minimum found.
3066        return $retVal;
3067  }  }
3068    
3069    =head3 Max
3070    
3071  =head3 TraceParms      my $max = Max($value1, $value2, ... $valueN);
   
 C<< Tracer::TraceParms($cgi); >>  
3072    
3073  Trace the CGI parameters at trace level CGI => 3 and the environment variables  Return the maximum argument. The arguments are treated as numbers.
 at level CGI => 4.  
3074    
3075  =over 4  =over 4
3076    
3077  =item cgi  =item $value1, $value2, ... $valueN
3078    
3079  CGI query object containing the parameters to trace.  List of numbers to compare.
3080    
3081    =item RETURN
3082    
3083    Returns the highest number in the list.
3084    
3085  =back  =back
3086    
3087  =cut  =cut
3088    
3089  sub TraceParms {  sub Max {
3090      # Get the parameters.      # Get the parameters. Note that we prime the return value with the first parameter.
3091      my ($cgi) = @_;      my ($retVal, @values) = @_;
3092      if (T(CGI => 3)) {      # Loop through the remaining parameters, looking for the highest.
3093          # Here we want to trace the parameter data.      for my $value (@values) {
3094          my @names = $cgi->param;          if ($value > $retVal) {
3095          for my $parmName (sort @names) {              $retVal = $value;
             # Note we skip the Trace parameters, which are for our use only.  
             if ($parmName ne 'Trace' && $parmName ne 'TF') {  
                 my @values = $cgi->param($parmName);  
                 Trace("CGI: $parmName = " . join(", ", @values));  
             }  
         }  
         # Display the request method.  
         my $method = $cgi->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}");  
3096          }          }
3097      }      }
3098        # Return the maximum found.
3099        return $retVal;
3100  }  }
3101    
3102  =head3 ScriptFinish  =head3 Strip
   
 C<< ScriptFinish($webData, $varHash); >>  
   
 Output a web page at the end of a script. Either the string to be output or the  
 name of a template file can be specified. If the second parameter is omitted,  
 it is assumed we have a string to be output; otherwise, it is assumed we have the  
 name of a template file. The template should have the variable C<DebugData>  
 specified in any form that invokes a standard script. If debugging mode is turned  
 on, a form field will be put in that allows the user to enter tracing data.  
 Trace messages will be placed immediately before the terminal C<BODY> tag in  
 the output, formatted as a list.  
   
 A typical standard script would loook like the following.  
   
     BEGIN {  
         # Print the HTML header.  
         print "CONTENT-TYPE: text/html\n\n";  
     }  
     use Tracer;  
     use CGI;  
     use FIG;  
     # ... more uses ...  
3103    
3104      my ($cgi, $varHash) = ScriptSetup();      my $string = Tracer::Strip($line);
     eval {  
         # ... get data from $cgi, put it in $varHash ...  
     };  
     if ($@) {  
         Trace("Script Error: $@") if T(0);  
     }  
     ScriptFinish("Html/MyTemplate.html", $varHash);  
3105    
3106  The idea here is that even if the script fails, you'll see trace messages and  Strip all line terminators off a string. This is necessary when dealing with files
3107  useful output.  that may have been transferred back and forth several times among different
3108    operating environments.
3109    
3110  =over 4  =over 4
3111    
3112  =item webData  =item line
3113    
3114  A string containing either the full web page to be written to the output or the  Line of text to be stripped.
 name of a template file from which the page is to be constructed. If the name  
 of a template file is specified, then the second parameter must be present;  
 otherwise, it must be absent.  
3115    
3116  =item varHash (optional)  =item RETURN
3117    
3118  If specified, then a reference to a hash mapping variable names for a template  The same line of text with all the line-ending characters chopped from the end.
 to their values. The template file will be read into memory, and variable markers  
 will be replaced by data in this hash reference.  
3119    
3120  =back  =back
3121    
3122  =cut  =cut
3123    
3124  sub ScriptFinish {  sub Strip {
3125      # Get the parameters.      # Get a copy of the parameter string.
3126      my ($webData, $varHash) = @_;      my ($string) = @_;
3127      # Check for a template file situation.      my $retVal = (defined $string ? $string : "");
3128      my $outputString;      # Strip the line terminator characters.
3129      if (defined $varHash) {      $retVal =~ s/(\r|\n)+$//g;
3130          # Here we have a template file. We need to determine the template type.      # Return the result.
3131          my $template;      return $retVal;
         if ($FIG_Config::template_url && $webData =~ /\.php$/) {  
             $template = "$FIG_Config::template_url/$webData";  
         } else {  
             $template = "<<$webData";  
         }  
         $outputString = PageBuilder::Build($template, $varHash, "Html");  
     } else {  
         # Here the user gave us a raw string.  
         $outputString = $webData;  
     }  
     # Check for trace messages.  
     if ($Destination ne "NONE" && $TraceLevel > 0) {  
         # 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;  
         }  
         # If the trace messages were queued, we unroll them. Otherwise, we display the  
         # destination.  
         my $traceHtml;  
         if ($Destination eq "QUEUE") {  
             $traceHtml = QTrace('Html');  
         } elsif ($Destination =~ /^>>(.+)$/) {  
             # Here the tracing output it to a file. We code it as a hyperlink so the user  
             # can copy the file name into the clipboard easily.  
             my $actualDest = $1;  
             $traceHtml = "<p>Tracing output to <a href=\"$actualDest\">$actualDest</a>.</p>\n";  
         } else {  
             # Here we have one of the special destinations.  
             $traceHtml = "<P>Tracing output type is $Destination.</p>\n";  
         }  
         substr $outputString, $pos, 0, $traceHtml;  
     }  
     # Write the output string.  
     print $outputString;  
3132  }  }
3133    
3134  =head3 Insure  =head3 Pad
3135    
3136  C<< Insure($dirName); >>      my $paddedString = Tracer::Pad($string, $len, $left, $padChar);
3137    
3138  Insure a directory is present.  Pad a string to a specified length. The pad character will be a
3139    space, and the padding will be on the right side unless specified
3140    in the third parameter.
3141    
3142  =over 4  =over 4
3143    
3144  =item dirName  =item string
   
 Name of the directory to check. If it does not exist, it will be created.  
3145    
3146  =back  String to be padded.
3147    
3148  =cut  =item len
3149    
3150  sub Insure {  Desired length of the padded string.
     my ($dirName) = @_;  
     if (! -d $dirName) {  
         Trace("Creating $dirName directory.") if T(2);  
         eval { mkpath $dirName; };  
         if ($@) {  
             Confess("Error creating $dirName: $@");  
         }  
     }  
 }  
3151    
3152  =head3 ChDir  =item left (optional)
3153    
3154  C<< ChDir($dirName); >>  TRUE if the string is to be left-padded; otherwise it will be padded on the right.
3155    
3156  Change to the specified directory.  =item padChar (optional)
3157    
3158  =over 4  Character to use for padding. The default is a space.
3159    
3160  =item dirName  =item RETURN
3161    
3162  Name of the directory to which we want to change.  Returns a copy of the original string with the pad character added to the
3163    specified end so that it achieves the desired length.
3164    
3165  =back  =back
3166    
3167  =cut  =cut
3168    
3169  sub ChDir {  sub Pad {
3170      my ($dirName) = @_;      # Get the parameters.
3171      if (! -d $dirName) {      my ($string, $len, $left, $padChar) = @_;
3172          Confess("Cannot change to directory $dirName: no such directory.");      # Compute the padding character.
3173        if (! defined $padChar) {
3174            $padChar = " ";
3175        }
3176        # Compute the number of spaces needed.
3177        my $needed = $len - length $string;
3178        # Copy the string into the return variable.
3179        my $retVal = $string;
3180        # Only proceed if padding is needed.
3181        if ($needed > 0) {
3182            # Create the pad string.
3183            my $pad = $padChar x $needed;
3184            # Affix it to the return value.
3185            if ($left) {
3186                $retVal = $pad . $retVal;
3187      } else {      } else {
3188          Trace("Changing to directory $dirName.") if T(4);              $retVal .= $pad;
         my $okFlag = chdir $dirName;  
         if (! $okFlag) {  
             Confess("Error switching to directory $dirName.");  
3189          }          }
3190      }      }
3191        # Return the result.
3192        return $retVal;
3193  }  }
3194    
3195  =head3 SendSMS  =head3 EOF
3196    
3197    This is a constant that is lexically greater than any useful string.
3198    
3199    =cut
3200    
3201  C<< my $msgID = Tracer::SendSMS($phoneNumber, $msg); >>  sub EOF {
3202        return "\xFF\xFF\xFF\xFF\xFF";
3203    }
3204    
3205  Send a text message to a phone number using Clickatell. The FIG_Config file must contain the  =head3 TICK
 user name, password, and API ID for the relevant account in the hash reference variable  
 I<$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  
3206    
3207      $phone =  { user => 'BruceTheHumanPet',      my @results = TICK($commandString);
                 password => 'silly',  
                 api_id => '2561022' };  
3208    
3209  The original purpose of this method was to insure Bruce would be notified immediately when the  Perform a back-tick operation on a command. If this is a Windows environment, any leading
3210  Sprout Load terminates. Care should be taken if you do not wish Bruce to be notified immediately  dot-slash (C<./> will be removed. So, for example, if you were doing
 when you call this method.  
3211    
3212  The message ID will be returned if successful, and C<undef> if an error occurs.      `./protein.cgi`
3213    
3214  =over 4  from inside a CGI script, it would work fine in Unix, but would issue an error message
3215    in Windows complaining that C<'.'> is not a valid command. If instead you code
3216    
3217  =item phoneNumber      TICK("./protein.cgi")
3218    
3219  Phone number to receive the message, in international format. A United States phone number  it will work correctly in both environments.
 would be prefixed by "1". A British phone number would be prefixed by "44".  
3220    
3221  =item msg  =over 4
3222    
3223  Message to send to the specified phone.  =item commandString
3224    
3225    The command string to pass to the system.
3226    
3227  =item RETURN  =item RETURN
3228    
3229  Returns the message ID if successful, and C<undef> if the message could not be sent.  Returns the standard output from the specified command, as a list.
3230    
3231  =back  =back
3232    
3233  =cut  =cut
3234    #: Return Type @;
3235  sub SendSMS {  sub TICK {
3236      # Get the parameters.      # Get the parameters.
3237      my ($phoneNumber, $msg) = @_;      my ($commandString) = @_;
3238      # Declare the return variable. If we do not change it, C<undef> will be returned.      # Chop off the dot-slash if this is Windows.
3239      my $retVal;      if ($FIG_Config::win_mode) {
3240      # Only proceed if we have phone support.          $commandString =~ s!^\./!!;
     if (! defined $FIG_Config::phone) {  
         Trace("Phone support not present in FIG_Config.") if T(1);  
     } else {  
         # Get the phone data.  
         my $parms = $FIG_Config::phone;  
         # Get the Clickatell URL.  
         my $url = "http://api.clickatell.com/http/";  
         # Create the user agent.  
         my $ua = LWP::UserAgent->new;  
         # Request a Clickatell session.  
         my $resp = $ua->post("$url/sendmsg", { user => $parms->{user},  
                                      password => $parms->{password},  
                                      api_id => $parms->{api_id},  
                                      to => $phoneNumber,  
                                      text => $msg});  
         # Check for an error.  
         if (! $resp->is_success) {  
             Trace("Alert failed.") if T(1);  
         } else {  
             # Get the message ID.  
             my $rstring = $resp->content;  
             if ($rstring =~ /^ID:\s+(.*)$/) {  
                 $retVal = $1;  
             } else {  
                 Trace("Phone attempt failed with $rstring") if T(1);  
             }  
         }  
3241      }      }
3242      # Return the result.      # Activate the command and return the result.
3243      return $retVal;      return `$commandString`;
3244  }  }
3245    
3246    
3247  =head3 CommaFormat  =head3 CommaFormat
3248    
3249  C<< my $formatted = Tracer::CommaFormat($number); >>      my $formatted = Tracer::CommaFormat($number);
3250    
3251  Insert commas into a number.  Insert commas into a number.
3252    
# Line 2503  Line 3279 
3279      # Return the result.      # Return the result.
3280      return $retVal;      return $retVal;
3281  }  }
 =head3 SetPermissions  
   
 C<< Tracer::SetPermissions($dirName, $group, $mask, %otherMasks); >>  
   
 Set the permissions for a directory and all the files and folders inside it.  
 In addition, the group ownership will be changed to the specified value.  
   
 This method is more vulnerable than most to permission and compatability  
 problems, so it does internal error recovery.  
3282    
 =over 4  
3283    
3284  =item dirName  =head3 CompareLists
3285    
3286  Name of the directory to process.      my ($inserted, $deleted) = Tracer::CompareLists(\@newList, \@oldList, $keyIndex);
3287    
3288  =item group  Compare two lists of tuples, and return a hash analyzing the differences. The lists
3289    are presumed to be sorted alphabetically by the value in the $keyIndex column.
3290    The return value contains a list of items that are only in the new list
3291    (inserted) and only in the old list (deleted).
3292    
3293  Name of the group to be assigned.  =over 4
3294    
3295  =item mask  =item newList
3296    
3297  Permission mask. Bits that are C<1> in this mask will be ORed into the  Reference to a list of new tuples.
 permission bits of any file or directory that does not already have them  
 set to 1.  
3298    
3299  =item otherMasks  =item oldList
3300    
3301  Map of search patterns to permission masks. If a directory name matches  Reference to a list of old tuples.
 one of the patterns, that directory and all its members and subdirectories  
 will be assigned the new pattern. For example, the following would  
 assign 01664 to most files, but would use 01777 for directories named C<tmp>.  
3302    
3303      Tracer::SetPermissions($dirName, 'fig', 01664, '^tmp$' => 01777);  =item keyIndex (optional)
3304    
3305  The list is ordered, so the following would use 0777 for C<tmp1> and  Index into each tuple of its key field. The default is 0.
 0666 for C<tmp>, C<tmp2>, or C<tmp3>.  
3306    
3307      Tracer::SetPermissions($dirName, 'fig', 01664, '^tmp1' => 0777,  =item RETURN
                                                    '^tmp' => 0666);  
3308    
3309  Note that the pattern matches are all case-insensitive, and only directory  Returns a 2-tuple consisting of a reference to the list of items that are only in the new
3310  names are matched, not file names.  list (inserted) followed by a reference to the list of items that are only in the old
3311    list (deleted).
3312    
3313  =back  =back
3314    
3315  =cut  =cut
3316    
3317  sub SetPermissions {  sub CompareLists {
3318      # Get the parameters.      # Get the parameters.
3319      my ($dirName, $group, $mask, @otherMasks) = @_;      my ($newList, $oldList, $keyIndex) = @_;
3320      # Set up for error recovery.      if (! defined $keyIndex) {
3321      eval {          $keyIndex = 0;
         # Switch to the specified directory.  
         ChDir($dirName);  
         # Get the group ID.  
         my $gid = getgrnam($group);  
         # Get the mask for tracing.  
         my $traceMask = sprintf("%04o", $mask) . "($mask)";  
         Trace("Fixing permissions for directory $dirName using group $group($gid) and mask $traceMask.") if T(2);  
         my $fixCount = 0;  
         my $lookCount = 0;  
         # @dirs will be a stack of directories to be processed.  
         my @dirs = (getcwd());  
         while (scalar(@dirs) > 0) {  
             # Get the current directory.  
             my $dir = pop @dirs;  
             # Check for a match to one of the specified directory names. To do  
             # that, we need to pull the individual part of the name off of the  
             # whole path.  
             my $simpleName = $dir;  
             if ($dir =~ m!/([^/]+)$!) {  
                 $simpleName = $1;  
             }  
             Trace("Simple directory name for $dir is $simpleName.") if T(4);  
             # Search for a match.  
             my $match = 0;  
             my $i;  
             for ($i = 0; $i < $#otherMasks && ! $match; $i += 2) {  
                 my $pattern = $otherMasks[$i];  
                 if ($simpleName =~ /$pattern/i) {  
                     $match = 1;  
                 }  
3322              }              }
3323              # Check for a match. Note we use $i-1 because the loop added 2      # Declare the return variables.
3324              # before terminating due to the match.      my ($inserted, $deleted) = ([], []);
3325              if ($match && $otherMasks[$i-1] != $mask) {      # Loop through the two lists simultaneously.
3326                  # This directory matches one of the incoming patterns, and it's      my ($newI, $oldI) = (0, 0);
3327                  # a different mask, so we process it recursively with that mask.      my ($newN, $oldN) = (scalar @{$newList}, scalar @{$oldList});
3328                  SetPermissions($dir, $group, $otherMasks[$i-1], @otherMasks);      while ($newI < $newN || $oldI < $oldN) {
3329            # Get the current object in each list. Note that if one
3330            # of the lists is past the end, we'll get undef.
3331            my $newItem = $newList->[$newI];
3332            my $oldItem = $oldList->[$oldI];
3333            if (! defined($newItem) || defined($oldItem) && $newItem->[$keyIndex] gt $oldItem->[$keyIndex]) {
3334                # The old item is not in the new list, so mark it deleted.
3335                push @{$deleted}, $oldItem;
3336                $oldI++;
3337            } elsif (! defined($oldItem) || $oldItem->[$keyIndex] gt $newItem->[$keyIndex]) {
3338                # The new item is not in the old list, so mark it inserted.
3339                push @{$inserted}, $newItem;
3340                $newI++;
3341              } else {              } else {
3342                  # Here we can process normally. Get all of the non-hidden members.              # The item is in both lists, so push forward.
3343                  my @submems = OpenDir($dir, 1);              $oldI++;
3344                  for my $submem (@submems) {              $newI++;
                     # Get the full name.  
                     my $thisMem = "$dir/$submem";  
                     Trace("Checking member $thisMem.") if T(4);  
                     $lookCount++;  
                     if ($lookCount % 1000 == 0) {  
                         Trace("$lookCount members examined. Current is $thisMem. Mask is $traceMask") if T(3);  
                     }  
                     # Fix the group.  
                     chown -1, $gid, $thisMem;  
                     # Insure this member is not a symlink.  
                     if (! -l $thisMem) {  
                         # Get its info.  
                         my $fileInfo = stat $thisMem;  
                         # Only proceed if we got the info. Otherwise, it's a hard link  
                         # and we want to skip it anyway.  
                         if ($fileInfo) {  
                             my $fileMode = $fileInfo->mode;  
                             if (($fileMode & $mask) != $mask) {  
                                 # Fix this member.  
                                 $fileMode |= $mask;  
                                 chmod $fileMode, $thisMem;  
                                 $fixCount++;  
                             }  
                             # If it's a subdirectory, stack it.  
                             if (-d $thisMem) {  
                                 push @dirs, $thisMem;  
                             }  
                         }  
3345                      }                      }
3346                  }                  }
3347        # Return the result.
3348        return ($inserted, $deleted);
3349              }              }
3350    
3351    =head3 Cmp
3352    
3353        my $cmp = Tracer::Cmp($a, $b);
3354    
3355    This method performs a universal sort comparison. Each value coming in is
3356    separated into a leading text part and a trailing number part. The text
3357    part is string compared, and if both parts are equal, then the number
3358    parts are compared numerically. A stream of just numbers or a stream of
3359    just strings will sort correctly, and a mixed stream will sort with the
3360    numbers first. Strings with a label and a number will sort in the
3361    expected manner instead of lexically.
3362    
3363    =over 4
3364    
3365    =item a
3366    
3367    First item to compare.
3368    
3369    =item b
3370    
3371    Second item to compare.
3372    
3373    =item RETURN