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revision 1.69, Mon Oct 2 02:59:47 2006 UTC revision 1.114, Thu Oct 16 22:27:09 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 qw(:DEFAULT :flock);
42    
43    
44  =head1 Tracing and Debugging Helpers  =head1 Tracing and Debugging Helpers
45    
46  =head2 Introduction  =head2 Tracing
47    
48  This package provides simple tracing for debugging and reporting purposes. To use it simply call the  This package provides simple tracing for debugging and reporting purposes. To use it simply call the
49  L</TSetup> method to set the options and call L</Trace> to write out trace messages. Each trace  L</TSetup> or L</ETracing> method to set the options and call L</Trace> to write out trace messages.
50  message has a I<trace level> and I<category> associated with it. In addition, the tracing package itself  L</TSetup> and L</ETracing> both establish a I<trace level> and a list of I<categories>. Similarly,
51  has a list of categories and a single trace level set by the B<TSetup> method. Only messages whose trace  each trace message has a I<trace level> and I<category> associated with it. Only messages whose trace
52  level is less than or equal to this package's trace level and whose category is activated will  level is less than or equal to the setup trace level and whose category is activated will
53  be written. Thus, a higher trace level on a message indicates that the message  be written. Thus, a higher trace level on a message indicates that the message
54  is less likely to be seen. A higher trace level passed to B<TSetup> means more trace messages will  is less likely to be seen, while a higher trace level passed to B<TSetup> means more trace messages will
55  appear. To generate a trace message, use the following syntax.  appear.
56    
57    =head3 Putting Trace Messages in Your Code
58    
59  C<< Trace($message) if T(errors => 4); >>  To generate a trace message, use the following syntax.
60    
61        Trace($message) if T(errors => 4);
62    
63  This statement will produce a trace message if the trace level is 4 or more and the C<errors>  This statement will produce a trace message if the trace level is 4 or more and the C<errors>
64  category is active. Note that the special category C<main> is always active, so  category is active. There is a special category C<main> that is always active, so
65    
66  C<< Trace($message) if T(main => 4); >>      Trace($message) if T(main => 4);
67    
68  will trace if the trace level is 4 or more.  will trace if the trace level is 4 or more.
69    
# Line 61  Line 71 
71  following call is made in the B<Sprout> package, it will appear if the C<Sprout> category is  following call is made in the B<Sprout> package, it will appear if the C<Sprout> category is
72  active and the trace level is 2 or more.  active and the trace level is 2 or more.
73    
74  C<< Trace($message) if T(2); >>      Trace($message) if T(2);
75    
76    In scripts, where no package name is available, the category defaults to C<main>.
77    
78    =head3 Custom Tracing
79    
80    Many programs have customized tracing configured using the L</TSetup> method. This is no longer
81    the preferred method, but a knowledge of how custom tracing works can make the more modern
82    L</Emergency Tracing> easier to understand.
83    
84  To set up tracing, you call the L</TSetup> method. The method takes as input a trace level, a list  To set up custom tracing, you call the L</TSetup> method. The method takes as input a trace level,
85  of category names, and a set of options. The trace level and list of category names are  a list of category names, and a destination. The trace level and list of category names are
86  specified as a space-delimited string. Thus  specified as a space-delimited string. Thus
87    
88  C<< TSetup('3 errors Sprout ERDB', 'HTML'); >>      TSetup('3 errors Sprout ERDB', 'TEXT');
89    
90  sets the trace level to 3, activates the C<errors>, C<Sprout>, and C<ERDB> categories, and  sets the trace level to 3, activates the C<errors>, C<Sprout>, and C<ERDB> categories, and
91  specifies that messages should be output as HTML paragraphs.  specifies that messages should be sent to the standard output.
92    
93  To turn on tracing for ALL categories, use an asterisk. The call below sets every category to  To turn on tracing for ALL categories, use an asterisk. The call below sets every category to
94  level 3 and writes the output to the standard error output. This sort of thing might be  level 3 and writes the output to the standard error output. This sort of thing might be
95  useful in a CGI environment.  useful in a CGI environment.
96    
97  C<< TSetup('3 *', 'WARN'); >>      TSetup('3 *', 'WARN');
98    
99  In addition to HTML and file output for trace messages, you can specify that the trace messages  In addition standard error and file output for trace messages, you can specify that the trace messages
100  be queued. The messages can then be retrieved by calling the L</QTrace> method. This approach  be queued. The messages can then be retrieved by calling the L</QTrace> method. This approach
101  is useful if you are building a web page. Instead of having the trace messages interspersed with  is useful if you are building a web page. Instead of having the trace messages interspersed with
102  the page output, they can be gathered together and displayed at the end of the page. This makes  the page output, they can be gathered together and displayed at the end of the page. This makes
103  it easier to debug page formatting problems.  it easier to debug page formatting problems.
104    
105  Finally, you can specify that all trace messages be emitted as warnings.  Finally, you can specify that all trace messages be emitted to a file, or the standard output and
106    a file at the same time. To trace to a file, specify the filename with an output character in front
107    of it.
108    
109        TSetup('4 SQL', ">$fileName");
110    
111    To trace to the standard output and a file at the same time, put a C<+> in front of the angle
112    bracket.
113    
114        TSetup('3 *', "+>$fileName");
115    
116  The flexibility of tracing makes it superior to simple use of directives like C<die> and C<warn>.  The flexibility of tracing makes it superior to simple use of directives like C<die> and C<warn>.
117  Tracer calls can be left in the code with minimal overhead and then turned on only when needed.  Tracer calls can be left in the code with minimal overhead and then turned on only when needed.
118  Thus, debugging information is available and easily retrieved even when the application is  Thus, debugging information is available and easily retrieved even when the application is
119  being used out in the field.  being used out in the field.
120    
121    =head3 Trace Levels
122    
123  There is no hard and fast rule on how to use trace levels. The following is therefore only  There is no hard and fast rule on how to use trace levels. The following is therefore only
124  a suggestion.  a suggestion.
125    
# Line 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: $!";
496            # Lock the file.
497            flock TRACING, LOCK_EX;
498            print TRACING "$formatted\n";
499            close TRACING;
500            # If the Tee flag is on, echo it to the standard output.
501            if ($TeeFlag) {
502                print "$formatted\n";
503            }
504        }
505    }
506    
507  =item categories  =head3 T
508    
509  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.  
510    
511  =item options      or
512    
513  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).  
514    
515  =item parmHelp  Return TRUE if the trace level is at or above a specified value and the specified category
516    is active, else FALSE. If no category is specified, the caller's package name is used.
517    
518  A string that vaguely describes the positional parameters. This is used  =over 4
 if the user specifies the C<-h> option.  
519    
520  =item argv  =item category
521    
522  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
523  precede the positional parameters and be prefixed by a hyphen.  used.
524    
525    =item traceLevel
526    
527    Relevant tracing level.
528    
529  =item RETURN  =item RETURN
530    
531  Returns a list. The first element of the list is the reference to a hash that  TRUE if a message at the specified trace level would appear in the trace, else FALSE.
 maps the command-line option switches to their values. These will either be the  
 default values or overrides specified on the command line. The remaining  
 elements of the list are the position parameters, in order.  
532    
533  =back  =back
534    
535  =cut  =cut
536    
537  sub StandardSetup {  sub T {
538        # Declare the return variable.
539        my $retVal = 0;
540        # Only proceed if tracing is turned on.
541        if ($Destination ne "NONE") {
542      # Get the parameters.      # Get the parameters.
543      my ($categories, $options, $parmHelp, @argv) = @_;          my ($category, $traceLevel) = @_;
544      # Add the tracing options.          if (!defined $traceLevel) {
545      if (! exists $options->{trace}) {              # Here we have no category, so we need to get the calling package.
546          $options->{trace} = [2, "tracing level"];              # The calling package is normally the first parameter. If it is
547      }              # omitted, the first parameter will be the tracelevel. So, the
548      $options->{sql} = [0, "turn on SQL tracing"];              # first thing we do is shift the so-called category into the
549      $options->{h} = [0, "display command-line options"];              # $traceLevel variable where it belongs.
550      $options->{user} = [$$, "trace log file name suffix"];              $traceLevel = $category;
551      $options->{background} = [0, "spool standard and error output"];              my ($package, $fileName, $line) = caller;
552      # Create a parsing hash from the options hash. The parsing hash              # If there is no calling package, we default to "main".
553      # contains the default values rather than the default value              if (!$package) {
554      # and the description. While we're at it, we'll memorize the                  $category = "main";
555      # length of the longest option name.              } else {
556      my $longestName = 0;                  my @cats = split /::/, $package;
557      my %parseOptions = ();                  $category = $cats[$#cats];
     for my $key (keys %{$options}) {  
         if (length $key > $longestName) {  
             $longestName = length $key;  
558          }          }
         $parseOptions{$key} = $options->{$key}->[0];  
559      }      }
560      # Parse the command line.          # Save the category name and level.
561      my ($retOptions, @retParameters) = ParseCommand(\%parseOptions, @argv);          $LastCategory = $category;
562      # Get the logfile suffix.          $LastLevel = $traceLevel;
563      my $suffix = $retOptions->{user};          # Convert it to lower case before we hash it.
564      # Check for background mode.          $category = lc $category;
565      if ($retOptions->{background}) {          # Validate the trace level.
566          my $outFileName = "$FIG_Config::temp/out$suffix.log";          if (ref $traceLevel) {
567          my $errFileName = "$FIG_Config::temp/err$suffix.log";              Confess("Bad trace level.");
568          open STDOUT, ">$outFileName";          } elsif (ref $TraceLevel) {
569          open STDERR, ">$errFileName";              Confess("Bad trace config.");
570      }      }
571      # Now we want to set up tracing. First, we need to know if SQL is to          # Make the check. Note that level 0 shows even if the category is turned off.
572      # be traced.          $retVal = ($traceLevel <= $TraceLevel && ($traceLevel == 0 || $AllTrace || exists $Categories{$category}));
     my @cats = @{$categories};  
     if ($retOptions->{sql}) {  
         push @cats, "SQL";  
573      }      }
574      # Add the default categories.      # Return the computed result.
575      push @cats, "Tracer";      return $retVal;
     # Next, we create the category string by joining the categories.  
     my $cats = join(" ", @cats);  
     # Check to determine whether or not the caller wants to turn off tracing  
     # to the standard output.  
     my $traceLevel = $retOptions->{trace};  
     my $textOKFlag = 1;  
     if ($traceLevel =~ /^(.)-/) {  
         $traceLevel = $1;  
         $textOKFlag = 0;  
576      }      }
577      # Now we set up the trace mode.  
578      my $traceMode;  =head3 QTrace
579      # Verify that we can open a file in the FIG temporary directory.  
580      my $traceFileName = "$FIG_Config::temp/trace$suffix.log";      my $data = QTrace($format);
581      if (open TESTTRACE, ">$traceFileName") {  
582          # Here we can trace to a file.  Return the queued trace data in the specified format.
583          $traceMode = ">$traceFileName";  
584          if ($textOKFlag) {  =over 4
585              # Echo to standard output if the text-OK flag is set.  
586              $traceMode = "+$traceMode";  =item format
587    
588    C<html> to format the data as an HTML list, C<text> to format it as straight text.
589    
590    =back
591    
592    =cut
593    
594    sub QTrace {
595        # Get the parameter.
596        my ($format) = @_;
597        # Create the return variable.
598        my $retVal = "";
599        # Only proceed if there is an actual queue.
600        if (@Queue) {
601            # Process according to the format.
602            if ($format =~ m/^HTML$/i) {
603                # Convert the queue into an HTML list.
604                $retVal = "<ul>\n";
605                for my $line (@Queue) {
606                    my $escapedLine = CGI::escapeHTML($line);
607                    $retVal .= "<li>$escapedLine</li>\n";
608          }          }
609          # Close the test file.              $retVal .= "</ul>\n";
610          close TESTTRACE;          } elsif ($format =~ m/^TEXT$/i) {
611                # Convert the queue into a list of text lines.
612                $retVal = join("\n", @Queue) . "\n";
613            }
614            # Clear the queue.
615            @Queue = ();
616        }
617        # Return the formatted list.
618        return $retVal;
619    }
620    
621    =head3 Confess
622    
623        Confess($message);
624    
625    Trace the call stack and abort the program with the specified message. When used with
626    the OR operator and the L</Assert> method, B<Confess> can function as a debugging assert.
627    So, for example
628    
629        Assert($recNum >= 0) || Confess("Invalid record number $recNum.");
630    
631    Will abort the program with a stack trace if the value of C<$recNum> is negative.
632    
633    =over 4
634    
635    =item message
636    
637    Message to include in the trace.
638    
639    =back
640    
641    =cut
642    
643    sub Confess {
644        # Get the parameters.
645        my ($message) = @_;
646        # Set up the category and level.
647        $LastCategory = "(confess)";
648        $LastLevel = 0;
649        if (! defined($FIG_Config::no_tool_hdr)) {
650            # Here we have a tool header. Display its length so that the user can adjust the line numbers.
651            my $toolHeaderFile = "$FIG_Config::fig_disk/dist/releases/current/$FIG_Config::arch/tool_hdr";
652            # Only proceed if the tool header file is actually present.
653            if (-f $toolHeaderFile) {
654                my $fh;
655                if (open $fh, "<$toolHeaderFile") {
656                    my @lines = <$fh>;
657                    Trace("Tool header has " . scalar(@lines) . " lines.");
658                }
659            }
660        }
661        # Trace the call stack.
662        Cluck($message);
663        # Abort the program.
664        croak(">>> $message");
665    }
666    
667    =head3 SaveCGI
668    
669        Tracer::SaveCGI($cgi);
670    
671    This method saves the CGI object but does not activate emergency tracing.
672    It is used to allow L</Warn> to work in situations where emergency
673    tracing is contra-indicated (e.g. the wiki).
674    
675    =over 4
676    
677    =item cgi
678    
679    Active CGI query object.
680    
681    =back
682    
683    =cut
684    
685    sub SaveCGI {
686        $SavedCGI = $_[0];
687    }
688    
689    =head3 Warn
690    
691        Warn($message, @options);
692    
693    This method traces an important message. If an RSS feed is configured
694    (via I<FIG_Config::error_feed>) and the tracing destination is C<WARN>,
695    then the message will be echoed to the feed. In general, a tracing
696    destination of C<WARN> indicates that the caller is running as a web
697    service in a production environment; however, this is not a requirement.
698    
699    To force warnings into the RSS feed even when the tracing destination
700    is not C<WARN>, simply specify the C<Feed> tracing module. This can be
701    configured automatically when L</StandardSetup> is used.
702    
703    The L</Cluck> method calls this one for its final message. Since
704    L</Confess> calls L</Cluck>, this means that any error which is caught
705    and confessed will put something in the feed. This insures that someone
706    will be alerted relatively quickly when a failure occurs.
707    
708    =over 4
709    
710    =item message
711    
712    Message to be traced.
713    
714    =item options
715    
716    A list containing zero or more options.
717    
718    =back
719    
720    The permissible options are as follows.
721    
722    =over 4
723    
724    =item noStack
725    
726    If specified, then the stack trace is not included in the output.
727    
728    =back
729    
730    =cut
731    
732    sub Warn {
733        # Get the parameters.
734        my $message = shift @_;
735        my %options = map { $_ => 1 } @_;
736        # Save $@;
737        my $savedError = $@;
738        # Trace the message.
739        Trace($message);
740        # This will contain the lock handle. If it's defined, it means we need to unlock.
741        my $lock;
742        # Check for feed forcing.
743        my $forceFeed = exists $Categories{feed};
744        # An error here would be disastrous. Note that if debug mode is specified,
745        # we do this stuff even in a test environment.
746        eval {
747            # Do we need to put this in the RSS feed?
748            if ($FIG_Config::error_feed && ($Destination eq 'WARN' || $forceFeed)) {
749                # Probably. We need to check first, however, to see if it's from an
750                # ignored IP. For non-CGI situations, we default the IP to the self-referent.
751                my $key = "127.0.0.1";
752                if (defined $SavedCGI) {
753                    # Get the IP address.
754                    $key = $ENV{HTTP_X_FORWARDED_FOR} || $ENV{REMOTE_ADDR};
755                }
756                # Is the IP address in the ignore list?
757                my $found = scalar(grep { $_ eq $key } @FIG_Config::error_ignore_ips);
758                if (! $found) {
759                    # No. We're good. We now need to compute the date, the link, and the title.
760                    # First, the date, in a very specific format.
761                    my $date = strftime("%a, %02e %b %H:%M:%S %Y ", localtime) .
762                        (tz_local_offset() / 30);
763                    # Environment data goes in here. We start with the date.
764                    my $environment = "$date.  ";
765                    # If we need to recap the message (because it's too long to be a title), we'll
766                    # put it in here.
767                    my $recap;
768                    # Copy the message and remove excess space.
769                    my $title = $message;
770                    $title =~ s/\s+/ /gs;
771                    # If it's too long, we have to split it up.
772                    if (length $title > 60) {
773                        # Put the full message in the environment string.
774                        $recap = $title;
775                        # Excerpt it as the title.
776                        $title = substr($title, 0, 50) . "...";
777                    }
778                    # If we have a CGI object, then this is a web error. Otherwise, it's
779                    # command-line.
780                    if (defined $SavedCGI) {
781                        # We're in a web service. The environment is the user's IP, and the link
782                        # is the URL that got us here.
783                        $environment .= "Event Reported at IP address $key process $$.";
784                        my $url = $SavedCGI->self_url();
785                        # We need the user agent string and (if available) the referrer.
786                        # The referrer will be the link.
787                        $environment .= " User Agent $ENV{HTTP_USER_AGENT}";
788                        if ($ENV{HTTP_REFERER}) {
789                            my $link = $ENV{HTTP_REFERER};
790                            $environment .= " referred from <a href=\"$link\">$link</a>.";
791                        } else {
792                            $environment .= " referrer unknown.";
793                        }
794                        # Close off the sentence with the original link.
795                        $environment .= " URL of event is <a href=\"$url\">$url</a>.";
796                    } else {
797                        # No CGI object, so we're a command-line tool. Use the tracing
798                        # key and the PID as the user identifier, and add the command.
799                        my $key = EmergencyKey();
800                        $environment .= "Event Reported by $key process $$.";
801                        if ($CommandLine) {
802                            # We're in a StandardSetup script, so we have the real command line.
803                            $environment .= "\n<pre>" . CGI::escapeHTML($CommandLine) . "</pre>\n";
804                        } elsif ($ENV{_}) {
805                            # We're in a BASH script, so the command has been stored in the _ variable.
806                            $environment .= "  Command = " . CGI::escapeHTML($ENV{_}) . "\n";
807                        }
808                    }
809                    # Build a GUID. We use the current time, the title, and the process ID,
810                    # then digest the result.
811                    my $guid = Digest::MD5::md5_base64(gettimeofday(), $title, $$);
812                    # Finally, the description. This is a stack trace plus various environmental stuff.
813                    # The trace is optional.
814                    my $stackTrace;
815                    if ($options{noStack}) {
816                        $stackTrace = "";
817                    } else {
818                        my @trace = LongMess();
819                        # Only proceed if we got something back.
820                        if (scalar(@trace) > 0) {
821                            $trace[0] =~ s/Tracer::Warn.+?called/Event occurred/;
822                            $stackTrace = "Stack trace:<pre>" . join("\n", @trace, "</pre>");
823                        }
824                    }
825                    # We got the stack trace. Now it's time to put it all together.
826                    # We have a goofy thing here in that we need to HTML-escape some sections of the description
827                    # twice. They will be escaped once here, and then once when written by XML::Simple. They are
828                    # unescaped once when processed by the RSS reader, and stuff in the description is treated as
829                    # HTML. So, anything escaped here is treated as a literal when viewed in the RSS reader, but
830                    # our <br>s and <pre>s are used to format the description.
831                    $recap = (defined $recap ? "<em>" . CGI::escapeHTML($recap) . "</em><br /><br />" : "");
832                    my $description = "$recap$environment  $stackTrace";
833                    # Okay, we have all the pieces. Create a hash of the new event.
834                    my $newItem = { title => $title,
835                                    description => $description,
836                                    category => $LastCategory,
837                                    pubDate => $date,
838                                    guid => $guid,
839                                  };
840                    # We need XML capability for this.
841                    require XML::Simple;
842                    # The RSS document goes in here.
843                    my $rss;
844                    # Get the name of the RSS file. It's in the FIG temporary directory.
845                    my $fileName = "$FIG_Config::temp/$FIG_Config::error_feed";
846                    # Open the config file and lock it.
847                    $lock = Open(undef, "<$FIG_Config::fig_disk/config/FIG_Config.pm");
848                    flock $lock, LOCK_EX;
849                    # Does it exist?
850                    if (-s $fileName) {
851                        # Slurp it in.
852                        $rss = XML::Simple::XMLin($fileName, ForceArray => ['item']);
853                    } else {
854                        my $size = -s $fileName;
855                        # Create an empty channel.
856                        $rss = {
857                            channel => {
858                                title => 'NMPDR Warning Feed',
859                                link => "$FIG_Config::temp_url/$FIG_Config::error_feed",
860                                description => "Important messages regarding the status of the NMPDR.",
861                                generator => "NMPDR Trace Facility",
862                                docs => "http://blogs.law.harvard.edu/tech/rss",
863                                item => []
864                            },
865                        };
866                    }
867                    # Get the channel object.
868                    my $channel = $rss->{channel};
869                    # Update the last-build date.
870                    $channel->{lastBuildDate} = $date;
871                    # Get the item array.
872                    my $items = $channel->{item};
873                    # Insure it has only 100 entries.
874                    while (scalar @{$items} > 100) {
875                        pop @{$items};
876                    }
877                    # Add our new item at the front.
878                    unshift @{$items}, $newItem;
879                    # Create the XML. Note we do not include the root or the declaration. XML Simple can't handle
880                    # the requirements for those.
881                    my $xml = XML::Simple::XMLout($channel, NoAttr => 1, RootName => 'channel', XmlDecl => '');
882                    # Here we put in the root and declaration. The problem is that the root has to have the version attribute
883                    # in it. So, we suppress the root and do it by hand, and that requires suppressing the declaration, too.
884                    $xml = "<?xml version=\"1.0\" encoding=\"utf-8\"?>\n<rss version=\"2.0\">$xml\n</rss>";
885                    # We don't use Open here because we can't afford an error.
886                    if (open XMLOUT, ">$fileName") {
887                        print XMLOUT $xml;
888                        close XMLOUT;
889                    }
890                }
891            }
892        };
893        if ($@) {
894            # If the feed failed, we need to know why. The error will be traced, but this method will not be involved
895            # (which is a good thing).
896            my $error = $@;
897            Trace("Feed Error: $error") if T(Feed => 0);
898        }
899        # Be sure to unlock.
900        if ($lock) {
901            flock $lock, LOCK_UN;
902            undef $lock;
903        }
904        # Restore the error message.
905        $@ = $savedError;
906    }
907    
908    
909    
910    
911    =head3 Assert
912    
913        Assert($condition1, $condition2, ... $conditionN);
914    
915    Return TRUE if all the conditions are true. This method can be used in conjunction with
916    the OR operator and the L</Confess> method as a debugging assert.
917    So, for example
918    
919        Assert($recNum >= 0) || Confess("Invalid record number $recNum.");
920    
921    Will abort the program with a stack trace if the value of C<$recNum> is negative.
922    
923    =cut
924    sub Assert {
925        my $retVal = 1;
926        LOOP: for my $condition (@_) {
927            if (! $condition) {
928                $retVal = 0;
929                last LOOP;
930            }
931        }
932        return $retVal;
933    }
934    
935    =head3 Cluck
936    
937        Cluck($message);
938    
939    Trace the call stack. Note that for best results, you should qualify the call with a
940    trace condition. For example,
941    
942        Cluck("Starting record parse.") if T(3);
943    
944    will only trace the stack if the trace level for the package is 3 or more.
945    
946    =over 4
947    
948    =item message
949    
950    Message to include in the trace.
951    
952    =back
953    
954    =cut
955    
956    sub Cluck {
957        # Get the parameters.
958        my ($message) = @_;
959        # Trace what's happening.
960        Trace("Stack trace for event: $message");
961        # Get the stack trace.
962        my @trace = LongMess();
963        # Convert the trace to a series of messages.
964        for my $line (@trace) {
965            # Replace the tab at the beginning with spaces.
966            $line =~ s/^\t/    /;
967            # Trace the line.
968            Trace($line);
969        }
970        # Issue a warning. This displays the event message and inserts it into the RSS error feed.
971        Warn($message);
972    }
973    
974    =head3 LongMess
975    
976        my @lines = Tracer::LongMess();
977    
978    Return a stack trace with all tracing methods removed. The return will be in the form of a list
979    of message strings.
980    
981    =cut
982    
983    sub LongMess {
984        # Declare the return variable.
985        my @retVal = ();
986        my $confession = longmess("");
987        for my $line (split /\s*\n/, $confession) {
988            unless ($line =~ /Tracer\.pm/) {
989                # Here we have a line worth keeping. Push it onto the result list.
990                push @retVal, $line;
991            }
992        }
993        # Return the result.
994        return @retVal;
995    }
996    
997    =head3 ETracing
998    
999        ETracing($parameter);
1000    
1001    Set up emergency tracing. Emergency tracing is tracing that is turned
1002    on automatically for any program that calls this method. The emergency
1003    tracing parameters are stored in a a file identified by a tracing key.
1004    If this method is called with a CGI object, then the tracing key is
1005    taken from a cookie. If it is called with no parameters, then the tracing
1006    key is taken from an environment variable. If it is called with a string,
1007    the tracing key is that string.
1008    
1009    =over 4
1010    
1011    =item parameter
1012    
1013    A parameter from which the tracing key is computed. If it is a scalar,
1014    that scalar is used as the tracing key. If it is a CGI object, the
1015    tracing key is taken from the C<IP> cookie. If it is omitted, the
1016    tracing key is taken from the C<TRACING> environment variable. If it
1017    is a CGI object and emergency tracing is not on, the C<Trace> and
1018    C<TF> parameters will be used to determine the type of tracing.
1019    
1020    =back
1021    
1022    =cut
1023    
1024    sub ETracing {
1025        # Get the parameter.
1026        my ($parameter) = @_;
1027        # Check for CGI mode.
1028        if (defined $parameter && ref $parameter eq 'CGI') {
1029            $SavedCGI = $parameter;
1030      } else {      } else {
1031          # Here we can't trace to a file. We trace to the standard output if it's          $SavedCGI = undef;
1032          # okay, and the error log otherwise.      }
1033          if ($textOKFlag) {      # Default to no tracing except errors.
1034              $traceMode = "TEXT";      my ($tracing, $dest) = ("0", "WARN");
1035        # Check for emergency tracing.
1036        my $tkey = EmergencyKey($parameter);
1037        my $emergencyFile = EmergencyFileName($tkey);
1038        if (-e $emergencyFile) {
1039            # We have the file. Read in the data.
1040            my @tracing = GetFile($emergencyFile);
1041            # Pull off the time limit.
1042            my $expire = shift @tracing;
1043            # Convert it to seconds.
1044            $expire *= 3600;
1045            # Check the file data.
1046            my $stat = stat($emergencyFile);
1047            my ($now) = gettimeofday;
1048            if ($now - $stat->mtime > $expire) {
1049                # Delete the expired file.
1050                unlink $emergencyFile;
1051          } else {          } else {
1052              $traceMode = "WARN";              # Emergency tracing is on. Pull off the destination and
1053                # the trace level;
1054                $dest = shift @tracing;
1055                my $level = shift @tracing;
1056                # Convert the destination to a real tracing destination.
1057                # temp directory.
1058                $dest = EmergencyTracingDest($tkey, $dest);
1059                # Insure Tracer is specified.
1060                my %moduleHash = map { $_ => 1 } @tracing;
1061                $moduleHash{Tracer} = 1;
1062                # Set the trace parameter.
1063                $tracing = join(" ", $level, sort keys %moduleHash);
1064          }          }
1065        } elsif (defined $SavedCGI) {
1066            # There's no emergency tracing, but we have a CGI object, so check
1067            # for tracing from the form parameters.
1068            if ($SavedCGI->param('Trace')) {
1069                # Here the user has requested tracing via a form.
1070                $dest = ($SavedCGI->param('TF') ? ">$FIG_Config::temp/Trace$$.log" : "QUEUE");
1071                $tracing = $SavedCGI->param('Trace') . " Tracer";
1072      }      }
     # Now set up the tracing.  
     TSetup("$traceLevel $cats", $traceMode);  
     # Check for the "h" option. If it is specified, dump the command-line  
     # options and exit the program.  
     if ($retOptions->{h}) {  
         $0 =~ m#[/\\](\w+)(\.pl)?$#i;  
         print "$1 [options] $parmHelp\n";  
         for my $key (sort keys %{$options}) {  
             my $name = Pad($key, $longestName, 0, ' ');  
             my $desc = $options->{$key}->[1];  
             if ($options->{$key}->[0]) {  
                 $desc .= " (default " . $options->{$key}->[0] . ")";  
1073              }              }
1074              print "  $name $desc\n";      # Setup the tracing we've determined from all the stuff above.
1075        TSetup($tracing, $dest);
1076        # Check to see if we're a web script.
1077        if (defined $SavedCGI) {
1078            # Yes we are. Trace the form and environment data.
1079            TraceParms($SavedCGI);
1080            # Check for RAW mode. In raw mode, we print a fake header so that we see everything
1081            # emitted by the script in its raw form.
1082            if (T(Raw => 3)) {
1083                print CGI::header(-type => 'text/plain', -tracing => 'Raw');
1084          }          }
         exit(0);  
1085      }      }
     # Return the parsed parameters.  
     return ($retOptions, @retParameters);  
1086  }  }
1087    
1088  =head3 Setups  =head3 EmergencyFileName
1089    
1090  C<< my $count = Tracer::Setups(); >>      my $fileName = Tracer::EmergencyFileName($tkey);
1091    
1092  Return the number of times L</TSetup> has been called.  Return the emergency tracing file name. This is the file that specifies
1093    the tracing information.
1094    
1095  This method allows for the creation of conditional tracing setups where, for example, we  =over 4
1096  may want to set up tracing if nobody else has done it before us.  
1097    =item tkey
1098    
1099    Tracing key for the current program.
1100    
1101    =item RETURN
1102    
1103    Returns the name of the file to contain the emergency tracing information.
1104    
1105    =back
1106    
1107  =cut  =cut
1108    
1109  sub Setups {  sub EmergencyFileName {
1110      return $SetupCount;      # Get the parameters.
1111        my ($tkey) = @_;
1112        # Compute the emergency tracing file name.
1113        return "$FIG_Config::temp/Emergency$tkey.txt";
1114    }
1115    
1116    =head3 EmergencyFileTarget
1117    
1118        my $fileName = Tracer::EmergencyFileTarget($tkey);
1119    
1120    Return the emergency tracing target file name. This is the file that receives
1121    the tracing output for file-based tracing.
1122    
1123    =over 4
1124    
1125    =item tkey
1126    
1127    Tracing key for the current program.
1128    
1129    =item RETURN
1130    
1131    Returns the name of the file to contain the trace output.
1132    
1133    =back
1134    
1135    =cut
1136    
1137    sub EmergencyFileTarget {
1138        # Get the parameters.
1139        my ($tkey) = @_;
1140        # Compute the emergency tracing file name.
1141        return "$FIG_Config::temp/trace$tkey.log";
1142    }
1143    
1144    =head3 EmergencyTracingDest
1145    
1146        my $dest = Tracer::EmergencyTracingDest($tkey, $myDest);
1147    
1148    This method converts an emergency tracing destination to a real
1149    tracing destination. The main difference is that if the
1150    destination is C<FILE> or C<APPEND>, we convert it to file
1151    output. If the destination is C<DUAL>, we convert it to file
1152    and standard output.
1153    
1154    =over 4
1155    
1156    =item tkey
1157    
1158    Tracing key for this environment.
1159    
1160    =item myDest
1161    
1162    Destination from the emergency tracing file.
1163    
1164    =item RETURN
1165    
1166    Returns a destination that can be passed into L</TSetup>.
1167    
1168    =back
1169    
1170    =cut
1171    
1172    sub EmergencyTracingDest {
1173        # Get the parameters.
1174        my ($tkey, $myDest) = @_;
1175        # Declare the return variable.
1176        my $retVal = $myDest;
1177        # Process according to the destination value.
1178        if ($myDest eq 'FILE') {
1179            $retVal = ">" . EmergencyFileTarget($tkey);
1180        } elsif ($myDest eq 'APPEND') {
1181            $retVal = ">>" . EmergencyFileTarget($tkey);
1182        } elsif ($myDest eq 'DUAL') {
1183            $retVal = "+>" . EmergencyFileTarget($tkey);
1184        } elsif ($myDest eq 'WARN') {
1185            $retVal = "WARN";
1186        }
1187        # Return the result.
1188        return $retVal;
1189    }
1190    
1191    =head3 Emergency
1192    
1193        Emergency($key, $hours, $dest, $level, @modules);
1194    
1195    Turn on emergency tracing. This method is normally invoked over the web from
1196    a debugging console, but it can also be called by the C<trace.pl> script.
1197    The caller specifies the duration of the emergency in hours, the desired tracing
1198    destination, the trace level, and a list of the trace modules to activate.
1199    For the length of the duration, when a program in an environment with the
1200    specified tracing key active invokes a Sprout CGI script, tracing will be
1201    turned on automatically. See L</TSetup> for more about tracing setup and
1202    L</ETracing> for more about emergency tracing.
1203    
1204    =over 4
1205    
1206    =item tkey
1207    
1208    The tracing key. This is used to identify the control file and the trace file.
1209    
1210    =item hours
1211    
1212    Number of hours to keep emergency tracing alive.
1213    
1214    =item dest
1215    
1216    Tracing destination. If no path information is specified for a file
1217    destination, it is put in the FIG temporary directory.
1218    
1219    =item level
1220    
1221    Tracing level. A higher level means more trace messages.
1222    
1223    =item modules
1224    
1225    A list of the tracing modules to activate.
1226    
1227    =back
1228    
1229    =cut
1230    
1231    sub Emergency {
1232        # Get the parameters.
1233        my ($tkey, $hours, $dest, $level, @modules) = @_;
1234        # Create the emergency file.
1235        my $specFile = EmergencyFileName($tkey);
1236        my $outHandle = Open(undef, ">$specFile");
1237        print $outHandle join("\n", $hours, $dest, $level, @modules, "");
1238    }
1239    
1240    =head3 EmergencyKey
1241    
1242        my $tkey = EmergencyKey($parameter);
1243    
1244    Return the Key to be used for emergency tracing. This could be an IP address,
1245     a session ID, or a user name, depending on the environment.
1246    
1247    =over 4
1248    
1249    =item parameter
1250    
1251    Parameter defining the method for finding the tracing key. If it is a scalar,
1252    then it is presumed to be the tracing key itself. If it is a CGI object, then
1253    the tracing key is taken from the C<IP> cookie. Otherwise, the tracing key is
1254    taken from the C<TRACING> environment variable.
1255    
1256    =item RETURN
1257    
1258    Returns the key to be used for labels in emergency tracing.
1259    
1260    =back
1261    
1262    =cut
1263    
1264    sub EmergencyKey {
1265        # Get the parameters.
1266        my ($parameter) = @_;
1267        # Declare the return variable.
1268        my $retVal;
1269        # Determine the parameter type.
1270        if (! defined $parameter || defined($ENV{TRACING})) {
1271            # Here we're supposed to check the environment. If that fails, we
1272            # get the effective login ID.
1273            $retVal = $ENV{TRACING} || scalar getpwuid($<);
1274        } else {
1275            my $ptype = ref $parameter;
1276            if ($ptype eq 'CGI') {
1277                # Here we were invoked from a web page. Look for a cookie.
1278                $retVal = $parameter->cookie('IP');
1279            } elsif (! $ptype) {
1280                # Here the key was passed in.
1281                $retVal = $parameter;
1282            }
1283        }
1284        # If no luck finding a key, use the PID.
1285        if (! defined $retVal) {
1286            $retVal = $$;
1287        }
1288        # Return the result.
1289        return $retVal;
1290    }
1291    
1292    
1293    =head3 TraceParms
1294    
1295        Tracer::TraceParms($cgi);
1296    
1297    Trace the CGI parameters at trace level CGI => 3 and the environment variables
1298    at level CGI => 4. A self-referencing URL is traced at level CGI => 2.
1299    
1300    =over 4
1301    
1302    =item cgi
1303    
1304    CGI query object containing the parameters to trace.
1305    
1306    =back
1307    
1308    =cut
1309    
1310    sub TraceParms {
1311        # Get the parameters.
1312        my ($cgi) = @_;
1313        if (T(CGI => 2)) {
1314            # Here we trace the GET-style URL for the script.
1315            Trace("[URL] " . $cgi->url(-relative => 1, -query => 1));
1316        }
1317        if (T(CGI => 3)) {
1318            # Here we want to trace the parameter data.
1319            my @names = $cgi->param;
1320            for my $parmName (sort @names) {
1321                # Note we skip the Trace parameters, which are for our use only.
1322                if ($parmName ne 'Trace' && $parmName ne 'TF') {
1323                    my @values = $cgi->param($parmName);
1324                    Trace("[CGI] $parmName = " . join(", ", @values));
1325                }
1326            }
1327            # Display the request method.
1328            my $method = $cgi->request_method();
1329            Trace("Method: $method");
1330        }
1331        if (T(CGI => 4)) {
1332            # Here we want the environment data too.
1333            for my $envName (sort keys %ENV) {
1334                Trace("[ENV] $envName = $ENV{$envName}");
1335            }
1336        }
1337  }  }
1338    
1339  =head3 Open  =head3 TraceImages
   
 C<< my $handle = Open($fileHandle, $fileSpec, $message); >>  
1340    
1341  Open a file.      Tracer::TraceImages($htmlString);
1342    
1343  The I<$fileSpec> is essentially the second argument of the PERL C<open>  Trace information about all of an html document's images. The tracing
1344  function. The mode is specified using Unix-like shell information. So, for  will be for type "IMG" at level 3. The image's source string
1345  example,  will be displayed. This is generally either the URL of the image or
1346    raw data for the image itself. If the source is too long, only the first 300
1347    characters will be shown at trace level 3. The entire source will be shown,
1348    however, at trace level 4. This method is not very smart, and might catch
1349    Javascript code, but it is still useful when debugging the arcane
1350    behavior of images in multiple browser environments.
1351    
1352      Open(\*LOGFILE, '>>/usr/spool/news/twitlog', "Could not open twit log.");  =over 4
1353    
1354  would open for output appended to the specified file, and  =item htmlString
1355    
1356      Open(\*DATASTREAM, "| sort -u >$outputFile", "Could not open $outputFile.");  HTML text for an outgoing web page.
1357    
1358  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.  
1359    
1360      my $logFile = Open(undef, '>>/usr/spool/news/twitlog', "Could not open twit log.");  =cut
1361    
1362  The I<$message> parameter is used if the open fails. If it is set to C<0>, then  sub TraceImages {
1363  the open returns TRUE if successful and FALSE if an error occurred. Otherwise, a      # Only proceed if we're at the proper trace level.
1364  failed open will throw an exception and the third parameter will be used to construct      if (T(IMG => 3)) {
1365  an error message. If the parameter is omitted, a standard message is constructed          # For performance reasons we're manipulating $_[0] instead of retrieving the string
1366  using the file spec.          # into a variable called "$htmlString". This is because we expect html strings to be
1367            # long, and don't want to copy them any more than we have to.
1368            Trace(length($_[0]) . " characters in web page.");
1369            # Loop through the HTML, culling image tags.
1370            while ($_[0] =~ /<img\s+[^>]+?src="([^"]+)"/sgi) {
1371                # Extract the source string and determine whether or not it's too long.
1372                my $srcString = $1;
1373                my $pos = pos($_[0]) - length($srcString);
1374                my $excess = length($srcString) - 300;
1375                # We'll put the display string in here.
1376                my $srcDisplay = $srcString;
1377                # If it's a data string, split it at the comma.
1378                $srcDisplay =~ s/^(data[^,]+,)/$1\n/;
1379                # If there's no excess or we're at trace level 4, we're done. At level 3 with
1380                # a long string, however, we only show the first 300 characters.
1381                if ($excess > 0 && ! T(IMG => 4)) {
1382                    $srcDisplay = substr($srcDisplay,0,300) . "\nplus $excess characters.";
1383                }
1384                # Output the trace message.
1385                Trace("Image tag at position $pos:\n$srcDisplay");
1386            }
1387        }
1388    }
1389    
1390      Could not open "/usr/spool/news/twitlog"  =head2 Command-Line Utility Methods
1391    
1392  Note that the mode characters are automatically cleaned from the file name.  =head3 SendSMS
 The actual error message from the file system will be captured and appended to the  
 message in any case.  
1393    
1394      Could not open "/usr/spool/news/twitlog": file not found.      my $msgID = Tracer::SendSMS($phoneNumber, $msg);
1395    
1396  In some versions of PERL the only error message we get is a number, which  Send a text message to a phone number using Clickatell. The FIG_Config file must contain the
1397  corresponds to the C++ C<errno> value.  user name, password, and API ID for the relevant account in the hash reference variable
1398    I<$FIG_Config::phone>, using the keys C<user>, C<password>, and C<api_id>. For
1399    example, if the user name is C<BruceTheHumanPet>, the password is C<silly>, and the API ID
1400    is C<2561022>, then the FIG_Config file must contain
1401    
1402      Could not open "/usr/spool/news/twitlog": 6.      $phone =  { user => 'BruceTheHumanPet',
1403                    password => 'silly',
1404                    api_id => '2561022' };
1405    
1406  =over 4  The original purpose of this method was to insure Bruce would be notified immediately when the
1407    Sprout Load terminates. Care should be taken if you do not wish Bruce to be notified immediately
1408    when you call this method.
1409    
1410  =item fileHandle  The message ID will be returned if successful, and C<undef> if an error occurs.
1411    
1412  File handle. If this parameter is C<undef>, a file handle will be generated  =over 4
 and returned as the value of this method.  
1413    
1414  =item fileSpec  =item phoneNumber
1415    
1416  File name and mode, as per the PERL C<open> function.  Phone number to receive the message, in international format. A United States phone number
1417    would be prefixed by "1". A British phone number would be prefixed by "44".
1418    
1419  =item message (optional)  =item msg
1420    
1421  Error message to use if the open fails. If omitted, a standard error message  Message to send to the specified phone.
 will be generated. In either case, the error information from the file system  
 is appended to the message. To specify a conditional open that does not throw  
 an error if it fails, use C<0>.  
1422    
1423  =item RETURN  =item RETURN
1424    
1425  Returns the name of the file handle assigned to the file, or C<undef> if the  Returns the message ID if successful, and C<undef> if the message could not be sent.
 open failed.  
1426    
1427  =back  =back
1428    
1429  =cut  =cut
1430    
1431  sub Open {  sub SendSMS {
1432      # Get the parameters.      # Get the parameters.
1433      my ($fileHandle, $fileSpec, $message) = @_;      my ($phoneNumber, $msg) = @_;
1434      # Attempt to open the file.      # Declare the return variable. If we do not change it, C<undef> will be returned.
1435      my $rv = open $fileHandle, $fileSpec;      my $retVal;
1436      # If the open failed, generate an error message.      # Only proceed if we have phone support.
1437      if (! $rv) {      if (! defined $FIG_Config::phone) {
1438          # Save the system error message.          Trace("Phone support not present in FIG_Config.") if T(1);
1439          my $sysMessage = $!;      } else {
1440          # See if we need a default message.          # Get the phone data.
1441          if (!$message) {          my $parms = $FIG_Config::phone;
1442              # Clean any obvious mode characters and leading spaces from the          # Get the Clickatell URL.
1443              # filename.          my $url = "http://api.clickatell.com/http/";
1444              my ($fileName) = FindNamePart($fileSpec);          # Create the user agent.
1445              $message = "Could not open \"$fileName\"";          my $ua = LWP::UserAgent->new;
1446            # Request a Clickatell session.
1447            my $resp = $ua->post("$url/sendmsg", { user => $parms->{user},
1448                                         password => $parms->{password},
1449                                         api_id => $parms->{api_id},
1450                                         to => $phoneNumber,
1451                                         text => $msg});
1452            # Check for an error.
1453            if (! $resp->is_success) {
1454                Trace("Alert failed.") if T(1);
1455            } else {
1456                # Get the message ID.
1457                my $rstring = $resp->content;
1458                if ($rstring =~ /^ID:\s+(.*)$/) {
1459                    $retVal = $1;
1460                } else {
1461                    Trace("Phone attempt failed with $rstring") if T(1);
1462          }          }
         # Terminate with an error using the supplied message and the  
         # error message from the file system.  
         Confess("$message: $!");  
1463      }      }
1464      # Return the file handle.      }
1465      return $fileHandle;      # Return the result.
1466        return $retVal;
1467  }  }
1468    
1469  =head3 FindNamePart  =head3 StandardSetup
1470    
1471  C<< my ($fileName, $start, $len) = Tracer::FindNamePart($fileSpec); >>      my ($options, @parameters) = StandardSetup(\@categories, \%options, $parmHelp, @ARGV);
1472    
1473  Extract the portion of a file specification that contains the file name.  This method performs standard command-line parsing and tracing setup. The return
1474    values are a hash of the command-line options and a list of the positional
1475    parameters. Tracing is automatically set up and the command-line options are
1476    validated.
1477    
1478  A file specification is the string passed to an C<open> call. It specifies the file  This is a complex method that does a lot of grunt work. The parameters can
1479  mode and name. In a truly complex situation, it can specify a pipe sequence. This  be more easily understood, however, once they are examined individually.
 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>.  
1480    
1481      >>/usr/fig/myfile.txt  The I<categories> parameter is the most obtuse. It is a reference to a list of
1482      </usr/fig/myfile.txt  special-purpose tracing categories. Most tracing categories are PERL package
1483      | sort -u > /usr/fig/myfile.txt  names. So, for example, if you wanted to turn on tracing inside the B<Sprout>,
1484    B<ERDB>, and B<SproutLoad> packages, you would specify the categories
1485    
1486  If the method cannot find a file name using its normal methods, it will return the      ["Sprout", "SproutLoad", "ERDB"]
1487  whole incoming string.  
1488    This would cause trace messages in the specified three packages to appear in
1489    the output. There are two special tracing categories that are automatically
1490    handled by this method. In other words, if you used L</TSetup> you would need
1491    to include these categories manually, but if you use this method they are turned
1492    on automatically.
1493    
1494  =over 4  =over 4
1495    
1496  =item fileSpec  =item SQL
1497    
1498  File specification string from which the file name is to be extracted.  Traces SQL commands and activity.
1499    
1500  =item RETURN  =item Tracer
1501    
1502  Returns a three-element list. The first element contains the file name portion of  Traces error messages and call stacks.
 the specified string, or the whole string if a file name cannot be found via normal  
 methods. The second element contains the start position of the file name portion and  
 the third element contains the length.  
1503    
1504  =back  =back
1505    
1506  =cut  C<SQL> is only turned on if the C<-sql> option is specified in the command line.
1507  #: Return Type $;  The trace level is specified using the C<-trace> command-line option. For example,
1508  sub FindNamePart {  the following command line for C<TransactFeatures> turns on SQL tracing and runs
1509      # Get the parameters.  all tracing at level 3.
     my ($fileSpec) = @_;  
     # Default to the whole input string.  
     my ($retVal, $pos, $len) = ($fileSpec, 0, length $fileSpec);  
     # Parse out the file name if we can.  
     if ($fileSpec =~ m/(<|>>?)(.+?)(\s*)$/) {  
         $retVal = $2;  
         $len = length $retVal;  
         $pos = (length $fileSpec) - (length $3) - $len;  
     }  
     # Return the result.  
     return ($retVal, $pos, $len);  
 }  
1510    
1511  =head3 OpenDir      TransactFeatures -trace=3 -sql register ../xacts IDs.tbl
1512    
1513    Standard tracing is output to the standard output and echoed to the file
1514    C<trace>I<$$>C<.log> in the FIG temporary directory, where I<$$> is the
1515    process ID. You can also specify the C<user> parameter to put a user ID
1516    instead of a process ID in the trace file name. So, for example
1517    
1518  C<< my @files = OpenDir($dirName, $filtered, $flag); >>  The default trace level is 2. To get all messages, specify a trace level of 4.
1519    For a genome-by-genome update, use 3.
1520    
1521  Open a directory and return all the file names. This function essentially performs      TransactFeatures -trace=3 -sql -user=Bruce register ../xacts IDs.tbl
 the functions of an C<opendir> and C<readdir>. If the I<$filtered> parameter is  
 set to TRUE, all filenames beginning with a period (C<.>), dollar sign (C<$>),  
 or pound sign (C<#>) and all filenames ending with a tilde C<~>) will be  
 filtered out of the return list. If the directory does not open and I<$flag> is not  
 set, an exception is thrown. So, for example,  
1522    
1523      my @files = OpenDir("/Volumes/fig/contigs", 1);  would send the trace output to C<traceBruce.log> in the temporary directory.
1524    
1525  is effectively the same as  The I<options> parameter is a reference to a hash containing the command-line
1526    options, their default values, and an explanation of what they mean. Command-line
1527    options may be in the form of switches or keywords. In the case of a switch, the
1528    option value is 1 if it is specified and 0 if it is not specified. In the case
1529    of a keyword, the value is separated from the option name by an equal sign. You
1530    can see this last in the command-line example above.
1531    
1532      opendir(TMP, "/Volumes/fig/contigs") || Confess("Could not open /Volumes/fig/contigs.");  You can specify a different default trace level by setting C<$options->{trace}>
1533      my @files = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir(TMP);  prior to calling this method.
1534    
1535  Similarly, the following code  An example at this point would help. Consider, for example, the command-line utility
1536    C<TransactFeatures>. It accepts a list of positional parameters plus the options
1537    C<safe>, C<noAlias>, C<start>, and C<tblFiles>. To start up this command, we execute
1538    the following code.
1539    
1540      my @files = grep { $_ =~ /^\d/ } OpenDir("/Volumes/fig/orgs", 0, 1);      my ($options, @parameters) = Tracer::StandardSetup(["DocUtils"],
1541                            { safe => [0, "use database transactions"],
1542                              noAlias => [0, "do not expect aliases in CHANGE transactions"],
1543                              start => [' ', "start with this genome"],
1544                              tblFiles => [0, "output TBL files containing the corrected IDs"] },
1545                            "<command> <transactionDirectory> <IDfile>",
1546                          @ARGV);
1547    
 Returns the names of all files in C</Volumes/fig/orgs> that begin with digits and  
 automatically returns an empty list if the directory fails to open.  
1548    
1549  =over 4  The call to C<ParseCommand> specifies the default values for the options and
1550    stores the actual options in a hash that is returned as C<$options>. The
1551    positional parameters are returned in C<@parameters>.
1552    
1553  =item dirName  The following is a sample command line for C<TransactFeatures>.
1554    
1555  Name of the directory to open.      TransactFeatures -trace=2 -noAlias register ../xacts IDs.tbl
1556    
1557  =item filtered  Single and double hyphens are equivalent. So, you could also code the
1558    above command as
1559    
1560        TransactFeatures --trace=2 --noAlias register ../xacts IDs.tbl
1561    
1562    In this case, C<register>, C<../xacts>, and C<IDs.tbl> are the positional
1563    parameters, and would find themselves in I<@parameters> after executing the
1564    above code fragment. The tracing would be set to level 2, and the categories
1565    would be C<Tracer>, and <DocUtils>. C<Tracer> is standard,
1566    and C<DocUtils> was included because it came in within the first parameter
1567    to this method. The I<$options> hash would be
1568    
1569        { trace => 2, sql => 0, safe => 0,
1570          noAlias => 1, start => ' ', tblFiles => 0 }
1571    
1572    Use of C<StandardSetup> in this way provides a simple way of performing
1573    standard tracing setup and command-line parsing. Note that the caller is
1574    not even aware of the command-line switches C<-trace> and C<-sql>, which
1575    are used by this method to control the tracing. If additional tracing features
1576    need to be added in the future, they can be processed by this method without
1577    upsetting the command-line utilities.
1578    
1579  TRUE if files whose names begin with a period (C<.>) should be automatically removed  If the C<background> option is specified on the command line, then the
1580  from the list, else FALSE.  standard and error outputs will be directed to files in the temporary
1581    directory, using the same suffix as the trace file. So, if the command
1582    line specified
1583    
1584  =item flag      -user=Bruce -background
1585    
1586  TRUE if a failure to open is okay, else FALSE  then the trace output would go to C<traceBruce.log>, the standard output to
1587    C<outBruce.log>, and the error output to C<errBruce.log>. This is designed to
1588    simplify starting a command in the background.
1589    
1590  =back  The user name is also used as the tracing key for L</Emergency Tracing>.
1591    Specifying a value of C<E> for the trace level causes emergency tracing to
1592    be used instead of custom tracing. If the user name is not specified,
1593    the tracing key is taken from the C<Tracing> environment variable. If there
1594    is no value for that variable, the tracing key will be computed from the active
1595    login ID.
1596    
1597    Since the default situation in StandardSetup is to trace to the standard
1598    output, errors that occur in command-line scripts will not generate
1599    RSS events. To force the events, use the C<warn> option.
1600    
1601  =cut      TransactFeatures -background -warn register ../xacts IDs.tbl
 #: Return Type @;  
 sub OpenDir {  
     # Get the parameters.  
     my ($dirName, $filtered, $flag) = @_;  
     # Declare the return variable.  
     my @retVal = ();  
     # Open the directory.  
     if (opendir(my $dirHandle, $dirName)) {  
         # The directory opened successfully. Get the appropriate list according to the  
         # strictures of the filter parameter.  
         if ($filtered) {  
             @retVal = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir $dirHandle;  
         } else {  
             @retVal = readdir $dirHandle;  
         }  
     } elsif (! $flag) {  
         # Here the directory would not open and it's considered an error.  
         Confess("Could not open directory $dirName.");  
     }  
     # Return the result.  
     return @retVal;  
 }  
1602    
1603  =head3 SetLevel  Finally, if the special option C<-help> is specified, the option
1604    names will be traced at level 0 and the program will exit without processing.
1605    This provides a limited help capability. For example, if the user enters
1606    
1607  C<< Tracer::SetLevel($newLevel); >>      TransactFeatures -help
1608    
1609  Modify the trace level. A higher trace level will cause more messages to appear.  he would see the following output.
1610    
1611  =over 4      TransactFeatures [options] <command> <transactionDirectory> <IDfile>
1612            -trace    tracing level (default E)
1613            -sql      trace SQL commands
1614            -safe     use database transactions
1615            -noAlias  do not expect aliases in CHANGE transactions
1616            -start    start with this genome
1617            -tblFiles output TBL files containing the corrected IDs
1618            -forked   do not erase the trace file before tracing
1619    
1620  =item newLevel  The caller has the option of modifying the tracing scheme by placing a value
1621    for C<trace> in the incoming options hash. The default value can be overridden,
1622    or the tracing to the standard output can be turned off by suffixing a minus
1623    sign to the trace level. So, for example,
1624    
1625  Proposed new trace level.      { trace => [0, "tracing level (default 0)"],
1626           ...
1627    
1628  =back  would set the default trace level to 0 instead of E, while
1629    
1630  =cut      { trace => ["2-", "tracing level (default 2)"],
1631           ...
1632    
1633  sub SetLevel {  would set the default to 2, but trace only to the log file, not to the
1634      $TraceLevel = $_[0];  standard output.
 }  
1635    
1636  =head3 Now  The parameters to this method are as follows.
1637    
1638  C<< my $string = Tracer::Now(); >>  =over 4
1639    
1640  Return a displayable time stamp containing the local time.  =item categories
1641    
1642  =cut  Reference to a list of tracing category names. These should be names of
1643    packages whose internal workings will need to be debugged to get the
1644    command working.
1645    
1646  sub Now {  =item options
     my ($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 $retVal;  
 }  
1647    
1648  # Pad a number to 2 digits.  Reference to a hash containing the legal options for the current command mapped
1649  sub _p2 {  to their default values and descriptions. The user can override the defaults
1650      my ($value) = @_;  by specifying the options as command-line switches prefixed by a hyphen.
1651      $value = "0$value" if ($value < 10);  Tracing-related options may be added to this hash. If the C<-h> option is
1652      return $value;  specified on the command line, the option descriptions will be used to
1653  }  explain the options. To turn off tracing to the standard output, add a
1654    minus sign to the value for C<trace> (see above).
1655    
1656  =head3 LogErrors  =item parmHelp
1657    
1658  C<< Tracer::LogErrors($fileName); >>  A string that vaguely describes the positional parameters. This is used
1659    if the user specifies the C<-h> option.
1660    
1661  Route the standard error output to a log file.  =item argv
1662    
1663  =over 4  List of command line parameters, including the option switches, which must
1664    precede the positional parameters and be prefixed by a hyphen.
1665    
1666  =item fileName  =item RETURN
1667    
1668  Name of the file to receive the error output.  Returns a list. The first element of the list is the reference to a hash that
1669    maps the command-line option switches to their values. These will either be the
1670    default values or overrides specified on the command line. The remaining
1671    elements of the list are the position parameters, in order.
1672    
1673  =back  =back
1674    
1675  =cut  =cut
1676    
1677  sub LogErrors {  sub StandardSetup {
1678      # Get the file name.      # Get the parameters.
1679      my ($fileName) = @_;      my ($categories, $options, $parmHelp, @argv) = @_;
1680      # Open the file as the standard error output.      # Get the default tracing key.
1681      open STDERR, '>', $fileName;      my $tkey = EmergencyKey();
1682        # Save the command line.
1683        $CommandLine = join(" ", $0, map { $_ =~ /\s/ ? "\"$_\"" : $_ } @argv);
1684        # Add the tracing options.
1685        if (! exists $options->{trace}) {
1686            $options->{trace} = ['2', "tracing level (E for emergency tracing)"];
1687        }
1688        if (! exists $options->{forked}) {
1689            $options->{forked} = [0, "keep old trace file"];
1690        }
1691        $options->{sql} = [0, "turn on SQL tracing"];
1692        $options->{help} = [0, "display command-line options"];
1693        $options->{user} = [$tkey, "tracing key"];
1694        $options->{background} = [0, "spool standard and error output"];
1695        $options->{warn} = [0, "send errors to RSS feed"];
1696        $options->{moreTracing} = ["", "comma-delimited list of additional trace modules for debugging"];
1697        # Create a parsing hash from the options hash. The parsing hash
1698        # contains the default values rather than the default value
1699        # and the description. While we're at it, we'll memorize the
1700        # length of the longest option name.
1701        my $longestName = 0;
1702        my %parseOptions = ();
1703        for my $key (keys %{$options}) {
1704            if (length $key > $longestName) {
1705                $longestName = length $key;
1706            }
1707            $parseOptions{$key} = $options->{$key}->[0];
1708        }
1709        # Parse the command line.
1710        my ($retOptions, @retParameters) = ParseCommand(\%parseOptions, @argv);
1711        # Get the logfile suffix.
1712        my $suffix = $retOptions->{user};
1713        # We'll put the trace file name in here. We need it later if background
1714        # mode is on.
1715        my $traceFileName;
1716        # Now we want to set up tracing. First, we need to know if the user
1717        # wants emergency tracing.
1718        if ($retOptions->{trace} eq 'E') {
1719            ETracing($retOptions->{user});
1720        } else {
1721            # Here the tracing is controlled from the command line.
1722            my @cats = @{$categories};
1723            if ($retOptions->{sql}) {
1724                push @cats, "SQL";
1725            }
1726            if ($retOptions->{warn}) {
1727                push @cats, "Feed";
1728            }
1729            # Add the default categories.
1730            push @cats, "Tracer";
1731            # Check for more tracing groups.
1732            if ($retOptions->{moreTracing}) {
1733                push @cats, split /,/, $retOptions->{moreTracing};
1734            }
1735            # Next, we create the category string by joining the categories.
1736            my $cats = join(" ", @cats);
1737            # Check to determine whether or not the caller wants to turn off tracing
1738            # to the standard output.
1739            my $traceLevel = $retOptions->{trace};
1740            my $textOKFlag = 1;
1741            if ($traceLevel =~ /^(.)-/) {
1742                $traceLevel = $1;
1743                $textOKFlag = 0;
1744            }
1745            # Now we set up the trace mode.
1746            my $traceMode;
1747            # Verify that we can open a file in the FIG temporary directory.
1748            my $traceFileName = "$FIG_Config::temp/trace$suffix.log";
1749            my $traceFileSpec = ($retOptions->{forked} ? ">>$traceFileName" : ">$traceFileName");
1750            if (open TESTTRACE, "$traceFileSpec") {
1751                # Here we can trace to a file.
1752                $traceMode = ">>$traceFileName";
1753                if ($textOKFlag) {
1754                    # Echo to standard output if the text-OK flag is set.
1755                    $traceMode = "+$traceMode";
1756                }
1757                # Close the test file.
1758                close TESTTRACE;
1759            } else {
1760                # Here we can't trace to a file. Complain about this.
1761                warn "Could not open trace file $traceFileName: $!\n";
1762                # We trace to the standard output if it's
1763                # okay, and the error log otherwise.
1764                if ($textOKFlag) {
1765                    $traceMode = "TEXT";
1766                } else {
1767                    $traceMode = "WARN";
1768                }
1769            }
1770            # Now set up the tracing.
1771            TSetup("$traceLevel $cats", $traceMode);
1772        }
1773        # Check for background mode.
1774        if ($retOptions->{background}) {
1775            my $outFileName = "$FIG_Config::temp/out$suffix$$.log";
1776            my $errFileName = "$FIG_Config::temp/err$suffix$$.log";
1777            # Spool the output.
1778            open STDOUT, ">$outFileName";
1779            # If we have a trace file, trace the errors to the log. Otherwise,
1780            # spool the errors.
1781            if (defined $traceFileName) {
1782                open STDERR, "| Tracer $traceFileName";
1783            } else {
1784                open STDERR, ">$errFileName";
1785            }
1786            # Check for phone support. If we have phone support and a phone number,
1787            # we want to turn it on.
1788            if ($ENV{PHONE} && defined($FIG_Config::phone)) {
1789                $retOptions->{phone} = $ENV{PHONE};
1790            }
1791        }
1792        # Check for the "help" option. If it is specified, dump the command-line
1793        # options and exit the program.
1794        if ($retOptions->{help}) {
1795            $0 =~ m#[/\\](\w+)(\.pl)?$#i;
1796            print "$1 [options] $parmHelp\n";
1797            for my $key (sort keys %{$options}) {
1798                my $name = Pad($key, $longestName, 0, ' ');
1799                my $desc = $options->{$key}->[1];
1800                if ($options->{$key}->[0]) {
1801                    $desc .= " (default " . $options->{$key}->[0] . ")";
1802                }
1803                print "  $name $desc\n";
1804            }
1805            exit(0);
1806        }
1807        # Trace the options, if applicable.
1808        if (T(3)) {
1809            my @parms = grep { $retOptions->{$_} } keys %{$retOptions};
1810            Trace("Selected options: " . join(", ", sort @parms) . ".");
1811        }
1812        # Return the parsed parameters.
1813        return ($retOptions, @retParameters);
1814  }  }
1815    
1816  =head3 ReadOptions  =head3 ReadOptions
1817    
1818  C<< my %options = Tracer::ReadOptions($fileName); >>      my %options = Tracer::ReadOptions($fileName);
1819    
1820  Read a set of options from a file. Each option is encoded in a line of text that has the  Read a set of options from a file. Each option is encoded in a line of text that has the
1821  format  format
# Line 855  Line 1876 
1876    
1877  =head3 GetOptions  =head3 GetOptions
1878    
1879  C<< Tracer::GetOptions(\%defaults, \%options); >>      Tracer::GetOptions(\%defaults, \%options);
1880    
1881  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
1882  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 1885 
1885    
1886  Consider the following example.  Consider the following example.
1887    
1888  C<< my $optionTable = GetOptions({ dbType => 'mySQL', trace => 0 }, $options); >>      my $optionTable = GetOptions({ dbType => 'mySQL', trace => 0 }, $options);
1889    
1890  In this example, the variable B<$options> is expected to contain at most two options-- B<dbType> and  In this example, the variable B<$options> is expected to contain at most two options-- B<dbType> and
1891  B<trace>. The default database type is C<mySQL> and the default trace level is C<0>. If the value of  B<trace>. The default database type is C<mySQL> and the default trace level is C<0>. If the value of
# Line 872  Line 1893 
1893  the trace level will remain at 0. If B<$options> is undefined, then the database type and trace level  the trace level will remain at 0. If B<$options> is undefined, then the database type and trace level
1894  will remain C<mySQL> and C<0>. If, on the other hand, B<$options> is defined as  will remain C<mySQL> and C<0>. If, on the other hand, B<$options> is defined as
1895    
1896  C<< {databaseType => 'Oracle'} >>      {databaseType => 'Oracle'}
1897    
1898  an error will occur because the B<databaseType> option does not exist.  an error will occur because the B<databaseType> option does not exist.
1899    
# Line 916  Line 1937 
1937    
1938  =head3 MergeOptions  =head3 MergeOptions
1939    
1940  C<< Tracer::MergeOptions(\%table, \%defaults); >>      Tracer::MergeOptions(\%table, \%defaults);
1941    
1942  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
1943  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 948  Line 1969 
1969      }      }
1970  }  }
1971    
1972  =head3 Trace  =head3 UnparseOptions
   
 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); >>  
1973    
1974  Return TRUE if the trace level is at or above a specified value and the specified category      my $optionString = Tracer::UnparseOptions(\%options);
 is active, else FALSE. If no category is specified, the caller's package name is used.  
   
 =over 4  
1975    
1976  =item category  Convert an option hash into a command-line string. This will not
1977    necessarily be the same text that came in, but it will nonetheless
1978  Category to which the message belongs. If not specified, the caller's package name is  produce the same ultimate result when parsed by L</StandardSetup>.
 used.  
1979    
1980  =item traceLevel  =over 4
1981    
1982  Relevant tracing level.  =item options
1983    
1984    Reference to a hash of options to convert into an option string.
1985    
1986  =item RETURN  =item RETURN
1987    
1988  TRUE if a message at the specified trace level would appear in the trace, else FALSE.  Returns a string that will parse to the same set of options when
1989    parsed by L</StandardSetup>.
1990    
1991  =back  =back
1992    
1993  =cut  =cut
1994    
1995  sub T {  sub UnparseOptions {
     # Declare the return variable.  
     my $retVal = 0;  
     # Only proceed if tracing is turned on.  
     if ($Destination ne "NONE") {  
1996          # Get the parameters.          # Get the parameters.
1997          my ($category, $traceLevel) = @_;      my ($options) = @_;
1998          if (!defined $traceLevel) {      # The option segments will be put in here.
1999              # Here we have no category, so we need to get the calling package.      my @retVal = ();
2000              # The calling package is normally the first parameter. If it is      # Loop through the options.
2001              # omitted, the first parameter will be the tracelevel. So, the      for my $key (keys %$options) {
2002              # first thing we do is shift the so-called category into the          # Get the option value.
2003              # $traceLevel variable where it belongs.          my $value = $options->{$key};
2004              $traceLevel = $category;          # Only use it if it's nonempty.
2005              my ($package, $fileName, $line) = caller;          if (defined $value && $value ne "") {
2006              # If there is no calling package, we default to "main".              my $segment = "--$key=$value";
2007              if (!$package) {              # Quote it if necessary.
2008                  $category = "main";              if ($segment =~ /[ |<>*]/) {
2009              } else {                  $segment = '"' . $segment . '"';
                 $category = $package;  
             }  
2010          }          }
2011          # Save the category name.              # Add it to the return list.
2012          $LastCategory = $category;              push @retVal, $segment;
         # 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.");  
2013          }          }
         $retVal = ($traceLevel <= $TraceLevel && ($AllTrace || exists $Categories{$category}));  
2014      }      }
2015      # Return the computed result.      # Return the result.
2016      return $retVal;      return join(" ", @retVal);
2017  }  }
2018    
2019  =head3 ParseCommand  =head3 ParseCommand
2020    
2021  C<< my ($options, @arguments) = Tracer::ParseCommand(\%optionTable, @inputList); >>      my ($options, @arguments) = Tracer::ParseCommand(\%optionTable, @inputList);
2022    
2023  Parse a command line consisting of a list of parameters. The initial parameters may be option  Parse a command line consisting of a list of parameters. The initial parameters may be option
2024  specifiers of the form C<->I<option> or C<->I<option>C<=>I<value>. The options are stripped  specifiers of the form C<->I<option> or C<->I<option>C<=>I<value>. The options are stripped
2025  off and merged into a table of default options. The remainder of the command line is  off and merged into a table of default options. The remainder of the command line is
2026  returned as a list of positional arguments. For example, consider the following invocation.  returned as a list of positional arguments. For example, consider the following invocation.
2027    
2028  C<< my ($options, @arguments) = ParseCommand({ errors => 0, logFile => 'trace.log'}, @words); >>      my ($options, @arguments) = ParseCommand({ errors => 0, logFile => 'trace.log'}, @words);
2029    
2030  In this case, the list @words will be treated as a command line. There are two options available,  In this case, the list @words will be treated as a command line and there are two options available,
2031  B<errors> and B<logFile>. If @words has the following format  B<errors> and B<logFile>. If @words has the following format
2032    
2033  C<< -logFile=error.log apple orange rutabaga >>      -logFile=error.log apple orange rutabaga
2034    
2035  then at the end of the invocation, C<$options> will be  then at the end of the invocation, C<$options> will be
2036    
2037  C<< { errors => 0, logFile => 'error.log' } >>      { errors => 0, logFile => 'error.log' }
2038    
2039  and C<@arguments> will contain  and C<@arguments> will contain
2040    
2041  C<< apple orange rutabaga >>      apple orange rutabaga
2042    
2043  The parser allows for some escape sequences. See L</UnEscape> for a description. There is no  The parser allows for some escape sequences. See L</UnEscape> for a description. There is no
2044  support for quote characters.  support for quote characters. Options can be specified with single or double hyphens.
2045    
2046  =over 4  =over 4
2047    
# Line 1119  Line 2066 
2066      my ($optionTable, @inputList) = @_;      my ($optionTable, @inputList) = @_;
2067      # Process any options in the input list.      # Process any options in the input list.
2068      my %overrides = ();      my %overrides = ();
2069      while ((@inputList > 0) && ($inputList[0] =~ /^-/)) {      while ((@inputList > 0) && ($inputList[0] =~ /^--?/)) {
2070          # Get the current option.          # Get the current option.
2071          my $arg = shift @inputList;          my $arg = shift @inputList;
2072          # Pull out the option name.          # Pull out the option name.
2073          $arg =~ /^-([^=]*)/g;          $arg =~ /^--?([^=]*)/g;
2074          my $name = $1;          my $name = $1;
2075          # Check for an option value.          # Check for an option value.
2076          if ($arg =~ /\G=(.*)$/g) {          if ($arg =~ /\G=(.*)$/g) {
# Line 1145  Line 2092 
2092      return ($optionTable, @retVal);      return ($optionTable, @retVal);
2093  }  }
2094    
 =head3 Escape  
2095    
2096  C<< my $codedString = Tracer::Escape($realString); >>  =head2 File Utility Methods
2097    
2098  Escape a string for use in a command length. Tabs will be replaced by C<\t>, new-lines  =head3 GetFile
2099  replaced by C<\n>, carriage returns will be deleted, and backslashes will be doubled. The  
2100  result is to reverse the effect of L</UnEscape>.      my @fileContents = Tracer::GetFile($fileName);
2101    
2102        or
2103    
2104        my $fileContents = Tracer::GetFile($fileName);
2105    
2106    Return the entire contents of a file. In list context, line-ends are removed and
2107    each line is a list element. In scalar context, line-ends are replaced by C<\n>.
2108    
2109  =over 4  =over 4
2110    
2111  =item realString  =item fileName
2112    
2113  String to escape.  Name of the file to read.
2114    
2115  =item RETURN  =item RETURN
2116    
2117  Escaped equivalent of the real string.  In a list context, returns the entire file as a list with the line terminators removed.
2118    In a scalar context, returns the entire file as a string. If an error occurs opening
2119    the file, an empty list will be returned.
2120    
2121  =back  =back
2122    
2123  =cut  =cut
2124    
2125  sub Escape {  sub GetFile {
2126      # Get the parameter.      # Get the parameters.
2127      my ($realString) = @_;      my ($fileName) = @_;
2128      # Initialize the return variable.      # Declare the return variable.
2129      my $retVal = "";      my @retVal = ();
2130      # Loop through the parameter string, looking for sequences to escape.      # Open the file for input.
2131      while (length $realString > 0) {      my $handle = Open(undef, "<$fileName");
2132          # Look for the first sequence to escape.      # Read the whole file into the return variable, stripping off any terminator
2133          if ($realString =~ /^(.*?)([\n\t\r\\])/) {      # characters.
2134              # Here we found it. The text preceding the sequence is in $1. The sequence      my $lineCount = 0;
2135              # itself is in $2. First, move the clear text to the return variable.      while (my $line = <$handle>) {
2136              $retVal .= $1;          $lineCount++;
2137              # Strip the processed section off the real string.          $line = Strip($line);
2138              $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;  
2139              }              }
2140        # Close it.
2141        close $handle;
2142        my $actualLines = @retVal;
2143        Trace("$actualLines lines read from file $fileName.") if T(File => 2);
2144        # Return the file's contents in the desired format.
2145        if (wantarray) {
2146            return @retVal;
2147          } else {          } else {
2148              # Here there are no more escape sequences. The rest of the string is          return join "\n", @retVal;
             # transferred unmodified.  
             $retVal .= $realString;  
             $realString = "";  
         }  
2149      }      }
     # Return the result.  
     return $retVal;  
2150  }  }
2151    
2152  =head3 UnEscape  =head3 PutFile
2153    
2154  C<< my $realString = Tracer::UnEscape($codedString); >>      Tracer::PutFile($fileName, \@lines);
2155    
2156  Replace escape sequences with their actual equivalents. C<\t> will be replaced by  Write out a file from a list of lines of text.
 a tab, C<\n> by a new-line character, and C<\\> by a backslash. C<\r> codes will  
 be deleted.  
2157    
2158  =over 4  =over 4
2159    
2160  =item codedString  =item fileName
2161    
2162  String to un-escape.  Name of the output file.
2163    
2164  =item RETURN  =item lines
2165    
2166  Returns a copy of the original string with the escape sequences converted to their actual  Reference to a list of text lines. The lines will be written to the file in order, with trailing
2167  values.  new-line characters. Alternatively, may be a string, in which case the string will be written without
2168    modification.
2169    
2170  =back  =back
2171    
2172  =cut  =cut
2173    
2174  sub UnEscape {  sub PutFile {
2175      # Get the parameter.      # Get the parameters.
2176      my ($codedString) = @_;      my ($fileName, $lines) = @_;
2177      # Initialize the return variable.      # Open the output file.
2178      my $retVal = "";      my $handle = Open(undef, ">$fileName");
2179      # Only proceed if the incoming string is nonempty.      # Count the lines written.
2180      if (defined $codedString) {      if (ref $lines ne 'ARRAY') {
2181          # Loop through the parameter string, looking for escape sequences. We can't do          # Here we have a scalar, so we write it raw.
2182          # translating because it causes problems with the escaped slash. ("\\t" becomes          print $handle $lines;
2183          # "\<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;  
                 }  
2184              } else {              } else {
2185                  # Here there are no more escape sequences. The rest of the string is          # Write the lines one at a time.
2186                  # transferred unmodified.          my $count = 0;
2187                  $retVal .= $codedString;          for my $line (@{$lines}) {
2188                  $codedString = "";              print $handle "$line\n";
2189              }              $count++;
2190          }          }
2191            Trace("$count lines put to file $fileName.") if T(File => 3);
2192      }      }
2193      # Return the result.      # Close the output file.
2194      return $retVal;      close $handle;
2195  }  }
2196    
2197  =head3 ParseRecord  =head3 ParseRecord
2198    
2199  C<< my @fields = Tracer::ParseRecord($line); >>      my @fields = Tracer::ParseRecord($line);
2200    
2201  Parse a tab-delimited data line. The data line is split into field values. Embedded tab  Parse a tab-delimited data line. The data line is split into field values. Embedded tab
2202  and new-line characters in the data line must be represented as C<\t> and C<\n>, respectively.  and new-line characters in the data line must be represented as C<\t> and C<\n>, respectively.
# Line 1307  Line 2241 
2241    
2242  =head3 Merge  =head3 Merge
2243    
2244  C<< my @mergedList = Tracer::Merge(@inputList); >>      my @mergedList = Tracer::Merge(@inputList);
2245    
2246  Sort a list of strings and remove duplicates.  Sort a list of strings and remove duplicates.
2247    
# Line 1339  Line 2273 
2273              # Find out how many elements duplicate the current entry.              # Find out how many elements duplicate the current entry.
2274              my $j = $i + 1;              my $j = $i + 1;
2275              my $dup1 = $i + 1;              my $dup1 = $i + 1;
2276              while ($j < @inputList && $inputList[$j] eq $thisEntry) { $j++; };              while ($j < @inputList && $inputList[$j] eq $thisEntry) { $j++; };
2277              # If the number is nonzero, splice out the duplicates found.              # If the number is nonzero, splice out the duplicates found.
2278              if ($j > $dup1) {              if ($j > $dup1) {
2279                  splice @inputList, $dup1, $j - $dup1;                  splice @inputList, $dup1, $j - $dup1;
2280              }              }
2281              # 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
2282              # at position $i. We push $i forward one position and start again.              # at position $i. We push $i forward one position and start again.
2283              $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;  
2284      }      }
     # Close it.  
     close $handle;  
     my $actualLines = @retVal;  
     # Return the file's contents in the desired format.  
     if (wantarray) {  
         return @retVal;  
     } else {  
         return join "\n", @retVal;  
2285      }      }
2286        # Return the merged list.
2287        return @inputList;
2288  }  }
2289    
2290  =head3 PutFile  =head3 Open
2291    
2292  C<< Tracer::PutFile($fileName, \@lines); >>      my $handle = Open($fileHandle, $fileSpec, $message);
2293    
2294  Write out a file from a list of lines of text.  Open a file.
2295    
2296  =over 4  The I<$fileSpec> is essentially the second argument of the PERL C<open>
2297    function. The mode is specified using Unix-like shell information. So, for
2298    example,
2299    
2300  =item fileName      Open(\*LOGFILE, '>>/usr/spool/news/twitlog', "Could not open twit log.");
2301    
2302  Name of the output file.  would open for output appended to the specified file, and
2303    
2304  =item lines      Open(\*DATASTREAM, "| sort -u >$outputFile", "Could not open $outputFile.");
2305    
2306  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
2307  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,
2308  modification.  code as follows.
2309    
2310  =back      my $logFile = Open(undef, '>>/usr/spool/news/twitlog', "Could not open twit log.");
2311    
2312  =cut  The I<$message> parameter is used if the open fails. If it is set to C<0>, then
2313    the open returns TRUE if successful and FALSE if an error occurred. Otherwise, a
2314    failed open will throw an exception and the third parameter will be used to construct
2315    an error message. If the parameter is omitted, a standard message is constructed
2316    using the file spec.
2317    
2318  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;  
 }  
2319    
2320  =head3 QTrace  Note that the mode characters are automatically cleaned from the file name.
2321    The actual error message from the file system will be captured and appended to the
2322    message in any case.
2323    
2324  C<< my $data = QTrace($format); >>      Could not open "/usr/spool/news/twitlog": file not found.
2325    
2326  Return the queued trace data in the specified format.  In some versions of PERL the only error message we get is a number, which
2327    corresponds to the C++ C<errno> value.
2328    
2329        Could not open "/usr/spool/news/twitlog": 6.
2330    
2331  =over 4  =over 4
2332    
2333  =item format  =item fileHandle
2334    
2335  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
2336    and returned as the value of this method.
2337    
2338    =item fileSpec
2339    
2340    File name and mode, as per the PERL C<open> function.
2341    
2342    =item message (optional)
2343    
2344    Error message to use if the open fails. If omitted, a standard error message
2345    will be generated. In either case, the error information from the file system
2346    is appended to the message. To specify a conditional open that does not throw
2347    an error if it fails, use C<0>.
2348    
2349    =item RETURN
2350    
2351    Returns the name of the file handle assigned to the file, or C<undef> if the
2352    open failed.
2353    
2354  =back  =back
2355    
2356  =cut  =cut
2357    
2358  sub QTrace {  sub Open {
2359      # Get the parameter.      # Get the parameters.
2360      my ($format) = @_;      my ($fileHandle, $fileSpec, $message) = @_;
2361      # Create the return variable.      # Attempt to open the file.
2362      my $retVal = "";      my $rv = open $fileHandle, $fileSpec;
2363      # Only proceed if there is an actual queue.      # If the open failed, generate an error message.
2364      if (@Queue) {      if (! $rv) {
2365          # Process according to the format.          # Save the system error message.
2366          if ($format =~ m/^HTML$/i) {          my $sysMessage = $!;
2367              # Convert the queue into an HTML list.          # See if we need a default message.
2368              $retVal = "<ul>\n";          if (!$message) {
2369              for my $line (@Queue) {              # Clean any obvious mode characters and leading spaces from the
2370                  my $escapedLine = CGI::escapeHTML($line);              # filename.
2371                  $retVal .= "<li>$escapedLine</li>\n";              my ($fileName) = FindNamePart($fileSpec);
2372              }              $message = "Could not open \"$fileName\"";
             $retVal .= "</ul>\n";  
         } elsif ($format =~ m/^TEXT$/i) {  
             # Convert the queue into a list of text lines.  
             $retVal = join("\n", @Queue) . "\n";  
2373          }          }
2374          # Clear the queue.          # Terminate with an error using the supplied message and the
2375          @Queue = ();          # error message from the file system.
2376            Confess("$message: $!");
2377      }      }
2378      # Return the formatted list.      # Return the file handle.
2379      return $retVal;      return $fileHandle;
2380  }  }
2381    
2382  =head3 Confess  =head3 FindNamePart
2383    
2384  C<< Confess($message); >>      my ($fileName, $start, $len) = Tracer::FindNamePart($fileSpec);
2385    
2386  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  
2387    
2388  C<< Assert($recNum >= 0) || Confess("Invalid record number $recNum."); >>  A file specification is the string passed to an C<open> call. It specifies the file
2389    mode and name. In a truly complex situation, it can specify a pipe sequence. This
2390    method assumes that the file name is whatever follows the first angle bracket
2391    sequence.  So, for example, in the following strings the file name is
2392    C</usr/fig/myfile.txt>.
2393    
2394  Will abort the program with a stack trace if the value of C<$recNum> is negative.      >>/usr/fig/myfile.txt
2395        </usr/fig/myfile.txt
2396        | sort -u > /usr/fig/myfile.txt
2397    
2398    If the method cannot find a file name using its normal methods, it will return the
2399    whole incoming string.
2400    
2401  =over 4  =over 4
2402    
2403  =item message  =item fileSpec
2404    
2405  Message to include in the trace.  File specification string from which the file name is to be extracted.
2406    
2407    =item RETURN
2408    
2409    Returns a three-element list. The first element contains the file name portion of
2410    the specified string, or the whole string if a file name cannot be found via normal
2411    methods. The second element contains the start position of the file name portion and
2412    the third element contains the length.
2413    
2414  =back  =back
2415    
2416  =cut  =cut
2417    #: Return Type $;
2418  sub Confess {  sub FindNamePart {
2419      # Get the parameters.      # Get the parameters.
2420      my ($message) = @_;      my ($fileSpec) = @_;
2421      # Trace the call stack.      # Default to the whole input string.
2422      Cluck($message);      my ($retVal, $pos, $len) = ($fileSpec, 0, length $fileSpec);
2423      # Abort the program.      # Parse out the file name if we can.
2424      croak(">>> $message");      if ($fileSpec =~ m/(<|>>?)(.+?)(\s*)$/) {
2425            $retVal = $2;
2426            $len = length $retVal;
2427            $pos = (length $fileSpec) - (length $3) - $len;
2428        }
2429        # Return the result.
2430        return ($retVal, $pos, $len);
2431  }  }
2432    
2433  =head3 Assert  =head3 OpenDir
2434    
2435  C<< Assert($condition1, $condition2, ... $conditionN); >>      my @files = OpenDir($dirName, $filtered, $flag);
2436    
2437  Return TRUE if all the conditions are true. This method can be used in conjunction with  Open a directory and return all the file names. This function essentially performs
2438  the OR operator and the L</Confess> method as a debugging assert.  the functions of an C<opendir> and C<readdir>. If the I<$filtered> parameter is
2439  So, for example  set to TRUE, all filenames beginning with a period (C<.>), dollar sign (C<$>),
2440    or pound sign (C<#>) and all filenames ending with a tilde C<~>) will be
2441    filtered out of the return list. If the directory does not open and I<$flag> is not
2442    set, an exception is thrown. So, for example,
2443    
2444  C<< Assert($recNum >= 0) || Confess("Invalid record number $recNum."); >>      my @files = OpenDir("/Volumes/fig/contigs", 1);
2445    
2446  Will abort the program with a stack trace if the value of C<$recNum> is negative.  is effectively the same as
2447    
2448  =cut      opendir(TMP, "/Volumes/fig/contigs") || Confess("Could not open /Volumes/fig/contigs.");
2449  sub Assert {      my @files = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir(TMP);
     my $retVal = 1;  
     LOOP: for my $condition (@_) {  
         if (! $condition) {  
             $retVal = 0;  
             last LOOP;  
         }  
     }  
     return $retVal;  
 }  
2450    
2451  =head3 Cluck  Similarly, the following code
2452    
2453  C<< Cluck($message); >>      my @files = grep { $_ =~ /^\d/ } OpenDir("/Volumes/fig/orgs", 0, 1);
2454    
2455  Trace the call stack. Note that for best results, you should qualify the call with a  Returns the names of all files in C</Volumes/fig/orgs> that begin with digits and
2456  trace condition. For example,  automatically returns an empty list if the directory fails to open.
2457    
2458  C<< Cluck("Starting record parse.") if T(3); >>  =over 4
2459    
2460  will only trace the stack if the trace level for the package is 3 or more.  =item dirName
2461    
2462  =over 4  Name of the directory to open.
2463    
2464  =item message  =item filtered
2465    
2466  Message to include in the trace.  TRUE if files whose names begin with a period (C<.>) should be automatically removed
2467    from the list, else FALSE.
2468    
2469    =item flag
2470    
2471    TRUE if a failure to open is okay, else FALSE
2472    
2473  =back  =back
2474    
2475  =cut  =cut
2476    #: Return Type @;
2477  sub Cluck {  sub OpenDir {
2478      # Get the parameters.      # Get the parameters.
2479      my ($message) = @_;      my ($dirName, $filtered, $flag) = @_;
2480      # Trace what's happening.      # Declare the return variable.
2481      Trace("Stack trace for event: $message");      my @retVal = ();
2482      my $confession = longmess($message);      # Open the directory.
2483      # Convert the confession to a series of trace messages. Note we skip any      if (opendir(my $dirHandle, $dirName)) {
2484      # messages relating to calls into Tracer.          # The directory opened successfully. Get the appropriate list according to the
2485      for my $line (split /\s*\n/, $confession) {          # strictures of the filter parameter.
2486          Trace($line) if ($line !~ /Tracer\.pm/);          if ($filtered) {
2487                @retVal = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir $dirHandle;
2488            } else {
2489                @retVal = readdir $dirHandle;
2490            }
2491        } elsif (! $flag) {
2492            # Here the directory would not open and it's considered an error.
2493            Confess("Could not open directory $dirName.");
2494      }      }
2495        # Return the result.
2496        return @retVal;
2497  }  }
2498    
 =head3 Min  
2499    
2500  C<< my $min = Min($value1, $value2, ... $valueN); >>  =head3 Insure
2501    
2502        Insure($dirName, $chmod);
2503    
2504  Return the minimum argument. The arguments are treated as numbers.  Insure a directory is present.
2505    
2506  =over 4  =over 4
2507    
2508  =item $value1, $value2, ... $valueN  =item dirName
2509    
2510  List of numbers to compare.  Name of the directory to check. If it does not exist, it will be created.
2511    
2512  =item RETURN  =item chmod (optional)
2513    
2514  Returns the lowest number in the list.  Security privileges to be given to the directory if it is created.
2515    
2516  =back  =back
2517    
2518  =cut  =cut
2519    
2520  sub Min {  sub Insure {
2521      # Get the parameters. Note that we prime the return value with the first parameter.      my ($dirName, $chmod) = @_;
2522      my ($retVal, @values) = @_;      if (! -d $dirName) {
2523      # Loop through the remaining parameters, looking for the lowest.          Trace("Creating $dirName directory.") if T(2);
2524      for my $value (@values) {          eval {
2525          if ($value < $retVal) {              mkpath $dirName;
2526              $retVal = $value;              # If we have permissions specified, set them here.
2527                if (defined($chmod)) {
2528                    chmod $chmod, $dirName;
2529                }
2530            };
2531            if ($@) {
2532                Confess("Error creating $dirName: $@");
2533          }          }
2534      }      }
     # Return the minimum found.  
     return $retVal;  
2535  }  }
2536    
2537  =head3 Max  =head3 ChDir
2538    
2539  C<< my $max = Max($value1, $value2, ... $valueN); >>      ChDir($dirName);
2540    
2541  Return the maximum argument. The arguments are treated as numbers.  Change to the specified directory.
2542    
2543  =over 4  =over 4
2544    
2545  =item $value1, $value2, ... $valueN  =item dirName
   
 List of numbers to compare.  
   
 =item RETURN  
2546    
2547  Returns the highest number in the list.  Name of the directory to which we want to change.
2548    
2549  =back  =back
2550    
2551  =cut  =cut
2552    
2553  sub Max {  sub ChDir {
2554      # Get the parameters. Note that we prime the return value with the first parameter.      my ($dirName) = @_;
2555      my ($retVal, @values) = @_;      if (! -d $dirName) {
2556      # Loop through the remaining parameters, looking for the highest.          Confess("Cannot change to directory $dirName: no such directory.");
2557      for my $value (@values) {      } else {
2558          if ($value > $retVal) {          Trace("Changing to directory $dirName.") if T(File => 4);
2559              $retVal = $value;          my $okFlag = chdir $dirName;
2560            if (! $okFlag) {
2561                Confess("Error switching to directory $dirName.");
2562          }          }
2563      }      }
     # Return the maximum found.  
     return $retVal;  
2564  }  }
2565    
2566  =head3 AddToListMap  =head3 SetPermissions
2567    
2568        Tracer::SetPermissions($dirName, $group, $mask, %otherMasks);
2569    
2570  C<< Tracer::AddToListMap(\%hash, $key, $value1, $value2, ... valueN); >>  Set the permissions for a directory and all the files and folders inside it.
2571    In addition, the group ownership will be changed to the specified value.
2572    
2573  Add a key-value pair to a hash of lists. If no value exists for the key, a singleton list  This method is more vulnerable than most to permission and compatability
2574  is created for the key. Otherwise, the new value is pushed onto the list.  problems, so it does internal error recovery.
2575    
2576  =over 4  =over 4
2577    
2578  =item hash  =item dirName
2579    
2580  Reference to the target hash.  Name of the directory to process.
2581    
2582  =item key  =item group
2583    
2584  Key for which the value is to be added.  Name of the group to be assigned.
2585    
2586  =item value1, value2, ... valueN  =item mask
2587    
2588  List of values to add to the key's value list.  Permission mask. Bits that are C<1> in this mask will be ORed into the
2589    permission bits of any file or directory that does not already have them
2590    set to 1.
2591    
2592  =back  =item otherMasks
2593    
2594  =cut  Map of search patterns to permission masks. If a directory name matches
2595    one of the patterns, that directory and all its members and subdirectories
2596    will be assigned the new pattern. For example, the following would
2597    assign 0664 to most files, but would use 0777 for directories named C<tmp>.
2598    
2599  sub AddToListMap {      Tracer::SetPermissions($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;  
     }  
 }  
2600    
2601  =head3 DebugMode  The list is ordered, so the following would use 0777 for C<tmp1> and
2602    0666 for C<tmp>, C<tmp2>, or C<tmp3>.
2603    
2604  C<< if (Tracer::DebugMode) { ...code... } >>      Tracer::SetPermissions($dirName, 'fig', 01664, '^tmp1' => 0777,
2605                                                       '^tmp' => 0666);
2606    
2607  Return TRUE if debug mode has been turned on, else abort.  Note that the pattern matches are all case-insensitive, and only directory
2608    names are matched, not file names.
2609    
2610  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.  
2611    
2612  =cut  =cut
2613    
2614  sub DebugMode {  sub SetPermissions {
2615      # Declare the return variable.      # Get the parameters.
2616      my $retVal = 0;      my ($dirName, $group, $mask, @otherMasks) = @_;
2617      # Check the debug configuration.      # Set up for error recovery.
2618      my $password = CGI::cookie("DebugMode");      eval {
2619      my $encrypted = Digest::MD5::md5_hex($password);          # Switch to the specified directory.
2620      if ($encrypted eq "252dec43280e0c0d6a75ffcec486e61d") {          ChDir($dirName);
2621          $retVal = 1;          # Get the group ID.
2622            my $gid = getgrnam($group);
2623            # Get the mask for tracing.
2624            my $traceMask = sprintf("%04o", $mask) . "($mask)";
2625            Trace("Fixing permissions for directory $dirName using group $group($gid) and mask $traceMask.") if T(File => 2);
2626            my $fixCount = 0;
2627            my $lookCount = 0;
2628            # @dirs will be a stack of directories to be processed.
2629            my @dirs = (getcwd());
2630            while (scalar(@dirs) > 0) {
2631                # Get the current directory.
2632                my $dir = pop @dirs;
2633                # Check for a match to one of the specified directory names. To do
2634                # that, we need to pull the individual part of the name off of the
2635                # whole path.
2636                my $simpleName = $dir;
2637                if ($dir =~ m!/([^/]+)$!) {
2638                    $simpleName = $1;
2639                }
2640                Trace("Simple directory name for $dir is $simpleName.") if T(File => 4);
2641                # Search for a match.
2642                my $match = 0;
2643                my $i;
2644                for ($i = 0; $i < $#otherMasks && ! $match; $i += 2) {
2645                    my $pattern = $otherMasks[$i];
2646                    if ($simpleName =~ /$pattern/i) {
2647                        $match = 1;
2648                    }
2649                }
2650                # Find out if we have a match. Note we use $i-1 because the loop added 2
2651                # before terminating due to the match.
2652                if ($match && $otherMasks[$i-1] != $mask) {
2653                    # This directory matches one of the incoming patterns, and it's
2654                    # a different mask, so we process it recursively with that mask.
2655                    SetPermissions($dir, $group, $otherMasks[$i-1], @otherMasks);
2656      } else {      } else {
2657          # Here debug mode is off, so we generate an error.                  # Here we can process normally. Get all of the non-hidden members.
2658          Confess("Cannot use this facility without logging in.");                  my @submems = OpenDir($dir, 1);
2659                    for my $submem (@submems) {
2660                        # Get the full name.
2661                        my $thisMem = "$dir/$submem";
2662                        Trace("Checking member $thisMem.") if T(4);
2663                        $lookCount++;
2664                        if ($lookCount % 1000 == 0) {
2665                            Trace("$lookCount members examined. Current is $thisMem. Mask is $traceMask") if T(File => 3);
2666      }      }
2667      # Return the determination indicator.                      # Fix the group.
2668      return $retVal;                      chown -1, $gid, $thisMem;
2669                        # Insure this member is not a symlink.
2670                        if (! -l $thisMem) {
2671                            # Get its info.
2672                            my $fileInfo = stat $thisMem;
2673                            # Only proceed if we got the info. Otherwise, it's a hard link
2674                            # and we want to skip it anyway.
2675                            if ($fileInfo) {
2676                                my $fileMode = $fileInfo->mode;
2677                                if (($fileMode & $mask) != $mask) {
2678                                    # Fix this member.
2679                                    $fileMode |= $mask;
2680                                    chmod $fileMode, $thisMem;
2681                                    $fixCount++;
2682                                }
2683                                # If it's a subdirectory, stack it.
2684                                if (-d $thisMem) {
2685                                    push @dirs, $thisMem;
2686                                }
2687                            }
2688                        }
2689                    }
2690                }
2691            }
2692            Trace("$lookCount files and directories processed, $fixCount fixed.") if T(File => 2);
2693        };
2694        # Check for an error.
2695        if ($@) {
2696            Confess("SetPermissions error: $@");
2697  }  }
   
 =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;  
2698  }  }
2699    
2700  =head3 Pad  =head3 GetLine
2701    
2702  C<< my $paddedString = Tracer::Pad($string, $len, $left, $padChar); >>      my @data = Tracer::GetLine($handle);
2703    
2704  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.  
2705    
2706  =over 4  =over 4
2707    
2708  =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)  
2709    
2710  Character to use for padding. The default is a space.  Open file handle from which to read.
2711    
2712  =item RETURN  =item RETURN
2713    
2714  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
2715  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
2716    returned. If an empty line is read, a single list item consisting of a null
2717    string will be returned.
2718    
2719  =back  =back
2720    
2721  =cut  =cut
2722    
2723  sub Pad {  sub GetLine {
2724      # Get the parameters.      # Get the parameters.
2725      my ($string, $len, $left, $padChar) = @_;      my ($handle) = @_;
2726      # Compute the padding character.      # Declare the return variable.
2727      if (! defined $padChar) {      my @retVal = ();
2728          $padChar = " ";      Trace("File position is " . tell($handle) . ". EOF flag is " . eof($handle) . ".") if T(File => 4);
2729      }      # Read from the file.
2730      # Compute the number of spaces needed.      my $line = <$handle>;
2731      my $needed = $len - length $string;      # Only proceed if we found something.
2732      # Copy the string into the return variable.      if (defined $line) {
2733      my $retVal = $string;          # Remove the new-line. We are a bit over-cautious here because the file may be coming in via an
2734      # Only proceed if padding is needed.          # upload control and have a nonstandard EOL combination.
2735      if ($needed > 0) {          $line =~ s/(\r|\n)+$//;
2736          # Create the pad string.          # Here we do some fancy tracing to help in debugging complicated EOL marks.
2737          my $pad = $padChar x $needed;          if (T(File => 4)) {
2738          # Affix it to the return value.              my $escapedLine = $line;
2739          if ($left) {              $escapedLine =~ s/\n/\\n/g;
2740              $retVal = $pad . $retVal;              $escapedLine =~ s/\r/\\r/g;
2741                $escapedLine =~ s/\t/\\t/g;
2742                Trace("Line read: -->$escapedLine<--");
2743            }
2744            # If the line is empty, return a single empty string; otherwise, parse
2745            # it into fields.
2746            if ($line eq "") {
2747                push @retVal, "";
2748          } else {          } else {
2749              $retVal .= $pad;              push @retVal, split /\t/,$line;
2750          }          }
2751        } else {
2752            # Trace the reason the read failed.
2753            Trace("End of file: $!") if T(File => 3);
2754      }      }
2755      # Return the result.      # Return the result.
2756      return $retVal;      return @retVal;
2757  }  }
2758    
2759  =head3 EOF  =head3 PutLine
2760    
2761  This is a constant that is lexically greater than any useful string.      Tracer::PutLine($handle, \@fields, $eol);
2762    
2763  =cut  Write a line of data to a tab-delimited file. The specified field values will be
2764    output in tab-separated form, with a trailing new-line.
2765    
2766  sub EOF {  =over 4
     return "\xFF\xFF\xFF\xFF\xFF";  
 }  
2767    
2768  =head3 TICK  =item handle
2769    
2770  C<< my @results = TICK($commandString); >>  Output file handle.
2771    
2772  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  
2773    
2774      `./protein.cgi`  List of field values.
2775    
2776  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  
2777    
2778      TICK("./protein.cgi")  End-of-line character (default is "\n").
2779    
2780  it will work correctly in both environments.  =back
2781    
2782  =over 4  =cut
2783    
2784  =item commandString  sub PutLine {
2785        # Get the parameters.
2786        my ($handle, $fields, $eol) = @_;
2787        # Write the data.
2788        print $handle join("\t", @{$fields}) . ($eol || "\n");
2789    }
2790    
 The command string to pass to the system.  
2791    
2792  =item RETURN  =head3 PrintLine
2793    
2794  Returns the standard output from the specified command, as a list.      Tracer::PrintLine($line);
2795    
2796    Print a line of text with a trailing new-line.
2797    
2798    =over 4
2799    
2800    =item line
2801    
2802    Line of text to print.
2803    
2804  =back  =back
2805    
2806  =cut  =cut
2807  #: Return Type @;  
2808  sub TICK {  sub PrintLine {
2809      # Get the parameters.      # Get the parameters.
2810      my ($commandString) = @_;      my ($line) = @_;
2811      # Chop off the dot-slash if this is Windows.      # Print the line.
2812      if ($FIG_Config::win_mode) {      print "$line\n";
         $commandString =~ s!^\./!!;  
     }  
     # Activate the command and return the result.  
     return `$commandString`;  
2813  }  }
2814    
 =head3 ScriptSetup  
2815    
2816  C<< my ($cgi, $varHash) = ScriptSetup($noTrace); >>  =head2 Other Useful Methods
2817    
2818  Perform standard tracing and debugging setup for scripts. The value returned is  =head3 ParseParm
 the CGI object followed by a pre-built variable hash.  
2819    
2820  The C<Trace> query parameter is used to determine whether or not tracing is active and      my $listValue = Tracer::ParseParm($string);
2821  which trace modules (other than C<Tracer> itself) should be turned on. Specifying  
2822  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,
2823  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
2824  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.  
2825    
2826  =over 4  =over 4
2827    
2828  =item noTrace (optional)  =item string
2829    
2830  If specified, tracing will be suppressed. This is useful if the script wants to set up  Incoming string.
 tracing manually.  
2831    
2832  =item RETURN  =item RETURN
2833    
2834  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
2835  the output page.  was undefined.
2836    
2837  =back  =back
2838    
2839  =cut  =cut
2840    
2841  sub ScriptSetup {  sub ParseParm {
2842      # Get the parameters.      # Get the parameters.
2843      my ($noTrace) = @_;      my ($string) = @_;
2844      # Get the CGI query object.      # Declare the return variable.
2845      my $cgi = CGI->new();      my $retVal;
2846      # Set up tracing if it's not suppressed.      # Check for data.
2847      CGITrace($cgi) unless $noTrace;      if (defined $string) {
2848      # Create the variable hash.          # We have some, so split it into a list.
2849      my $varHash = { results => '' };          $retVal = [ split /\s*,\s*/, $string];
2850      # Return the query object and variable hash.      }
2851      return ($cgi, $varHash);      # Return the result.
2852        return $retVal;
2853    }
2854    
2855    =head3 Now
2856    
2857        my $string = Tracer::Now();
2858    
2859    Return a displayable time stamp containing the local time. Whatever format this
2860    method produces must be parseable by L</ParseDate>.
2861    
2862    =cut
2863    
2864    sub Now {
2865        return DisplayTime(time);
2866  }  }
2867    
2868  =head3 CGITrace  =head3 DisplayTime
2869    
2870  C<< Tracer::CGITrace($cgi); >>      my $string = Tracer::DisplayTime($time);
2871    
2872  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
2873    method produces must be parseable by L</ParseDate>.
2874    
2875  =over 4  =over 4
2876    
2877  =item cgi  =item time
2878    
2879    Time to display, in seconds since the epoch, or C<undef> if the time is unknown.
2880    
2881    =item RETURN
2882    
2883  Ths CGI query object for this script.  Returns a displayable time, or C<(n/a)> if the incoming time is undefined.
2884    
2885  =back  =back
2886    
2887  =cut  =cut
2888    
2889  sub CGITrace {  sub DisplayTime {
2890      # Get the parameters.      my ($time) = @_;
2891      my ($cgi) = @_;      my $retVal = "(n/a)";
2892      # Default to no tracing except errors.      if (defined $time) {
2893      my ($tracing, $dest) = ("0", "WARN");          my ($sec,$min,$hour,$mday,$mon,$year,$wday,$yday,$isdst) = localtime($time);
2894      # Check for emergency tracing.          $retVal = _p2($mon+1) . "/" . _p2($mday) . "/" . ($year + 1900) . " " .
2895      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));  
2896          }          }
2897      } 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 = $cgi->param('Trace') . " Tracer";  
2898      }      }
2899      # Setup the tracing we've determined from all the stuff above.  
2900      TSetup($tracing, $dest);  # Pad a number to 2 digits.
2901      # Trace the parameter and environment data.  sub _p2 {
2902      TraceParms($cgi);      my ($value) = @_;
2903        $value = "0$value" if ($value < 10);
2904        return $value;
2905  }  }
2906    
2907  =head3 EmergencyFileName  =head3 Escape
2908    
2909  C<< my $fileName = Tracer::EmergencyFileName($ip); >>      my $codedString = Tracer::Escape($realString);
2910    
2911  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
2912  the tracing information.  replaced by C<\n>, carriage returns will be deleted, and backslashes will be doubled. The
2913    result is to reverse the effect of L</UnEscape>.
2914    
2915  =over 4  =over 4
2916    
2917  =item ip  =item realString
2918    
2919  IP address of the user who wants tracing, as taken from the C<< $cgi->remote_host() >>  String to escape.
 method.  
2920    
2921  =item RETURN  =item RETURN
2922    
2923  Returns the name of the file to contain the emergency tracing information.  Escaped equivalent of the real string.
2924    
2925  =back  =back
2926    
2927  =cut  =cut
2928    
2929  sub EmergencyFileName {  sub Escape {
2930      # Get the parameters.      # Get the parameter.
2931      my ($ip) = @_;      my ($realString) = @_;
2932      # Compute the emergency tracing file name.      # Initialize the return variable.
2933      return "$FIG_Config::temp/Emergency$ip.txt";      my $retVal = "";
2934        # Loop through the parameter string, looking for sequences to escape.
2935        while (length $realString > 0) {
2936            # Look for the first sequence to escape.
2937            if ($realString =~ /^(.*?)([\n\t\r\\])/) {
2938                # Here we found it. The text preceding the sequence is in $1. The sequence
2939                # itself is in $2. First, move the clear text to the return variable.
2940                $retVal .= $1;
2941                # Strip the processed section off the real string.
2942                $realString = substr $realString, (length $2) + (length $1);
2943                # Get the matched character.
2944                my $char = $2;
2945                # If we have a CR, we are done.
2946                if ($char ne "\r") {
2947                    # It's not a CR, so encode the escape sequence.
2948                    $char =~ tr/\t\n/tn/;
2949                    $retVal .= "\\" . $char;
2950                }
2951            } else {
2952                # Here there are no more escape sequences. The rest of the string is
2953                # transferred unmodified.
2954                $retVal .= $realString;
2955                $realString = "";
2956            }
2957        }
2958        # Return the result.
2959        return $retVal;
2960  }  }
2961    
2962  =head3 EmergencyFileTarget  =head3 UnEscape
2963    
2964  C<< my $fileName = Tracer::EmergencyFileTarget($ip); >>      my $realString = Tracer::UnEscape($codedString);
2965    
2966  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
2967  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
2968    be deleted.
2969    
2970  =over 4  =over 4
2971    
2972  =item ip  =item codedString
2973    
2974  IP address of the user who wants tracing, as taken from the C<< $cgi->remote_host() >>  String to un-escape.
 method.  
2975    
2976  =item RETURN  =item RETURN
2977    
2978  Returns the name of the file to contain the emergency tracing information.  Returns a copy of the original string with the escape sequences converted to their actual
2979    values.
2980    
2981  =back  =back
2982    
2983  =cut  =cut
2984    
2985  sub EmergencyFileTarget {  sub UnEscape {
2986      # Get the parameters.      # Get the parameter.
2987      my ($ip) = @_;      my ($codedString) = @_;
2988      # Compute the emergency tracing file name.      # Initialize the return variable.
2989      return "$FIG_Config::temp/Emergency$ip.log";      my $retVal = "";
2990        # Only proceed if the incoming string is nonempty.
2991        if (defined $codedString) {
2992            # Loop through the parameter string, looking for escape sequences. We can't do
2993            # translating because it causes problems with the escaped slash. ("\\t" becomes
2994            # "\<tab>" no matter what we do.)
2995            while (length $codedString > 0) {
2996                # Look for the first escape sequence.
2997                if ($codedString =~ /^(.*?)\\(\\|n|t|r)/) {
2998                    # Here we found it. The text preceding the sequence is in $1. The sequence
2999                    # itself is in $2. First, move the clear text to the return variable.
3000                    $retVal .= $1;
3001                    $codedString = substr $codedString, (2 + length $1);
3002                    # Get the escape value.
3003                    my $char = $2;
3004                    # If we have a "\r", we are done.
3005                    if ($char ne 'r') {
3006                        # Here it's not an 'r', so we convert it.
3007                        $char =~ tr/\\tn/\\\t\n/;
3008                        $retVal .= $char;
3009                    }
3010                } else {
3011                    # Here there are no more escape sequences. The rest of the string is
3012                    # transferred unmodified.
3013                    $retVal .= $codedString;
3014                    $codedString = "";
3015                }
3016            }
3017        }
3018        # Return the result.
3019        return $retVal;
3020  }  }
3021    
3022  =head3 EmergencyTracingDest  =head3 Percent
3023    
3024  C<< my $dest = Tracer::EmergencyTracingDest($ip, $myDest); >>      my $percent = Tracer::Percent($number, $base);
3025    
3026  This method converts an emergency tracing destination to a real  Returns the percent of the base represented by the given number. If the base
3027  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.  
3028    
3029  =over 4  =over 4
3030    
3031  =item ip  =item number
3032    
3033  IP address of the user who wants tracing, as taken from the C<< $cgi->remote_host() >>  Percent numerator.
 method.  
3034    
3035  =item myDest  =item base
3036    
3037  Destination from the emergency tracing file.  Percent base.
3038    
3039  =item RETURN  =item RETURN
3040    
3041  Returns a destination that can be passed into L</TSetup>.  Returns the percentage of the base represented by the numerator.
3042    
3043  =back  =back
3044    
3045  =cut  =cut
3046    
3047  sub EmergencyTracingDest {  sub Percent {
3048      # Get the parameters.      # Get the parameters.
3049      my ($ip, $myDest) = @_;      my ($number, $base) = @_;
3050      # Declare the return variable.      # Declare the return variable.
3051      my $retVal;      my $retVal = 0;
3052      # Process according to the destination value.      # Compute the percent.
3053      if ($myDest eq 'FILE') {      if ($base != 0) {
3054          $retVal = ">" . EmergencyFileTarget($ip);          $retVal = $number * 100 / $base;
     } elsif ($myDest eq 'APPEND') {  
         $retVal = ">>" . EmergencyFileTarget($ip);  
     } else {  
         $retVal = $myDest;  
3055      }      }
3056      # Return the result.      # Return the result.
3057      return $retVal;      return $retVal;
3058  }  }
3059    
3060  =head3 Emergency  =head3 Constrain
3061    
3062  C<< Emergency($cgi, $hours, $dest, $level, @modules); >>      my $constrained = Constrain($value, $min, $max);
3063    
3064  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.  
3065    
3066  =over 4  =over 4
3067    
3068  =item cgi  =item value
   
 A CGI query object.  
3069    
3070  =item hours  Value to constrain.
   
 Number of hours to keep emergency tracing alive.  
3071    
3072  =item dest  =item min (optional)
3073    
3074  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.  
3075    
3076  =item level  =item max (optional)
3077    
3078  Tracing level. A higher level means more trace messages.  Maximum permissible value. If this parameter is undefined, no maximum constraint will be applied.
3079    
3080  =item modules  =item RETURN
3081    
3082  A list of the tracing modules to activate.  Returns the incoming value, constrained according to the other parameters.
3083    
3084  =back  =back
3085    
3086  =cut  =cut
3087    
3088  sub Emergency {  sub Constrain {
3089      # Get the parameters.      # Get the parameters.
3090      my ($cgi, $hours, $dest, $level, @modules) = @_;      my ($value, $min, $max) = @_;
3091      # Get the IP address.      # Declare the return variable.
3092      my $ip = EmergencyIP($cgi);      my $retVal = $value;
3093      # Create the emergency file.      # Apply the minimum constraint.
3094      my $specFile = EmergencyFileName($ip);      if (defined $min && $retVal < $min) {
3095      my $outHandle = Open(undef, ">$specFile");          $retVal = $min;
3096      print $outHandle join("\n",$hours, $dest, $level, @modules, "");      }
3097        # Apply the maximum constraint.
3098        if (defined $max && $retVal > $max) {
3099            $retVal = $max;
3100        }
3101        # Return the result.
3102        return $retVal;
3103  }  }
3104    
3105  =head3 EmergencyIP  =head3 Min
3106    
3107  C<< my $ip = EmergencyIP($cgi); >>      my $min = Min($value1, $value2, ... $valueN);
3108    
3109  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.  
3110    
3111  =over 4  =over 4
3112    
3113  =item cgi  =item $value1, $value2, ... $valueN
3114    
3115  CGI query object.  List of numbers to compare.
3116    
3117  =item RETURN  =item RETURN
3118    
3119  Returns the IP address to be used for labelling emergency tracing.  Returns the lowest number in the list.
3120    
3121  =back  =back
3122    
3123  =cut  =cut
3124    
3125  sub EmergencyIP {  sub Min {
3126      # Get the parameters.      # Get the parameters. Note that we prime the return value with the first parameter.
3127      my ($cgi) = @_;      my ($retVal, @values) = @_;
3128      # Return the result.      # Loop through the remaining parameters, looking for the lowest.
3129      return $cgi->remote_addr();      for my $value (@values) {
3130            if ($value < $retVal) {
3131                $retVal = $value;
3132            }
3133        }
3134        # Return the minimum found.
3135        return $retVal;
3136  }  }
3137    
3138    =head3 Max
3139    
3140  =head3 TraceParms      my $max = Max($value1, $value2, ... $valueN);
   
 C<< Tracer::TraceParms($cgi); >>  
3141    
3142  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.  
3143    
3144  =over 4  =over 4
3145    
3146  =item cgi  =item $value1, $value2, ... $valueN
3147    
3148  CGI query object containing the parameters to trace.  List of numbers to compare.
3149    
3150    =item RETURN
3151    
3152    Returns the highest number in the list.
3153    
3154  =back  =back
3155    
3156  =cut  =cut
3157    
3158  sub TraceParms {  sub Max {
3159      # Get the parameters.      # Get the parameters. Note that we prime the return value with the first parameter.
3160      my ($cgi) = @_;      my ($retVal, @values) = @_;
3161      if (T(CGI => 3)) {      # Loop through the remaining parameters, looking for the highest.
3162          # Here we want to trace the parameter data.      for my $value (@values) {
3163          my @names = $cgi->param;          if ($value > $retVal) {
3164          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}");  
3165          }          }
3166      }      }
3167        # Return the maximum found.
3168        return $retVal;
3169  }  }
3170    
3171  =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 ...  
3172    
3173      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", $varHash);  
3174    
3175  The idea here is that even if the script fails, you'll see trace messages and  Strip all line terminators off a string. This is necessary when dealing with files
3176  useful output.  that may have been transferred back and forth several times among different
3177    operating environments.
3178    
3179  =over 4  =over 4
3180    
3181  =item webData  =item line
3182    
3183  A string containing either the full web page to be written to the output or the  Line of text to be stripped.
 name of a template file from which the page is to be constructed. If the name  
 of a template file is specified, then the second parameter must be present;  
 otherwise, it must be absent.  
3184    
3185  =item varHash (optional)  =item RETURN
3186    
3187  If specified, then a reference to a hash mapping variable names for a template  The same line of text with all the line-ending characters chopped from the end.
 to their values. The template file will be read into memory, and variable markers  
 will be replaced by data in this hash reference.  
3188    
3189  =back  =back
3190    
3191  =cut  =cut
3192    
3193  sub ScriptFinish {  sub Strip {
3194      # Get the parameters.      # Get a copy of the parameter string.
3195      my ($webData, $varHash) = @_;      my ($string) = @_;
3196      # Check for a template file situation.      my $retVal = (defined $string ? $string : "");
3197      my $outputString;      # Strip the line terminator characters.
3198      if (defined $varHash) {      $retVal =~ s/(\r|\n)+$//g;
3199          # Here we have a template file. We need to determine the template type.      # Return the result.
3200          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 $outputString;  
3201  }  }
3202    
3203  =head3 Insure  =head3 Pad
3204    
3205  C<< Insure($dirName); >>      my $paddedString = Tracer::Pad($string, $len, $left, $padChar);
3206    
3207  Insure a directory is present.  Pad a string to a specified length. The pad character will be a
3208    space, and the padding will be on the right side unless specified
3209    in the third parameter.
3210    
3211  =over 4  =over 4
3212    
3213  =item dirName  =item string
   
 Name of the directory to check. If it does not exist, it will be created.  
3214    
3215  =back  String to be padded.
3216    
3217  =cut  =item len
3218    
3219  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: $@");  
         }  
     }  
 }  
3220    
3221  =head3 ChDir  =item left (optional)
3222    
3223  C<< ChDir($dirName); >>  TRUE if the string is to be left-padded; otherwise it will be padded on the right.
3224    
3225  Change to the specified directory.  =item padChar (optional)
3226    
3227  =over 4  Character to use for padding. The default is a space.
3228    
3229  =item dirName  =item RETURN
3230    
3231  Name of the directory to which we want to change.  Returns a copy of the original string with the pad character added to the
3232    specified end so that it achieves the desired length.
3233    
3234  =back  =back
3235    
3236  =cut  =cut
3237    
3238  sub ChDir {  sub Pad {
3239      my ($dirName) = @_;      # Get the parameters.
3240      if (! -d $dirName) {      my ($string, $len, $left, $padChar) = @_;
3241          Confess("Cannot change to directory $dirName: no such directory.");      # Compute the padding character.
3242        if (! defined $padChar) {
3243            $padChar = " ";
3244        }
3245        # Compute the number of spaces needed.
3246        my $needed = $len - length $string;
3247        # Copy the string into the return variable.
3248        my $retVal = $string;
3249        # Only proceed if padding is needed.
3250        if ($needed > 0) {
3251            # Create the pad string.
3252            my $pad = $padChar x $needed;
3253            # Affix it to the return value.
3254            if ($left) {
3255                $retVal = $pad . $retVal;
3256      } else {      } else {
3257          Trace("Changing to directory $dirName.") if T(4);              $retVal .= $pad;
         my $okFlag = chdir $dirName;  
         if (! $okFlag) {  
             Confess("Error switching to directory $dirName.");  
3258          }          }
3259      }      }
3260        # Return the result.
3261        return $retVal;
3262  }  }
3263    
3264  =head3 SendSMS  =head3 EOF
3265    
3266    This is a constant that is lexically greater than any useful string.
3267    
3268    =cut
3269    
3270  C<< my $msgID = Tracer::SendSMS($phoneNumber, $msg); >>  sub EOF {
3271        return "\xFF\xFF\xFF\xFF\xFF";
3272    }
3273    
3274  Send a text message to a phone number using Clickatell. The FIG_Config file must contain the  =head3 TICK
 user name, password, and API ID for the relevant account in the hash reference variable  
 I<$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  
3275    
3276      $phone =  { user => 'BruceTheHumanPet',      my @results = TICK($commandString);
                 password => 'silly',  
                 api_id => '2561022' };  
3277    
3278  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
3279  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.  
3280    
3281  The message ID will be returned if successful, and C<undef> if an error occurs.      `./protein.cgi`
3282    
3283  =over 4  from inside a CGI script, it would work fine in Unix, but would issue an error message
3284    in Windows complaining that C<'.'> is not a valid command. If instead you code
3285    
3286  =item phoneNumber      TICK("./protein.cgi")
3287    
3288  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".  
3289    
3290  =item msg  =over 4
3291    
3292  Message to send to the specified phone.  =item commandString
3293    
3294    The command string to pass to the system.
3295    
3296  =item RETURN  =item RETURN
3297    
3298  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.
3299    
3300  =back  =back
3301    
3302  =cut  =cut
3303    #: Return Type @;
3304  sub SendSMS {  sub TICK {
3305      # Get the parameters.      # Get the parameters.
3306      my ($phoneNumber, $msg) = @_;      my ($commandString) = @_;
3307      # Declare the return variable. If we do not change it, C<undef> will be returned.      # Chop off the dot-slash if this is Windows.
3308      my $retVal;      if ($FIG_Config::win_mode) {
3309      # 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);  
             }  
         }  
3310      }      }
3311      # Return the result.      # Activate the command and return the result.
3312      return $retVal;      return `$commandString`;
3313  }  }
3314    
3315    
3316  =head3 CommaFormat  =head3 CommaFormat
3317    
3318  C<< my $formatted = Tracer::CommaFormat($number); >>      my $formatted = Tracer::CommaFormat($number);
3319    
3320  Insert commas into a number.  Insert commas into a number.
3321    
# Line 2503  Line 3348 
3348      # Return the result.      # Return the result.
3349      return $retVal;      return $retVal;
3350  }  }
 =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.  
3351    
 =over 4  
3352    
3353  =item dirName  =head3 CompareLists
3354    
3355  Name of the directory to process.      my ($inserted, $deleted) = Tracer::CompareLists(\@newList, \@oldList, $keyIndex);
3356    
3357  =item group  Compare two lists of tuples, and return a hash analyzing the differences. The lists
3358    are presumed to be sorted alphabetically by the value in the $keyIndex column.
3359    The return value contains a list of items that are only in the new list
3360    (inserted) and only in the old list (deleted).
3361    
3362  Name of the group to be assigned.  =over 4
3363    
3364  =item mask  =item newList
3365    
3366  Permission mask. Bits that are C<1> in this mask will be ORed into the  Reference to a list of new tuples.
 permission bits of any file or directory that does not already have them  
 set to 1.  
3367    
3368  =item otherMasks  =item oldList
3369    
3370  Map of search patterns to permission masks. If a directory name matches  Reference to a list of old tuples.
 one of the patterns, that directory and all its members and subdirectories  
 will be assigned the new pattern. For example, the following would  
 assign 01664 to most files, but would use 01777 for directories named C<tmp>.  
3371    
3372      Tracer::SetPermissions($dirName, 'fig', 01664, '^tmp$' => 01777);  =item keyIndex (optional)
3373    
3374  The list is ordered, so the following would use 0777 for C<tmp1> and  Index into each tuple of its key field. The default is 0.
 0666 for C<tmp>, C<tmp2>, or C<tmp3>.  
3375    
3376      Tracer::SetPermissions($dirName, 'fig', 01664, '^tmp1' => 0777,  =item RETURN
                                                    '^tmp' => 0666);  
3377    
3378  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
3379  names are matched, not file names.  list (inserted) followed by a reference to the list of items that are only in the old
3380    list (deleted).
3381    
3382  =back  =back
3383    
3384  =cut  =cut
3385    
3386  sub SetPermissions {  sub CompareLists {
3387      # Get the parameters.      # Get the parameters.
3388      my ($dirName, $group, $mask, @otherMasks) = @_;      my ($newList, $oldList, $keyIndex) = @_;
3389      # Set up for error recovery.      if (! defined $keyIndex) {
3390      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;  
                 }  
3391              }              }
3392              # Check for a match. Note we use $i-1 because the loop added 2      # Declare the return variables.
3393              # before terminating due to the match.      my ($inserted, $deleted) = ([], []);
3394              if ($match && $otherMasks[$i-1] != $mask) {      # Loop through the two lists simultaneously.
3395                  # This directory matches one of the incoming patterns, and it's      my ($newI, $oldI) = (0, 0);
3396                  # a different mask, so we process it recursively with that mask.      my ($newN, $oldN) = (scalar @{$newList}, scalar @{$oldList});
3397                  SetPermissions($dir, $group, $otherMasks[$i-1], @otherMasks);      while ($newI < $newN || $oldI < $oldN) {
3398            # Get the current object in each list. Note that if one
3399            # of the lists is past the end, we'll get undef.
3400            my $newItem = $newList->[$newI];
3401            my $oldItem = $oldList->[$oldI];
3402            if (! defined($newItem) || defined($oldItem) && $newItem->[$keyIndex] gt $oldItem->[$keyIndex]) {
3403                # The old item is not in the new list, so mark it deleted.
3404                push @{$deleted}, $oldItem;
3405                $oldI++;
3406            } elsif (! defined($oldItem) || $oldItem->[$keyIndex] gt $newItem->[$keyIndex]) {
3407                # The new item is not in the old list, so mark it inserted.
3408                push @{$inserted}, $newItem;
3409                $newI++;
3410              } else {              } else {
3411                  # Here we can process normally. Get all of the non-hidden members.              # The item is in both lists, so push forward.
3412                  my @submems = OpenDir($dir, 1);              $oldI++;
3413                  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) {