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revision 1.69, Mon Oct 2 02:59:47 2006 UTC revision 1.112, Wed Oct 1 03:23:40 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) {
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        # Create a parsing hash from the options hash. The parsing hash
1697        # contains the default values rather than the default value
1698        # and the description. While we're at it, we'll memorize the
1699        # length of the longest option name.
1700        my $longestName = 0;
1701        my %parseOptions = ();
1702        for my $key (keys %{$options}) {
1703            if (length $key > $longestName) {
1704                $longestName = length $key;
1705            }
1706            $parseOptions{$key} = $options->{$key}->[0];
1707        }
1708        # Parse the command line.
1709        my ($retOptions, @retParameters) = ParseCommand(\%parseOptions, @argv);
1710        # Get the logfile suffix.
1711        my $suffix = $retOptions->{user};
1712        # Check for background mode.
1713        if ($retOptions->{background}) {
1714            my $outFileName = "$FIG_Config::temp/out$suffix$$.log";
1715            my $errFileName = "$FIG_Config::temp/err$suffix$$.log";
1716            open STDOUT, ">$outFileName";
1717            open STDERR, ">$errFileName";
1718            # Check for phone support. If we have phone support and a phone number,
1719            # we want to turn it on.
1720            if ($ENV{PHONE} && defined($FIG_Config::phone)) {
1721                $retOptions->{phone} = $ENV{PHONE};
1722            }
1723        }
1724        # Now we want to set up tracing. First, we need to know if the user
1725        # wants emergency tracing.
1726        if ($retOptions->{trace} eq 'E') {
1727            ETracing($retOptions->{user});
1728        } else {
1729            # Here the tracing is controlled from the command line.
1730            my @cats = @{$categories};
1731            if ($retOptions->{sql}) {
1732                push @cats, "SQL";
1733            }
1734            if ($retOptions->{warn}) {
1735                push @cats, "Feed";
1736            }
1737            # Add the default categories.
1738            push @cats, "Tracer";
1739            # Next, we create the category string by joining the categories.
1740            my $cats = join(" ", @cats);
1741            # Check to determine whether or not the caller wants to turn off tracing
1742            # to the standard output.
1743            my $traceLevel = $retOptions->{trace};
1744            my $textOKFlag = 1;
1745            if ($traceLevel =~ /^(.)-/) {
1746                $traceLevel = $1;
1747                $textOKFlag = 0;
1748            }
1749            # Now we set up the trace mode.
1750            my $traceMode;
1751            # Verify that we can open a file in the FIG temporary directory.
1752            my $traceFileName = "$FIG_Config::temp/trace$suffix.log";
1753            my $traceFileSpec = ($retOptions->{forked} ? ">>$traceFileName" : ">$traceFileName");
1754            if (open TESTTRACE, "$traceFileSpec") {
1755                # Here we can trace to a file.
1756                $traceMode = ">>$traceFileName";
1757                if ($textOKFlag) {
1758                    # Echo to standard output if the text-OK flag is set.
1759                    $traceMode = "+$traceMode";
1760                }
1761                # Close the test file.
1762                close TESTTRACE;
1763            } else {
1764                # Here we can't trace to a file. Complain about this.
1765                warn "Could not open trace file $traceFileName: $!\n";
1766                # We trace to the standard output if it's
1767                # okay, and the error log otherwise.
1768                if ($textOKFlag) {
1769                    $traceMode = "TEXT";
1770                } else {
1771                    $traceMode = "WARN";
1772                }
1773            }
1774            # Now set up the tracing.
1775            TSetup("$traceLevel $cats", $traceMode);
1776        }
1777        # Check for the "help" option. If it is specified, dump the command-line
1778        # options and exit the program.
1779        if ($retOptions->{help}) {
1780            $0 =~ m#[/\\](\w+)(\.pl)?$#i;
1781            print "$1 [options] $parmHelp\n";
1782            for my $key (sort keys %{$options}) {
1783                my $name = Pad($key, $longestName, 0, ' ');
1784                my $desc = $options->{$key}->[1];
1785                if ($options->{$key}->[0]) {
1786                    $desc .= " (default " . $options->{$key}->[0] . ")";
1787                }
1788                print "  $name $desc\n";
1789            }
1790            exit(0);
1791        }
1792        # Trace the options, if applicable.
1793        if (T(3)) {
1794            my @parms = grep { $retOptions->{$_} } keys %{$retOptions};
1795            Trace("Selected options: " . join(", ", sort @parms) . ".");
1796        }
1797        # Return the parsed parameters.
1798        return ($retOptions, @retParameters);
1799  }  }
1800    
1801  =head3 ReadOptions  =head3 ReadOptions
1802    
1803  C<< my %options = Tracer::ReadOptions($fileName); >>      my %options = Tracer::ReadOptions($fileName);
1804    
1805  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
1806  format  format
# Line 855  Line 1861 
1861    
1862  =head3 GetOptions  =head3 GetOptions
1863    
1864  C<< Tracer::GetOptions(\%defaults, \%options); >>      Tracer::GetOptions(\%defaults, \%options);
1865    
1866  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
1867  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 1870 
1870    
1871  Consider the following example.  Consider the following example.
1872    
1873  C<< my $optionTable = GetOptions({ dbType => 'mySQL', trace => 0 }, $options); >>      my $optionTable = GetOptions({ dbType => 'mySQL', trace => 0 }, $options);
1874    
1875  In this example, the variable B<$options> is expected to contain at most two options-- B<dbType> and  In this example, the variable B<$options> is expected to contain at most two options-- B<dbType> and
1876  B<trace>. The default database type is C<mySQL> and the default trace level is C<0>. If the value of  B<trace>. The default database type is C<mySQL> and the default trace level is C<0>. If the value of
# Line 872  Line 1878 
1878  the trace level will remain at 0. If B<$options> is undefined, then the database type and trace level  the trace level will remain at 0. If B<$options> is undefined, then the database type and trace level
1879  will remain C<mySQL> and C<0>. If, on the other hand, B<$options> is defined as  will remain C<mySQL> and C<0>. If, on the other hand, B<$options> is defined as
1880    
1881  C<< {databaseType => 'Oracle'} >>      {databaseType => 'Oracle'}
1882    
1883  an error will occur because the B<databaseType> option does not exist.  an error will occur because the B<databaseType> option does not exist.
1884    
# Line 916  Line 1922 
1922    
1923  =head3 MergeOptions  =head3 MergeOptions
1924    
1925  C<< Tracer::MergeOptions(\%table, \%defaults); >>      Tracer::MergeOptions(\%table, \%defaults);
1926    
1927  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
1928  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 1954 
1954      }      }
1955  }  }
1956    
1957  =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); >>  
1958    
1959  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  
1960    
1961  =item category  Convert an option hash into a command-line string. This will not
1962    necessarily be the same text that came in, but it will nonetheless
1963  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.  
1964    
1965  =item traceLevel  =over 4
1966    
1967  Relevant tracing level.  =item options
1968    
1969    Reference to a hash of options to convert into an option string.
1970    
1971  =item RETURN  =item RETURN
1972    
1973  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
1974    parsed by L</StandardSetup>.
1975    
1976  =back  =back
1977    
1978  =cut  =cut
1979    
1980  sub T {  sub UnparseOptions {
     # Declare the return variable.  
     my $retVal = 0;  
     # Only proceed if tracing is turned on.  
     if ($Destination ne "NONE") {  
1981          # Get the parameters.          # Get the parameters.
1982          my ($category, $traceLevel) = @_;      my ($options) = @_;
1983          if (!defined $traceLevel) {      # The option segments will be put in here.
1984              # Here we have no category, so we need to get the calling package.      my @retVal = ();
1985              # The calling package is normally the first parameter. If it is      # Loop through the options.
1986              # omitted, the first parameter will be the tracelevel. So, the      for my $key (keys %$options) {
1987              # first thing we do is shift the so-called category into the          # Get the option value.
1988              # $traceLevel variable where it belongs.          my $value = $options->{$key};
1989              $traceLevel = $category;          # Only use it if it's nonempty.
1990              my ($package, $fileName, $line) = caller;          if (defined $value && $value ne "") {
1991              # If there is no calling package, we default to "main".              my $segment = "--$key=$value";
1992              if (!$package) {              # Quote it if necessary.
1993                  $category = "main";              if ($segment =~ /[ |<>*]/) {
1994              } else {                  $segment = '"' . $segment . '"';
                 $category = $package;  
             }  
1995          }          }
1996          # Save the category name.              # Add it to the return list.
1997          $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.");  
1998          }          }
         $retVal = ($traceLevel <= $TraceLevel && ($AllTrace || exists $Categories{$category}));  
1999      }      }
2000      # Return the computed result.      # Return the result.
2001      return $retVal;      return join(" ", @retVal);
2002  }  }
2003    
2004  =head3 ParseCommand  =head3 ParseCommand
2005    
2006  C<< my ($options, @arguments) = Tracer::ParseCommand(\%optionTable, @inputList); >>      my ($options, @arguments) = Tracer::ParseCommand(\%optionTable, @inputList);
2007    
2008  Parse a command line consisting of a list of parameters. The initial parameters may be option  Parse a command line consisting of a list of parameters. The initial parameters may be option
2009  specifiers of the form C<->I<option> or C<->I<option>C<=>I<value>. The options are stripped  specifiers of the form C<->I<option> or C<->I<option>C<=>I<value>. The options are stripped
2010  off and merged into a table of default options. The remainder of the command line is  off and merged into a table of default options. The remainder of the command line is
2011  returned as a list of positional arguments. For example, consider the following invocation.  returned as a list of positional arguments. For example, consider the following invocation.
2012    
2013  C<< my ($options, @arguments) = ParseCommand({ errors => 0, logFile => 'trace.log'}, @words); >>      my ($options, @arguments) = ParseCommand({ errors => 0, logFile => 'trace.log'}, @words);
2014    
2015  In this case, the list @words will be treated as a command line. There are two options available,  In this case, the list @words will be treated as a command line and there are two options available,
2016  B<errors> and B<logFile>. If @words has the following format  B<errors> and B<logFile>. If @words has the following format
2017    
2018  C<< -logFile=error.log apple orange rutabaga >>      -logFile=error.log apple orange rutabaga
2019    
2020  then at the end of the invocation, C<$options> will be  then at the end of the invocation, C<$options> will be
2021    
2022  C<< { errors => 0, logFile => 'error.log' } >>      { errors => 0, logFile => 'error.log' }
2023    
2024  and C<@arguments> will contain  and C<@arguments> will contain
2025    
2026  C<< apple orange rutabaga >>      apple orange rutabaga
2027    
2028  The parser allows for some escape sequences. See L</UnEscape> for a description. There is no  The parser allows for some escape sequences. See L</UnEscape> for a description. There is no
2029  support for quote characters.  support for quote characters. Options can be specified with single or double hyphens.
2030    
2031  =over 4  =over 4
2032    
# Line 1119  Line 2051 
2051      my ($optionTable, @inputList) = @_;      my ($optionTable, @inputList) = @_;
2052      # Process any options in the input list.      # Process any options in the input list.
2053      my %overrides = ();      my %overrides = ();
2054      while ((@inputList > 0) && ($inputList[0] =~ /^-/)) {      while ((@inputList > 0) && ($inputList[0] =~ /^--?/)) {
2055          # Get the current option.          # Get the current option.
2056          my $arg = shift @inputList;          my $arg = shift @inputList;
2057          # Pull out the option name.          # Pull out the option name.
2058          $arg =~ /^-([^=]*)/g;          $arg =~ /^--?([^=]*)/g;
2059          my $name = $1;          my $name = $1;
2060          # Check for an option value.          # Check for an option value.
2061          if ($arg =~ /\G=(.*)$/g) {          if ($arg =~ /\G=(.*)$/g) {
# Line 1145  Line 2077 
2077      return ($optionTable, @retVal);      return ($optionTable, @retVal);
2078  }  }
2079    
 =head3 Escape  
2080    
2081  C<< my $codedString = Tracer::Escape($realString); >>  =head2 File Utility Methods
2082    
2083  Escape a string for use in a command length. Tabs will be replaced by C<\t>, new-lines  =head3 GetFile
2084  replaced by C<\n>, carriage returns will be deleted, and backslashes will be doubled. The  
2085  result is to reverse the effect of L</UnEscape>.      my @fileContents = Tracer::GetFile($fileName);
2086    
2087        or
2088    
2089        my $fileContents = Tracer::GetFile($fileName);
2090    
2091    Return the entire contents of a file. In list context, line-ends are removed and
2092    each line is a list element. In scalar context, line-ends are replaced by C<\n>.
2093    
2094  =over 4  =over 4
2095    
2096  =item realString  =item fileName
2097    
2098  String to escape.  Name of the file to read.
2099    
2100  =item RETURN  =item RETURN
2101    
2102  Escaped equivalent of the real string.  In a list context, returns the entire file as a list with the line terminators removed.
2103    In a scalar context, returns the entire file as a string. If an error occurs opening
2104    the file, an empty list will be returned.
2105    
2106  =back  =back
2107    
2108  =cut  =cut
2109    
2110  sub Escape {  sub GetFile {
2111      # Get the parameter.      # Get the parameters.
2112      my ($realString) = @_;      my ($fileName) = @_;
2113      # Initialize the return variable.      # Declare the return variable.
2114      my $retVal = "";      my @retVal = ();
2115      # Loop through the parameter string, looking for sequences to escape.      # Open the file for input.
2116      while (length $realString > 0) {      my $handle = Open(undef, "<$fileName");
2117          # Look for the first sequence to escape.      # Read the whole file into the return variable, stripping off any terminator
2118          if ($realString =~ /^(.*?)([\n\t\r\\])/) {      # characters.
2119              # Here we found it. The text preceding the sequence is in $1. The sequence      my $lineCount = 0;
2120              # itself is in $2. First, move the clear text to the return variable.      while (my $line = <$handle>) {
2121              $retVal .= $1;          $lineCount++;
2122              # Strip the processed section off the real string.          $line = Strip($line);
2123              $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;  
2124              }              }
2125        # Close it.
2126        close $handle;
2127        my $actualLines = @retVal;
2128        Trace("$actualLines lines read from file $fileName.") if T(File => 2);
2129        # Return the file's contents in the desired format.
2130        if (wantarray) {
2131            return @retVal;
2132          } else {          } else {
2133              # Here there are no more escape sequences. The rest of the string is          return join "\n", @retVal;
             # transferred unmodified.  
             $retVal .= $realString;  
             $realString = "";  
         }  
2134      }      }
     # Return the result.  
     return $retVal;  
2135  }  }
2136    
2137  =head3 UnEscape  =head3 PutFile
2138    
2139  C<< my $realString = Tracer::UnEscape($codedString); >>      Tracer::PutFile($fileName, \@lines);
2140    
2141  Replace escape sequences with their actual equivalents. C<\t> will be replaced by  Write out a file from a list of lines of text.
 a tab, C<\n> by a new-line character, and C<\\> by a backslash. C<\r> codes will  
 be deleted.  
2142    
2143  =over 4  =over 4
2144    
2145  =item codedString  =item fileName
2146    
2147  String to un-escape.  Name of the output file.
2148    
2149  =item RETURN  =item lines
2150    
2151  Returns a copy of the original string with the escape sequences converted to their actual  Reference to a list of text lines. The lines will be written to the file in order, with trailing
2152  values.  new-line characters. Alternatively, may be a string, in which case the string will be written without
2153    modification.
2154    
2155  =back  =back
2156    
2157  =cut  =cut
2158    
2159  sub UnEscape {  sub PutFile {
2160      # Get the parameter.      # Get the parameters.
2161      my ($codedString) = @_;      my ($fileName, $lines) = @_;
2162      # Initialize the return variable.      # Open the output file.
2163      my $retVal = "";      my $handle = Open(undef, ">$fileName");
2164      # Only proceed if the incoming string is nonempty.      # Count the lines written.
2165      if (defined $codedString) {      if (ref $lines ne 'ARRAY') {
2166          # Loop through the parameter string, looking for escape sequences. We can't do          # Here we have a scalar, so we write it raw.
2167          # translating because it causes problems with the escaped slash. ("\\t" becomes          print $handle $lines;
2168          # "\<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;  
                 }  
2169              } else {              } else {
2170                  # Here there are no more escape sequences. The rest of the string is          # Write the lines one at a time.
2171                  # transferred unmodified.          my $count = 0;
2172                  $retVal .= $codedString;          for my $line (@{$lines}) {
2173                  $codedString = "";              print $handle "$line\n";
2174              }              $count++;
2175          }          }
2176            Trace("$count lines put to file $fileName.") if T(File => 3);
2177      }      }
2178      # Return the result.      # Close the output file.
2179      return $retVal;      close $handle;
2180  }  }
2181    
2182  =head3 ParseRecord  =head3 ParseRecord
2183    
2184  C<< my @fields = Tracer::ParseRecord($line); >>      my @fields = Tracer::ParseRecord($line);
2185    
2186  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
2187  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 2226 
2226    
2227  =head3 Merge  =head3 Merge
2228    
2229  C<< my @mergedList = Tracer::Merge(@inputList); >>      my @mergedList = Tracer::Merge(@inputList);
2230    
2231  Sort a list of strings and remove duplicates.  Sort a list of strings and remove duplicates.
2232    
# Line 1339  Line 2258 
2258              # Find out how many elements duplicate the current entry.              # Find out how many elements duplicate the current entry.
2259              my $j = $i + 1;              my $j = $i + 1;
2260              my $dup1 = $i + 1;              my $dup1 = $i + 1;
2261              while ($j < @inputList && $inputList[$j] eq $thisEntry) { $j++; };              while ($j < @inputList && $inputList[$j] eq $thisEntry) { $j++; };
2262              # If the number is nonzero, splice out the duplicates found.              # If the number is nonzero, splice out the duplicates found.
2263              if ($j > $dup1) {              if ($j > $dup1) {
2264                  splice @inputList, $dup1, $j - $dup1;                  splice @inputList, $dup1, $j - $dup1;
2265              }              }
2266              # 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
2267              # at position $i. We push $i forward one position and start again.              # at position $i. We push $i forward one position and start again.
2268              $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;  
2269      }      }
     # Close it.  
     close $handle;  
     my $actualLines = @retVal;  
     # Return the file's contents in the desired format.  
     if (wantarray) {  
         return @retVal;  
     } else {  
         return join "\n", @retVal;  
2270      }      }
2271        # Return the merged list.
2272        return @inputList;
2273  }  }
2274    
2275  =head3 PutFile  =head3 Open
2276    
2277  C<< Tracer::PutFile($fileName, \@lines); >>      my $handle = Open($fileHandle, $fileSpec, $message);
2278    
2279  Write out a file from a list of lines of text.  Open a file.
2280    
2281  =over 4  The I<$fileSpec> is essentially the second argument of the PERL C<open>
2282    function. The mode is specified using Unix-like shell information. So, for
2283    example,
2284    
2285  =item fileName      Open(\*LOGFILE, '>>/usr/spool/news/twitlog', "Could not open twit log.");
2286    
2287  Name of the output file.  would open for output appended to the specified file, and
2288    
2289  =item lines      Open(\*DATASTREAM, "| sort -u >$outputFile", "Could not open $outputFile.");
2290    
2291  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
2292  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,
2293  modification.  code as follows.
2294    
2295  =back      my $logFile = Open(undef, '>>/usr/spool/news/twitlog', "Could not open twit log.");
2296    
2297  =cut  The I<$message> parameter is used if the open fails. If it is set to C<0>, then
2298    the open returns TRUE if successful and FALSE if an error occurred. Otherwise, a
2299    failed open will throw an exception and the third parameter will be used to construct
2300    an error message. If the parameter is omitted, a standard message is constructed
2301    using the file spec.
2302    
2303  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;  
 }  
2304    
2305  =head3 QTrace  Note that the mode characters are automatically cleaned from the file name.
2306    The actual error message from the file system will be captured and appended to the
2307    message in any case.
2308    
2309  C<< my $data = QTrace($format); >>      Could not open "/usr/spool/news/twitlog": file not found.
2310    
2311  Return the queued trace data in the specified format.  In some versions of PERL the only error message we get is a number, which
2312    corresponds to the C++ C<errno> value.
2313    
2314        Could not open "/usr/spool/news/twitlog": 6.
2315    
2316  =over 4  =over 4
2317    
2318  =item format  =item fileHandle
2319    
2320  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
2321    and returned as the value of this method.
2322    
2323    =item fileSpec
2324    
2325    File name and mode, as per the PERL C<open> function.
2326    
2327    =item message (optional)
2328    
2329    Error message to use if the open fails. If omitted, a standard error message
2330    will be generated. In either case, the error information from the file system
2331    is appended to the message. To specify a conditional open that does not throw
2332    an error if it fails, use C<0>.
2333    
2334    =item RETURN
2335    
2336    Returns the name of the file handle assigned to the file, or C<undef> if the
2337    open failed.
2338    
2339  =back  =back
2340    
2341  =cut  =cut
2342    
2343  sub QTrace {  sub Open {
2344      # Get the parameter.      # Get the parameters.
2345      my ($format) = @_;      my ($fileHandle, $fileSpec, $message) = @_;
2346      # Create the return variable.      # Attempt to open the file.
2347      my $retVal = "";      my $rv = open $fileHandle, $fileSpec;
2348      # Only proceed if there is an actual queue.      # If the open failed, generate an error message.
2349      if (@Queue) {      if (! $rv) {
2350          # Process according to the format.          # Save the system error message.
2351          if ($format =~ m/^HTML$/i) {          my $sysMessage = $!;
2352              # Convert the queue into an HTML list.          # See if we need a default message.
2353              $retVal = "<ul>\n";          if (!$message) {
2354              for my $line (@Queue) {              # Clean any obvious mode characters and leading spaces from the
2355                  my $escapedLine = CGI::escapeHTML($line);              # filename.
2356                  $retVal .= "<li>$escapedLine</li>\n";              my ($fileName) = FindNamePart($fileSpec);
2357              }              $message = "Could not open \"$fileName\"";
             $retVal .= "</ul>\n";  
         } elsif ($format =~ m/^TEXT$/i) {  
             # Convert the queue into a list of text lines.  
             $retVal = join("\n", @Queue) . "\n";  
2358          }          }
2359          # Clear the queue.          # Terminate with an error using the supplied message and the
2360          @Queue = ();          # error message from the file system.
2361            Confess("$message: $!");
2362      }      }
2363      # Return the formatted list.      # Return the file handle.
2364      return $retVal;      return $fileHandle;
2365  }  }
2366    
2367  =head3 Confess  =head3 FindNamePart
2368    
2369  C<< Confess($message); >>      my ($fileName, $start, $len) = Tracer::FindNamePart($fileSpec);
2370    
2371  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  
2372    
2373  C<< Assert($recNum >= 0) || Confess("Invalid record number $recNum."); >>  A file specification is the string passed to an C<open> call. It specifies the file
2374    mode and name. In a truly complex situation, it can specify a pipe sequence. This
2375    method assumes that the file name is whatever follows the first angle bracket
2376    sequence.  So, for example, in the following strings the file name is
2377    C</usr/fig/myfile.txt>.
2378    
2379  Will abort the program with a stack trace if the value of C<$recNum> is negative.      >>/usr/fig/myfile.txt
2380        </usr/fig/myfile.txt
2381        | sort -u > /usr/fig/myfile.txt
2382    
2383    If the method cannot find a file name using its normal methods, it will return the
2384    whole incoming string.
2385    
2386  =over 4  =over 4
2387    
2388  =item message  =item fileSpec
2389    
2390  Message to include in the trace.  File specification string from which the file name is to be extracted.
2391    
2392    =item RETURN
2393    
2394    Returns a three-element list. The first element contains the file name portion of
2395    the specified string, or the whole string if a file name cannot be found via normal
2396    methods. The second element contains the start position of the file name portion and
2397    the third element contains the length.
2398    
2399  =back  =back
2400    
2401  =cut  =cut
2402    #: Return Type $;
2403  sub Confess {  sub FindNamePart {
2404      # Get the parameters.      # Get the parameters.
2405      my ($message) = @_;      my ($fileSpec) = @_;
2406      # Trace the call stack.      # Default to the whole input string.
2407      Cluck($message);      my ($retVal, $pos, $len) = ($fileSpec, 0, length $fileSpec);
2408      # Abort the program.      # Parse out the file name if we can.
2409      croak(">>> $message");      if ($fileSpec =~ m/(<|>>?)(.+?)(\s*)$/) {
2410            $retVal = $2;
2411            $len = length $retVal;
2412            $pos = (length $fileSpec) - (length $3) - $len;
2413        }
2414        # Return the result.
2415        return ($retVal, $pos, $len);
2416  }  }
2417    
2418  =head3 Assert  =head3 OpenDir
2419    
2420  C<< Assert($condition1, $condition2, ... $conditionN); >>      my @files = OpenDir($dirName, $filtered, $flag);
2421    
2422  Return TRUE if all the conditions are true. This method can be used in conjunction with  Open a directory and return all the file names. This function essentially performs
2423  the OR operator and the L</Confess> method as a debugging assert.  the functions of an C<opendir> and C<readdir>. If the I<$filtered> parameter is
2424  So, for example  set to TRUE, all filenames beginning with a period (C<.>), dollar sign (C<$>),
2425    or pound sign (C<#>) and all filenames ending with a tilde C<~>) will be
2426    filtered out of the return list. If the directory does not open and I<$flag> is not
2427    set, an exception is thrown. So, for example,
2428    
2429  C<< Assert($recNum >= 0) || Confess("Invalid record number $recNum."); >>      my @files = OpenDir("/Volumes/fig/contigs", 1);
2430    
2431  Will abort the program with a stack trace if the value of C<$recNum> is negative.  is effectively the same as
2432    
2433  =cut      opendir(TMP, "/Volumes/fig/contigs") || Confess("Could not open /Volumes/fig/contigs.");
2434  sub Assert {      my @files = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir(TMP);
     my $retVal = 1;  
     LOOP: for my $condition (@_) {  
         if (! $condition) {  
             $retVal = 0;  
             last LOOP;  
         }  
     }  
     return $retVal;  
 }  
2435    
2436  =head3 Cluck  Similarly, the following code
2437    
2438  C<< Cluck($message); >>      my @files = grep { $_ =~ /^\d/ } OpenDir("/Volumes/fig/orgs", 0, 1);
2439    
2440  Trace the call stack. Note that for best results, you should qualify the call with a  Returns the names of all files in C</Volumes/fig/orgs> that begin with digits and
2441  trace condition. For example,  automatically returns an empty list if the directory fails to open.
2442    
2443  C<< Cluck("Starting record parse.") if T(3); >>  =over 4
2444    
2445  will only trace the stack if the trace level for the package is 3 or more.  =item dirName
2446    
2447  =over 4  Name of the directory to open.
2448    
2449  =item message  =item filtered
2450    
2451  Message to include in the trace.  TRUE if files whose names begin with a period (C<.>) should be automatically removed
2452    from the list, else FALSE.
2453    
2454    =item flag
2455    
2456    TRUE if a failure to open is okay, else FALSE
2457    
2458  =back  =back
2459    
2460  =cut  =cut
2461    #: Return Type @;
2462  sub Cluck {  sub OpenDir {
2463      # Get the parameters.      # Get the parameters.
2464      my ($message) = @_;      my ($dirName, $filtered, $flag) = @_;
2465      # Trace what's happening.      # Declare the return variable.
2466      Trace("Stack trace for event: $message");      my @retVal = ();
2467      my $confession = longmess($message);      # Open the directory.
2468      # Convert the confession to a series of trace messages. Note we skip any      if (opendir(my $dirHandle, $dirName)) {
2469      # messages relating to calls into Tracer.          # The directory opened successfully. Get the appropriate list according to the
2470      for my $line (split /\s*\n/, $confession) {          # strictures of the filter parameter.
2471          Trace($line) if ($line !~ /Tracer\.pm/);          if ($filtered) {
2472                @retVal = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir $dirHandle;
2473            } else {
2474                @retVal = readdir $dirHandle;
2475            }
2476        } elsif (! $flag) {
2477            # Here the directory would not open and it's considered an error.
2478            Confess("Could not open directory $dirName.");
2479      }      }
2480        # Return the result.
2481        return @retVal;
2482  }  }
2483    
 =head3 Min  
2484    
2485  C<< my $min = Min($value1, $value2, ... $valueN); >>  =head3 Insure
2486    
2487        Insure($dirName, $chmod);
2488    
2489  Return the minimum argument. The arguments are treated as numbers.  Insure a directory is present.
2490    
2491  =over 4  =over 4
2492    
2493  =item $value1, $value2, ... $valueN  =item dirName
2494    
2495  List of numbers to compare.  Name of the directory to check. If it does not exist, it will be created.
2496    
2497  =item RETURN  =item chmod (optional)
2498    
2499  Returns the lowest number in the list.  Security privileges to be given to the directory if it is created.
2500    
2501  =back  =back
2502    
2503  =cut  =cut
2504    
2505  sub Min {  sub Insure {
2506      # Get the parameters. Note that we prime the return value with the first parameter.      my ($dirName, $chmod) = @_;
2507      my ($retVal, @values) = @_;      if (! -d $dirName) {
2508      # Loop through the remaining parameters, looking for the lowest.          Trace("Creating $dirName directory.") if T(2);
2509      for my $value (@values) {          eval {
2510          if ($value < $retVal) {              mkpath $dirName;
2511              $retVal = $value;              # If we have permissions specified, set them here.
2512                if (defined($chmod)) {
2513                    chmod $chmod, $dirName;
2514                }
2515            };
2516            if ($@) {
2517                Confess("Error creating $dirName: $@");
2518          }          }
2519      }      }
     # Return the minimum found.  
     return $retVal;  
2520  }  }
2521    
2522  =head3 Max  =head3 ChDir
2523    
2524  C<< my $max = Max($value1, $value2, ... $valueN); >>      ChDir($dirName);
2525    
2526  Return the maximum argument. The arguments are treated as numbers.  Change to the specified directory.
2527    
2528  =over 4  =over 4
2529    
2530  =item $value1, $value2, ... $valueN  =item dirName
   
 List of numbers to compare.  
   
 =item RETURN  
2531    
2532  Returns the highest number in the list.  Name of the directory to which we want to change.
2533    
2534  =back  =back
2535    
2536  =cut  =cut
2537    
2538  sub Max {  sub ChDir {
2539      # Get the parameters. Note that we prime the return value with the first parameter.      my ($dirName) = @_;
2540      my ($retVal, @values) = @_;      if (! -d $dirName) {
2541      # Loop through the remaining parameters, looking for the highest.          Confess("Cannot change to directory $dirName: no such directory.");
2542      for my $value (@values) {      } else {
2543          if ($value > $retVal) {          Trace("Changing to directory $dirName.") if T(File => 4);
2544              $retVal = $value;          my $okFlag = chdir $dirName;
2545            if (! $okFlag) {
2546                Confess("Error switching to directory $dirName.");
2547          }          }
2548      }      }
     # Return the maximum found.  
     return $retVal;  
2549  }  }
2550    
2551  =head3 AddToListMap  =head3 SetPermissions
2552    
2553        Tracer::SetPermissions($dirName, $group, $mask, %otherMasks);
2554    
2555  C<< Tracer::AddToListMap(\%hash, $key, $value1, $value2, ... valueN); >>  Set the permissions for a directory and all the files and folders inside it.
2556    In addition, the group ownership will be changed to the specified value.
2557    
2558  Add a key-value pair to a hash of lists. If no value exists for the key, a singleton list  This method is more vulnerable than most to permission and compatability
2559  is created for the key. Otherwise, the new value is pushed onto the list.  problems, so it does internal error recovery.
2560    
2561  =over 4  =over 4
2562    
2563  =item hash  =item dirName
2564    
2565  Reference to the target hash.  Name of the directory to process.
2566    
2567  =item key  =item group
2568    
2569  Key for which the value is to be added.  Name of the group to be assigned.
2570    
2571  =item value1, value2, ... valueN  =item mask
2572    
2573  List of values to add to the key's value list.  Permission mask. Bits that are C<1> in this mask will be ORed into the
2574    permission bits of any file or directory that does not already have them
2575    set to 1.
2576    
2577  =back  =item otherMasks
2578    
2579  =cut  Map of search patterns to permission masks. If a directory name matches
2580    one of the patterns, that directory and all its members and subdirectories
2581    will be assigned the new pattern. For example, the following would
2582    assign 0664 to most files, but would use 0777 for directories named C<tmp>.
2583    
2584  sub AddToListMap {      Tracer::SetPermissions($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;  
     }  
 }  
2585    
2586  =head3 DebugMode  The list is ordered, so the following would use 0777 for C<tmp1> and
2587    0666 for C<tmp>, C<tmp2>, or C<tmp3>.
2588    
2589  C<< if (Tracer::DebugMode) { ...code... } >>      Tracer::SetPermissions($dirName, 'fig', 01664, '^tmp1' => 0777,
2590                                                       '^tmp' => 0666);
2591    
2592  Return TRUE if debug mode has been turned on, else abort.  Note that the pattern matches are all case-insensitive, and only directory
2593    names are matched, not file names.
2594    
2595  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.  
2596    
2597  =cut  =cut
2598    
2599  sub DebugMode {  sub SetPermissions {
2600      # Declare the return variable.      # Get the parameters.
2601      my $retVal = 0;      my ($dirName, $group, $mask, @otherMasks) = @_;
2602      # Check the debug configuration.      # Set up for error recovery.
2603      my $password = CGI::cookie("DebugMode");      eval {
2604      my $encrypted = Digest::MD5::md5_hex($password);          # Switch to the specified directory.
2605      if ($encrypted eq "252dec43280e0c0d6a75ffcec486e61d") {          ChDir($dirName);
2606          $retVal = 1;          # Get the group ID.
2607            my $gid = getgrnam($group);
2608            # Get the mask for tracing.
2609            my $traceMask = sprintf("%04o", $mask) . "($mask)";
2610            Trace("Fixing permissions for directory $dirName using group $group($gid) and mask $traceMask.") if T(File => 2);
2611            my $fixCount = 0;
2612            my $lookCount = 0;
2613            # @dirs will be a stack of directories to be processed.
2614            my @dirs = (getcwd());
2615            while (scalar(@dirs) > 0) {
2616                # Get the current directory.
2617                my $dir = pop @dirs;
2618                # Check for a match to one of the specified directory names. To do
2619                # that, we need to pull the individual part of the name off of the
2620                # whole path.
2621                my $simpleName = $dir;
2622                if ($dir =~ m!/([^/]+)$!) {
2623                    $simpleName = $1;
2624                }
2625                Trace("Simple directory name for $dir is $simpleName.") if T(File => 4);
2626                # Search for a match.
2627                my $match = 0;
2628                my $i;
2629                for ($i = 0; $i < $#otherMasks && ! $match; $i += 2) {
2630                    my $pattern = $otherMasks[$i];
2631                    if ($simpleName =~ /$pattern/i) {
2632                        $match = 1;
2633                    }
2634                }
2635                # Find out if we have a match. Note we use $i-1 because the loop added 2
2636                # before terminating due to the match.
2637                if ($match && $otherMasks[$i-1] != $mask) {
2638                    # This directory matches one of the incoming patterns, and it's
2639                    # a different mask, so we process it recursively with that mask.
2640                    SetPermissions($dir, $group, $otherMasks[$i-1], @otherMasks);
2641      } else {      } else {
2642          # Here debug mode is off, so we generate an error.                  # Here we can process normally. Get all of the non-hidden members.
2643          Confess("Cannot use this facility without logging in.");                  my @submems = OpenDir($dir, 1);
2644                    for my $submem (@submems) {
2645                        # Get the full name.
2646                        my $thisMem = "$dir/$submem";
2647                        Trace("Checking member $thisMem.") if T(4);
2648                        $lookCount++;
2649                        if ($lookCount % 1000 == 0) {
2650                            Trace("$lookCount members examined. Current is $thisMem. Mask is $traceMask") if T(File => 3);
2651      }      }
2652      # Return the determination indicator.                      # Fix the group.
2653      return $retVal;                      chown -1, $gid, $thisMem;
2654                        # Insure this member is not a symlink.
2655                        if (! -l $thisMem) {
2656                            # Get its info.
2657                            my $fileInfo = stat $thisMem;
2658                            # Only proceed if we got the info. Otherwise, it's a hard link
2659                            # and we want to skip it anyway.
2660                            if ($fileInfo) {
2661                                my $fileMode = $fileInfo->mode;
2662                                if (($fileMode & $mask) != $mask) {
2663                                    # Fix this member.
2664                                    $fileMode |= $mask;
2665                                    chmod $fileMode, $thisMem;
2666                                    $fixCount++;
2667                                }
2668                                # If it's a subdirectory, stack it.
2669                                if (-d $thisMem) {
2670                                    push @dirs, $thisMem;
2671                                }
2672                            }
2673                        }
2674                    }
2675                }
2676            }
2677            Trace("$lookCount files and directories processed, $fixCount fixed.") if T(File => 2);
2678        };
2679        # Check for an error.
2680        if ($@) {
2681            Confess("SetPermissions error: $@");
2682  }  }
   
 =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;  
2683  }  }
2684    
2685  =head3 Pad  =head3 GetLine
2686    
2687  C<< my $paddedString = Tracer::Pad($string, $len, $left, $padChar); >>      my @data = Tracer::GetLine($handle);
2688    
2689  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.  
2690    
2691  =over 4  =over 4
2692    
2693  =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)  
2694    
2695  Character to use for padding. The default is a space.  Open file handle from which to read.
2696    
2697  =item RETURN  =item RETURN
2698    
2699  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
2700  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
2701    returned. If an empty line is read, a single list item consisting of a null
2702    string will be returned.
2703    
2704  =back  =back
2705    
2706  =cut  =cut
2707    
2708  sub Pad {  sub GetLine {
2709      # Get the parameters.      # Get the parameters.
2710      my ($string, $len, $left, $padChar) = @_;      my ($handle) = @_;
2711      # Compute the padding character.      # Declare the return variable.
2712      if (! defined $padChar) {      my @retVal = ();
2713          $padChar = " ";      Trace("File position is " . tell($handle) . ". EOF flag is " . eof($handle) . ".") if T(File => 4);
2714      }      # Read from the file.
2715      # Compute the number of spaces needed.      my $line = <$handle>;
2716      my $needed = $len - length $string;      # Only proceed if we found something.
2717      # Copy the string into the return variable.      if (defined $line) {
2718      my $retVal = $string;          # Remove the new-line. We are a bit over-cautious here because the file may be coming in via an
2719      # Only proceed if padding is needed.          # upload control and have a nonstandard EOL combination.
2720      if ($needed > 0) {          $line =~ s/(\r|\n)+$//;
2721          # Create the pad string.          # Here we do some fancy tracing to help in debugging complicated EOL marks.
2722          my $pad = $padChar x $needed;          if (T(File => 4)) {
2723          # Affix it to the return value.              my $escapedLine = $line;
2724          if ($left) {              $escapedLine =~ s/\n/\\n/g;
2725              $retVal = $pad . $retVal;              $escapedLine =~ s/\r/\\r/g;
2726                $escapedLine =~ s/\t/\\t/g;
2727                Trace("Line read: -->$escapedLine<--");
2728            }
2729            # If the line is empty, return a single empty string; otherwise, parse
2730            # it into fields.
2731            if ($line eq "") {
2732                push @retVal, "";
2733          } else {          } else {
2734              $retVal .= $pad;              push @retVal, split /\t/,$line;
2735          }          }
2736        } else {
2737            # Trace the reason the read failed.
2738            Trace("End of file: $!") if T(File => 3);
2739      }      }
2740      # Return the result.      # Return the result.
2741      return $retVal;      return @retVal;
2742  }  }
2743    
2744  =head3 EOF  =head3 PutLine
2745    
2746  This is a constant that is lexically greater than any useful string.      Tracer::PutLine($handle, \@fields, $eol);
2747    
2748  =cut  Write a line of data to a tab-delimited file. The specified field values will be
2749    output in tab-separated form, with a trailing new-line.
2750    
2751  sub EOF {  =over 4
     return "\xFF\xFF\xFF\xFF\xFF";  
 }  
2752    
2753  =head3 TICK  =item handle
2754    
2755  C<< my @results = TICK($commandString); >>  Output file handle.
2756    
2757  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  
2758    
2759      `./protein.cgi`  List of field values.
2760    
2761  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  
2762    
2763      TICK("./protein.cgi")  End-of-line character (default is "\n").
2764    
2765  it will work correctly in both environments.  =back
2766    
2767  =over 4  =cut
2768    
2769  =item commandString  sub PutLine {
2770        # Get the parameters.
2771        my ($handle, $fields, $eol) = @_;
2772        # Write the data.
2773        print $handle join("\t", @{$fields}) . ($eol || "\n");
2774    }
2775    
 The command string to pass to the system.  
2776    
2777  =item RETURN  =head3 PrintLine
2778    
2779  Returns the standard output from the specified command, as a list.      Tracer::PrintLine($line);
2780    
2781    Print a line of text with a trailing new-line.
2782    
2783    =over 4
2784    
2785    =item line
2786    
2787    Line of text to print.
2788    
2789  =back  =back
2790    
2791  =cut  =cut
2792  #: Return Type @;  
2793  sub TICK {  sub PrintLine {
2794      # Get the parameters.      # Get the parameters.
2795      my ($commandString) = @_;      my ($line) = @_;
2796      # Chop off the dot-slash if this is Windows.      # Print the line.
2797      if ($FIG_Config::win_mode) {      print "$line\n";
         $commandString =~ s!^\./!!;  
     }  
     # Activate the command and return the result.  
     return `$commandString`;  
2798  }  }
2799    
 =head3 ScriptSetup  
2800    
2801  C<< my ($cgi, $varHash) = ScriptSetup($noTrace); >>  =head2 Other Useful Methods
2802    
2803  Perform standard tracing and debugging setup for scripts. The value returned is  =head3 ParseParm
 the CGI object followed by a pre-built variable hash.  
2804    
2805  The C<Trace> query parameter is used to determine whether or not tracing is active and      my $listValue = Tracer::ParseParm($string);
2806  which trace modules (other than C<Tracer> itself) should be turned on. Specifying  
2807  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,
2808  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
2809  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.  
2810    
2811  =over 4  =over 4
2812    
2813  =item noTrace (optional)  =item string
2814    
2815  If specified, tracing will be suppressed. This is useful if the script wants to set up  Incoming string.
 tracing manually.  
2816    
2817  =item RETURN  =item RETURN
2818    
2819  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
2820  the output page.  was undefined.
2821    
2822  =back  =back
2823    
2824  =cut  =cut
2825    
2826  sub ScriptSetup {  sub ParseParm {
2827      # Get the parameters.      # Get the parameters.
2828      my ($noTrace) = @_;      my ($string) = @_;
2829      # Get the CGI query object.      # Declare the return variable.
2830      my $cgi = CGI->new();      my $retVal;
2831      # Set up tracing if it's not suppressed.      # Check for data.
2832      CGITrace($cgi) unless $noTrace;      if (defined $string) {
2833      # Create the variable hash.          # We have some, so split it into a list.
2834      my $varHash = { results => '' };          $retVal = [ split /\s*,\s*/, $string];
2835      # Return the query object and variable hash.      }
2836      return ($cgi, $varHash);      # Return the result.
2837        return $retVal;
2838    }
2839    
2840    =head3 Now
2841    
2842        my $string = Tracer::Now();
2843    
2844    Return a displayable time stamp containing the local time. Whatever format this
2845    method produces must be parseable by L</ParseDate>.
2846    
2847    =cut
2848    
2849    sub Now {
2850        return DisplayTime(time);
2851  }  }
2852    
2853  =head3 CGITrace  =head3 DisplayTime
2854    
2855  C<< Tracer::CGITrace($cgi); >>      my $string = Tracer::DisplayTime($time);
2856    
2857  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
2858    method produces must be parseable by L</ParseDate>.
2859    
2860  =over 4  =over 4
2861    
2862  =item cgi  =item time
2863    
2864    Time to display, in seconds since the epoch, or C<undef> if the time is unknown.
2865    
2866    =item RETURN
2867    
2868  Ths CGI query object for this script.  Returns a displayable time, or C<(n/a)> if the incoming time is undefined.
2869    
2870  =back  =back
2871    
2872  =cut  =cut
2873    
2874  sub CGITrace {  sub DisplayTime {
2875      # Get the parameters.      my ($time) = @_;
2876      my ($cgi) = @_;      my $retVal = "(n/a)";
2877      # Default to no tracing except errors.      if (defined $time) {
2878      my ($tracing, $dest) = ("0", "WARN");          my ($sec,$min,$hour,$mday,$mon,$year,$wday,$yday,$isdst) = localtime($time);
2879      # Check for emergency tracing.          $retVal = _p2($mon+1) . "/" . _p2($mday) . "/" . ($year + 1900) . " " .
2880      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));  
2881          }          }
2882      } 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 = $cgi->param('Trace') . " Tracer";  
2883      }      }
2884      # Setup the tracing we've determined from all the stuff above.  
2885      TSetup($tracing, $dest);  # Pad a number to 2 digits.
2886      # Trace the parameter and environment data.  sub _p2 {
2887      TraceParms($cgi);      my ($value) = @_;
2888        $value = "0$value" if ($value < 10);
2889        return $value;
2890  }  }
2891    
2892  =head3 EmergencyFileName  =head3 Escape
2893    
2894  C<< my $fileName = Tracer::EmergencyFileName($ip); >>      my $codedString = Tracer::Escape($realString);
2895    
2896  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
2897  the tracing information.  replaced by C<\n>, carriage returns will be deleted, and backslashes will be doubled. The
2898    result is to reverse the effect of L</UnEscape>.
2899    
2900  =over 4  =over 4
2901    
2902  =item ip  =item realString
2903    
2904  IP address of the user who wants tracing, as taken from the C<< $cgi->remote_host() >>  String to escape.
 method.  
2905    
2906  =item RETURN  =item RETURN
2907    
2908  Returns the name of the file to contain the emergency tracing information.  Escaped equivalent of the real string.
2909    
2910  =back  =back
2911    
2912  =cut  =cut
2913    
2914  sub EmergencyFileName {  sub Escape {
2915      # Get the parameters.      # Get the parameter.
2916      my ($ip) = @_;      my ($realString) = @_;
2917      # Compute the emergency tracing file name.      # Initialize the return variable.
2918      return "$FIG_Config::temp/Emergency$ip.txt";      my $retVal = "";
2919        # Loop through the parameter string, looking for sequences to escape.
2920        while (length $realString > 0) {
2921            # Look for the first sequence to escape.
2922            if ($realString =~ /^(.*?)([\n\t\r\\])/) {
2923                # Here we found it. The text preceding the sequence is in $1. The sequence
2924                # itself is in $2. First, move the clear text to the return variable.
2925                $retVal .= $1;
2926                # Strip the processed section off the real string.
2927                $realString = substr $realString, (length $2) + (length $1);
2928                # Get the matched character.
2929                my $char = $2;
2930                # If we have a CR, we are done.
2931                if ($char ne "\r") {
2932                    # It's not a CR, so encode the escape sequence.
2933                    $char =~ tr/\t\n/tn/;
2934                    $retVal .= "\\" . $char;
2935                }
2936            } else {
2937                # Here there are no more escape sequences. The rest of the string is
2938                # transferred unmodified.
2939                $retVal .= $realString;
2940                $realString = "";
2941            }
2942        }
2943        # Return the result.
2944        return $retVal;
2945  }  }
2946    
2947  =head3 EmergencyFileTarget  =head3 UnEscape
2948    
2949  C<< my $fileName = Tracer::EmergencyFileTarget($ip); >>      my $realString = Tracer::UnEscape($codedString);
2950    
2951  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
2952  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
2953    be deleted.
2954    
2955  =over 4  =over 4
2956    
2957  =item ip  =item codedString
2958    
2959  IP address of the user who wants tracing, as taken from the C<< $cgi->remote_host() >>  String to un-escape.
 method.  
2960    
2961  =item RETURN  =item RETURN
2962    
2963  Returns the name of the file to contain the emergency tracing information.  Returns a copy of the original string with the escape sequences converted to their actual
2964    values.
2965    
2966  =back  =back
2967    
2968  =cut  =cut
2969    
2970  sub EmergencyFileTarget {  sub UnEscape {
2971      # Get the parameters.      # Get the parameter.
2972      my ($ip) = @_;      my ($codedString) = @_;
2973      # Compute the emergency tracing file name.      # Initialize the return variable.
2974      return "$FIG_Config::temp/Emergency$ip.log";      my $retVal = "";
2975        # Only proceed if the incoming string is nonempty.
2976        if (defined $codedString) {
2977            # Loop through the parameter string, looking for escape sequences. We can't do
2978            # translating because it causes problems with the escaped slash. ("\\t" becomes
2979            # "\<tab>" no matter what we do.)
2980            while (length $codedString > 0) {
2981                # Look for the first escape sequence.
2982                if ($codedString =~ /^(.*?)\\(\\|n|t|r)/) {
2983                    # Here we found it. The text preceding the sequence is in $1. The sequence
2984                    # itself is in $2. First, move the clear text to the return variable.
2985                    $retVal .= $1;
2986                    $codedString = substr $codedString, (2 + length $1);
2987                    # Get the escape value.
2988                    my $char = $2;
2989                    # If we have a "\r", we are done.
2990                    if ($char ne 'r') {
2991                        # Here it's not an 'r', so we convert it.
2992                        $char =~ tr/\\tn/\\\t\n/;
2993                        $retVal .= $char;
2994                    }
2995                } else {
2996                    # Here there are no more escape sequences. The rest of the string is
2997                    # transferred unmodified.
2998                    $retVal .= $codedString;
2999                    $codedString = "";
3000                }
3001            }
3002        }
3003        # Return the result.
3004        return $retVal;
3005  }  }
3006    
3007  =head3 EmergencyTracingDest  =head3 Percent
3008    
3009  C<< my $dest = Tracer::EmergencyTracingDest($ip, $myDest); >>      my $percent = Tracer::Percent($number, $base);
3010    
3011  This method converts an emergency tracing destination to a real  Returns the percent of the base represented by the given number. If the base
3012  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.  
3013    
3014  =over 4  =over 4
3015    
3016  =item ip  =item number
3017    
3018  IP address of the user who wants tracing, as taken from the C<< $cgi->remote_host() >>  Percent numerator.
 method.  
3019    
3020  =item myDest  =item base
3021    
3022  Destination from the emergency tracing file.  Percent base.
3023    
3024  =item RETURN  =item RETURN
3025    
3026  Returns a destination that can be passed into L</TSetup>.  Returns the percentage of the base represented by the numerator.
3027    
3028  =back  =back
3029    
3030  =cut  =cut
3031    
3032  sub EmergencyTracingDest {  sub Percent {
3033      # Get the parameters.      # Get the parameters.
3034      my ($ip, $myDest) = @_;      my ($number, $base) = @_;
3035      # Declare the return variable.      # Declare the return variable.
3036      my $retVal;      my $retVal = 0;
3037      # Process according to the destination value.      # Compute the percent.
3038      if ($myDest eq 'FILE') {      if ($base != 0) {
3039          $retVal = ">" . EmergencyFileTarget($ip);          $retVal = $number * 100 / $base;
     } elsif ($myDest eq 'APPEND') {  
         $retVal = ">>" . EmergencyFileTarget($ip);  
     } else {  
         $retVal = $myDest;  
3040      }      }
3041      # Return the result.      # Return the result.
3042      return $retVal;      return $retVal;
3043  }  }
3044    
3045  =head3 Emergency  =head3 Constrain
3046    
3047  C<< Emergency($cgi, $hours, $dest, $level, @modules); >>      my $constrained = Constrain($value, $min, $max);
3048    
3049  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.  
3050    
3051  =over 4  =over 4
3052    
3053  =item cgi  =item value
   
 A CGI query object.  
3054    
3055  =item hours  Value to constrain.
   
 Number of hours to keep emergency tracing alive.  
3056    
3057  =item dest  =item min (optional)
3058    
3059  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.  
3060    
3061  =item level  =item max (optional)
3062    
3063  Tracing level. A higher level means more trace messages.  Maximum permissible value. If this parameter is undefined, no maximum constraint will be applied.
3064    
3065  =item modules  =item RETURN
3066    
3067  A list of the tracing modules to activate.  Returns the incoming value, constrained according to the other parameters.
3068    
3069  =back  =back
3070    
3071  =cut  =cut
3072    
3073  sub Emergency {  sub Constrain {
3074      # Get the parameters.      # Get the parameters.
3075      my ($cgi, $hours, $dest, $level, @modules) = @_;      my ($value, $min, $max) = @_;
3076      # Get the IP address.      # Declare the return variable.
3077      my $ip = EmergencyIP($cgi);      my $retVal = $value;
3078      # Create the emergency file.      # Apply the minimum constraint.
3079      my $specFile = EmergencyFileName($ip);      if (defined $min && $retVal < $min) {
3080      my $outHandle = Open(undef, ">$specFile");          $retVal = $min;
3081      print $outHandle join("\n",$hours, $dest, $level, @modules, "");      }
3082        # Apply the maximum constraint.
3083        if (defined $max && $retVal > $max) {
3084            $retVal = $max;
3085        }
3086        # Return the result.
3087        return $retVal;
3088  }  }
3089    
3090  =head3 EmergencyIP  =head3 Min
3091    
3092  C<< my $ip = EmergencyIP($cgi); >>      my $min = Min($value1, $value2, ... $valueN);
3093    
3094  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.  
3095    
3096  =over 4  =over 4
3097    
3098  =item cgi  =item $value1, $value2, ... $valueN
3099    
3100  CGI query object.  List of numbers to compare.
3101    
3102  =item RETURN  =item RETURN
3103    
3104  Returns the IP address to be used for labelling emergency tracing.  Returns the lowest number in the list.
3105    
3106  =back  =back
3107    
3108  =cut  =cut
3109    
3110  sub EmergencyIP {  sub Min {
3111      # Get the parameters.      # Get the parameters. Note that we prime the return value with the first parameter.
3112      my ($cgi) = @_;      my ($retVal, @values) = @_;
3113      # Return the result.      # Loop through the remaining parameters, looking for the lowest.
3114      return $cgi->remote_addr();      for my $value (@values) {
3115            if ($value < $retVal) {
3116                $retVal = $value;
3117            }
3118        }
3119        # Return the minimum found.
3120        return $retVal;
3121  }  }
3122    
3123    =head3 Max
3124    
3125  =head3 TraceParms      my $max = Max($value1, $value2, ... $valueN);
   
 C<< Tracer::TraceParms($cgi); >>  
3126    
3127  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.  
3128    
3129  =over 4  =over 4
3130    
3131  =item cgi  =item $value1, $value2, ... $valueN
3132    
3133  CGI query object containing the parameters to trace.  List of numbers to compare.
3134    
3135    =item RETURN
3136    
3137    Returns the highest number in the list.
3138    
3139  =back  =back
3140    
3141  =cut  =cut
3142    
3143  sub TraceParms {  sub Max {
3144      # Get the parameters.      # Get the parameters. Note that we prime the return value with the first parameter.
3145      my ($cgi) = @_;      my ($retVal, @values) = @_;
3146      if (T(CGI => 3)) {      # Loop through the remaining parameters, looking for the highest.
3147          # Here we want to trace the parameter data.      for my $value (@values) {
3148          my @names = $cgi->param;          if ($value > $retVal) {
3149          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}");  
3150          }          }
3151      }      }
3152        # Return the maximum found.
3153        return $retVal;
3154  }  }
3155    
3156  =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 ...  
3157    
3158      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", $varHash);  
3159    
3160  The idea here is that even if the script fails, you'll see trace messages and  Strip all line terminators off a string. This is necessary when dealing with files
3161  useful output.  that may have been transferred back and forth several times among different
3162    operating environments.
3163    
3164  =over 4  =over 4
3165    
3166  =item webData  =item line
3167    
3168  A string containing either the full web page to be written to the output or the  Line of text to be stripped.
 name of a template file from which the page is to be constructed. If the name  
 of a template file is specified, then the second parameter must be present;  
 otherwise, it must be absent.  
3169    
3170  =item varHash (optional)  =item RETURN
3171    
3172  If specified, then a reference to a hash mapping variable names for a template  The same line of text with all the line-ending characters chopped from the end.
 to their values. The template file will be read into memory, and variable markers  
 will be replaced by data in this hash reference.  
3173    
3174  =back  =back
3175    
3176  =cut  =cut
3177    
3178  sub ScriptFinish {  sub Strip {
3179      # Get the parameters.      # Get a copy of the parameter string.
3180      my ($webData, $varHash) = @_;      my ($string) = @_;
3181      # Check for a template file situation.      my $retVal = (defined $string ? $string : "");
3182      my $outputString;      # Strip the line terminator characters.
3183      if (defined $varHash) {      $retVal =~ s/(\r|\n)+$//g;
3184          # Here we have a template file. We need to determine the template type.      # Return the result.
3185          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 $outputString;  
3186  }  }
3187    
3188  =head3 Insure  =head3 Pad
3189    
3190  C<< Insure($dirName); >>      my $paddedString = Tracer::Pad($string, $len, $left, $padChar);
3191    
3192  Insure a directory is present.  Pad a string to a specified length. The pad character will be a
3193    space, and the padding will be on the right side unless specified
3194    in the third parameter.
3195    
3196  =over 4  =over 4
3197    
3198  =item dirName  =item string
   
 Name of the directory to check. If it does not exist, it will be created.  
3199    
3200  =back  String to be padded.
3201    
3202  =cut  =item len
3203    
3204  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: $@");  
         }  
     }  
 }  
3205    
3206  =head3 ChDir  =item left (optional)
3207    
3208  C<< ChDir($dirName); >>  TRUE if the string is to be left-padded; otherwise it will be padded on the right.
3209    
3210  Change to the specified directory.  =item padChar (optional)
3211    
3212  =over 4  Character to use for padding. The default is a space.
3213    
3214  =item dirName  =item RETURN
3215    
3216  Name of the directory to which we want to change.  Returns a copy of the original string with the pad character added to the
3217    specified end so that it achieves the desired length.
3218    
3219  =back  =back
3220    
3221  =cut  =cut
3222    
3223  sub ChDir {  sub Pad {
3224      my ($dirName) = @_;      # Get the parameters.
3225      if (! -d $dirName) {      my ($string, $len, $left, $padChar) = @_;
3226          Confess("Cannot change to directory $dirName: no such directory.");      # Compute the padding character.
3227        if (! defined $padChar) {
3228            $padChar = " ";
3229        }
3230        # Compute the number of spaces needed.
3231        my $needed = $len - length $string;
3232        # Copy the string into the return variable.
3233        my $retVal = $string;
3234        # Only proceed if padding is needed.
3235        if ($needed > 0) {
3236            # Create the pad string.
3237            my $pad = $padChar x $needed;
3238            # Affix it to the return value.
3239            if ($left) {
3240                $retVal = $pad . $retVal;
3241      } else {      } else {
3242          Trace("Changing to directory $dirName.") if T(4);              $retVal .= $pad;
         my $okFlag = chdir $dirName;  
         if (! $okFlag) {  
             Confess("Error switching to directory $dirName.");  
3243          }          }
3244      }      }
3245        # Return the result.
3246        return $retVal;
3247  }  }
3248    
3249  =head3 SendSMS  =head3 EOF
3250    
3251    This is a constant that is lexically greater than any useful string.
3252    
3253    =cut
3254    
3255  C<< my $msgID = Tracer::SendSMS($phoneNumber, $msg); >>  sub EOF {
3256        return "\xFF\xFF\xFF\xFF\xFF";
3257    }
3258    
3259  Send a text message to a phone number using Clickatell. The FIG_Config file must contain the  =head3 TICK
 user name, password, and API ID for the relevant account in the hash reference variable  
 I<$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  
3260    
3261      $phone =  { user => 'BruceTheHumanPet',      my @results = TICK($commandString);
                 password => 'silly',  
                 api_id => '2561022' };  
3262    
3263  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
3264  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.  
3265    
3266  The message ID will be returned if successful, and C<undef> if an error occurs.      `./protein.cgi`
3267    
3268  =over 4  from inside a CGI script, it would work fine in Unix, but would issue an error message
3269    in Windows complaining that C<'.'> is not a valid command. If instead you code
3270    
3271  =item phoneNumber      TICK("./protein.cgi")
3272    
3273  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".  
3274    
3275  =item msg  =over 4
3276    
3277  Message to send to the specified phone.  =item commandString
3278    
3279    The command string to pass to the system.
3280    
3281  =item RETURN  =item RETURN
3282    
3283  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.
3284    
3285  =back  =back
3286    
3287  =cut  =cut
3288    #: Return Type @;
3289  sub SendSMS {  sub TICK {
3290      # Get the parameters.      # Get the parameters.
3291      my ($phoneNumber, $msg) = @_;      my ($commandString) = @_;
3292      # Declare the return variable. If we do not change it, C<undef> will be returned.      # Chop off the dot-slash if this is Windows.
3293      my $retVal;      if ($FIG_Config::win_mode) {
3294      # 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);  
             }  
         }  
3295      }      }
3296      # Return the result.      # Activate the command and return the result.
3297      return $retVal;      return `$commandString`;
3298  }  }
3299    
3300    
3301  =head3 CommaFormat  =head3 CommaFormat
3302    
3303  C<< my $formatted = Tracer::CommaFormat($number); >>      my $formatted = Tracer::CommaFormat($number);
3304    
3305  Insert commas into a number.  Insert commas into a number.
3306    
# Line 2503  Line 3333 
3333      # Return the result.      # Return the result.
3334      return $retVal;      return $retVal;
3335  }  }
 =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.  
3336    
 =over 4  
3337    
3338  =item dirName  =head3 CompareLists
3339    
3340  Name of the directory to process.      my ($inserted, $deleted) = Tracer::CompareLists(\@newList, \@oldList, $keyIndex);
3341    
3342  =item group  Compare two lists of tuples, and return a hash analyzing the differences. The lists
3343    are presumed to be sorted alphabetically by the value in the $keyIndex column.
3344    The return value contains a list of items that are only in the new list
3345    (inserted) and only in the old list (deleted).
3346    
3347  Name of the group to be assigned.  =over 4
3348    
3349  =item mask  =item newList
3350    
3351  Permission mask. Bits that are C<1> in this mask will be ORed into the  Reference to a list of new tuples.
 permission bits of any file or directory that does not already have them  
 set to 1.  
3352    
3353  =item otherMasks  =item oldList
3354    
3355  Map of search patterns to permission masks. If a directory name matches  Reference to a list of old tuples.
 one of the patterns, that directory and all its members and subdirectories  
 will be assigned the new pattern. For example, the following would  
 assign 01664 to most files, but would use 01777 for directories named C<tmp>.  
3356    
3357      Tracer::SetPermissions($dirName, 'fig', 01664, '^tmp$' => 01777);  =item keyIndex (optional)
3358    
3359  The list is ordered, so the following would use 0777 for C<tmp1> and  Index into each tuple of its key field. The default is 0.
 0666 for C<tmp>, C<tmp2>, or C<tmp3>.  
3360    
3361      Tracer::SetPermissions($dirName, 'fig', 01664, '^tmp1' => 0777,  =item RETURN
                                                    '^tmp' => 0666);  
3362    
3363  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
3364  names are matched, not file names.  list (inserted) followed by a reference to the list of items that are only in the old
3365    list (deleted).
3366    
3367  =back  =back
3368    
3369  =cut  =cut
3370    
3371  sub SetPermissions {  sub CompareLists {
3372      # Get the parameters.      # Get the parameters.
3373      my ($dirName, $group, $mask, @otherMasks) = @_;      my ($newList, $oldList, $keyIndex) = @_;
3374      # Set up for error recovery.      if (! defined $keyIndex) {
3375      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;  
                 }  
3376              }              }
3377              # Check for a match. Note we use $i-1 because the loop added 2      # Declare the return variables.
3378              # before terminating due to the match.      my ($inserted, $deleted) = ([], []);
3379              if ($match && $otherMasks[$i-1] != $mask) {      # Loop through the two lists simultaneously.
3380                  # This directory matches one of the incoming patterns, and it's      my ($newI, $oldI) = (0, 0);
3381                  # a different mask, so we process it recursively with that mask.      my ($newN, $oldN) = (scalar @{$newList}, scalar @{$oldList});
3382                  SetPermissions($dir, $group, $otherMasks[$i-1], @otherMasks);      while ($newI < $newN || $oldI < $oldN) {
3383            # Get the current object in each list. Note that if one
3384            # of the lists is past the end, we'll get undef.
3385            my $newItem = $newList->[$newI];
3386            my $oldItem = $oldList->[$oldI];
3387            if (! defined($newItem) || defined($oldItem) && $newItem->[$keyIndex] gt $oldItem->[$keyIndex]) {
3388                # The old item is not in the new list, so mark it deleted.
3389                push @{$deleted}, $oldItem;
3390                $oldI++;
3391            } elsif (! defined($oldItem) || $oldItem->[$keyIndex] gt $newItem->[$keyIndex]) {
3392                # The new item is not in the old list, so mark it inserted.
3393                push @{$inserted}, $newItem;
3394                $newI++;
3395              } else {              } else {
3396                  # Here we can process normally. Get all of the non-hidden members.              # The item is in both lists, so push forward.
3397                  my @submems = OpenDir($dir, 1);              $oldI++;
3398                  for my $submem (@submems) {              $newI++;
                     # Get the full name.  
                     my $thisMem = "$dir/$submem";  
                     Trace("Checking member $thisMem.") if T(4);  
                     $lookCount++;  
                     if ($lookCount % 1000 == 0) {  
                         Trace("$lookCount members examined. Current is $thisMem. Mask is $traceMask") if T(3);  
                     }  
                     # Fix the group.  
                     chown -1, $gid, $thisMem;  
                     # Insure this member is not a symlink.  
                     if (! -l $thisMem) {  
                         # Get its info.  
                         my $fileInfo = stat $thisMem;  
                         # Only proceed if we got the info. Otherwise, it's a hard link  
                         # and we want to skip it anyway.  
                         if ($fileInfo) {  
                             my $fileMode = $fileInfo->mode;  
                             if (($fileMode & $mask) != $mask) {  
                                 # Fix this member.  
                                 $fileMode |= $mask;  
                                 chmod $fileMode, $thisMem;  
                                 $fixCount++;  
                             }  
                             # If it's a subdirectory, stack it.  
                             if (-d $thisMem) {  
                                 push @dirs, $thisMem;  
                             }  
                         }  
3399                      }                      }