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revision 1.73, Tue Oct 3 12:04:50 2006 UTC revision 1.104, Fri May 9 06:22:49 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 EmergencyKey ETracing 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    
42    
43  =head1 Tracing and Debugging Helpers  =head1 Tracing and Debugging Helpers
44    
# Line 158  Line 163 
163    
164  Sometimes, you need a way for tracing to happen automatically without putting parameters  Sometimes, you need a way for tracing to happen automatically without putting parameters
165  in a form or on the command line. Emergency tracing does this. You invoke emergency tracing  in a form or on the command line. Emergency tracing does this. You invoke emergency tracing
166  from the debug form, which is accessed from I<MySeedInstance>C</FIG/Html/SetPassword.html>.  from the debug form, which is accessed from the [[DebugConsole]]. Emergency tracing requires
167  Emergency tracing requires you specify a tracing key. For command-line tools, the key is  that you specify a tracing key. For command-line tools, the key is
168  taken from the C<TRACING> environment variable. For web services, the key is taken from  taken from the C<TRACING> environment variable. For web services, the key is taken from
169  a cookie. Either way, the key tells the tracing facility who you are, so that you control  a cookie. Either way, the key tells the tracing facility who you are, so that you control
170  the tracing in your environment without stepping on other users.  the tracing in your environment without stepping on other users.
# Line 182  Line 187 
187    
188  The web script will look for the tracing key in the cookies, and the command-line  The web script will look for the tracing key in the cookies, and the command-line
189  script will look for it in the C<TRACING> environment variable. If you are  script will look for it in the C<TRACING> environment variable. If you are
190  using the L</StandardScript> or L</StandardSetup> methods, emergency tracing  using the L</StandardSetup> method or a [[WebApplication]], emergency tracing
191  will be configured automatically.  will be configured automatically.
192    
 =head3 Debugging Control Panel  
   
 The debugging control panel provides several tools to assist in development of  
 SEED and Sprout software. You access the debugging control panel from the URL  
 C</FIG/Html/SetPassword.html> in whichever seed instance you're using. (So,  
 for example, the panel access point for the development NMPDR system is  
 C<http://web-1.nmpdr.org/next/FIG/Html/SetPassword.html>. Contact Bruce to  
 find out what the password is. From this page, you can also specify a tracing  
 key. If you don't specify a key, one will be generated for you.  
   
 =head4 Emergency Tracing Form  
   
 At the bottom of the debugging control panel is a form that allows you to  
 specify a trace level and tracing categories. Special and common categories  
 are listed with check boxes. You can hold your mouse over a check box to see  
 what its category does. In general, however, a category name is the same as  
 the name of the package in which the trace message occurs.  
   
 Additional categories can be entered in an input box, delimited by spaces or commas.  
   
 The B<Activate> button turns on Emergency tracing at the level you specify with the  
 specified categories active. The B<Terminate> button turns tracing off. The  
 B<Show File> button displays the current contents of the trace file. The tracing  
 form at the bottom of the control panel is designed for emergency tracing, so it  
 will only affect programs that call L</ETracing>, L</StandardScript>,  
 or L</StandardSetup>.  
   
 =head4 Script Form  
   
 The top form of the debugging control panel allows you to enter a tiny script and  
 have the output generated in a formatted table. Certain object variables are  
 predefined in the script, including a FIG object (C<$fig>), a CGI object (C<$cgi>),  
 and-- if Sprout is active-- Sprout (C<$sprout>) and SFXlate (C<$sfx>) objects.  
   
 The last line of the script must be a scalar, but it can be a reference to a hash,  
 a list, a list of lists, and various other combinations. If you select the appropriate  
 data type in the dropdown box, the output will be formatted accordingly. The form  
 also has controls for specifying tracing. These controls override any emergency  
 tracing in effect.  
   
 =head4 Database Query Forms  
   
 The forms between the script form and the emergency tracing form allow you to  
 make queries against the database. The FIG query form allows simple queries against  
 a single FIG table. The Sprout query form uses the B<GetAll> method to do a  
 multi-table query against the Sprout database. B<GetAll> is located in the B<ERDB>  
 package, and it takes five parameters.  
   
     GetAll(\@objectNames, $filterClause, \@parameters, \@fields, $count);  
   
 Each of the five parameters corresponds to a text box on the query form:  
   
 =over 4  
   
 =item Objects  
   
 Comma-separated list containing the names of the entity and relationship objects to be retrieved.  
   
 =item Filter  
   
 WHERE/ORDER BY clause (without the WHERE) to be used to filter and sort the query. The WHERE clause can  
 be parameterized with parameter markers (C<?>). Each field used must be specified in the standard form  
 B<I<objectName>(I<fieldName>)> or B<$I<number>(I<fieldName>)> where I<fieldName> is the name of a  
 field, I<objectName> is the name of the entity or relationship object containing the field, and  
 I<number> is the 1-based position of the object in the object list. Any parameters  
 specified in the filter clause should be specified in the B<Params> field.  
 The fields in a filter clause can come from primary entity relations,  
 relationship relations, or secondary entity relations; however, all of the  
 entities and relationships involved must be included in the list of object names.  
   
 =item Params  
   
 List of the parameters to be substituted in for the parameters marks in the filter clause. This  
 is a comma-separated list without any quoting or escaping.  
   
 =item fields  
   
 Comma-separated list of the fields to be returned in each element of the list returned. Fields  
 are specified in the same manner as in the filter clause.  
   
 =item count  
   
 Maximum number of records to return. If omitted or 0, all available records will be returned.  
   
 =back  
   
 B<GetAll> automatically joins together the entities and relationships listed in the object  
 names. This simplifies the coding of the filter clause, but it means that some queries are  
 not possible, since they cannot be expressed in a linear sequence of joins. This is a limitation  
 that has yet to be addressed.  
   
193  =cut  =cut
194    
195  # Declare the configuration variables.  # Declare the configuration variables.
196    
197  my $Destination = "NONE";   # Description of where to send the trace output.  my $Destination = "WARN";   # Description of where to send the trace output.
198  my $TeeFlag = 0;            # TRUE if output is going to a file and to the  my $TeeFlag = 0;            # TRUE if output is going to a file and to the
199                              # standard output                              # standard output
200  my %Categories = ( main => 1 );  my %Categories = ( main => 1 );
201                              # hash of active category names                              # hash of active category names
202    my @LevelNames = qw(error warn notice info detail);
203  my $TraceLevel = 0;         # trace level; a higher trace level produces more  my $TraceLevel = 0;         # trace level; a higher trace level produces more
204                              # messages                              # messages
205  my @Queue = ();             # queued list of trace messages.  my @Queue = ();             # queued list of trace messages.
206  my $LastCategory = "main";  # name of the last category interrogated  my $LastCategory = "main";  # name of the last category interrogated
207    my $LastLevel = 0;          # level of the last test call
208  my $SetupCount = 0;         # number of times TSetup called  my $SetupCount = 0;         # number of times TSetup called
209  my $AllTrace = 0;           # TRUE if we are tracing all categories.  my $AllTrace = 0;           # TRUE if we are tracing all categories.
210    my $SavedCGI;               # CGI object passed to ETracing
211    my $CommandLine;            # Command line passed to StandardSetup
212    umask 2;                    # Fix the damn umask so everything is group-writable.
213    
214  =head2 Public Methods  =head2 Tracing Methods
215    
216    =head3 Setups
217    
218        my $count = Tracer::Setups();
219    
220    Return the number of times L</TSetup> has been called.
221    
222    This method allows for the creation of conditional tracing setups where, for example, we
223    may want to set up tracing if nobody else has done it before us.
224    
225    =cut
226    
227    sub Setups {
228        return $SetupCount;
229    }
230    
231  =head3 TSetup  =head3 TSetup
232    
233  C<< TSetup($categoryList, $target); >>      TSetup($categoryList, $target);
234    
235  This method is used to specify the trace options. The options are stored as package data  This method is used to specify the trace options. The options are stored as package data
236  and interrogated by the L</Trace> and L</T> methods.  and interrogated by the L</Trace> and L</T> methods.
# Line 346  Line 280 
280          }          }
281      }      }
282      # Now we need to process the destination information. The most important special      # Now we need to process the destination information. The most important special
283      # cases are the single ">", which requires we clear the file first, and the      # case is when we're writing to a file. This is indicated by ">" (overwrite) and
284      # "+" prefix which indicates a double echo.      # ">>" (append). A leading "+" for either indicates that we are also writing to
285        # the standard output (tee mode).
286      if ($target =~ m/^\+?>>?/) {      if ($target =~ m/^\+?>>?/) {
287          if ($target =~ m/^\+/) {          if ($target =~ m/^\+/) {
288              $TeeFlag = 1;              $TeeFlag = 1;
289              $target = substr($target, 1);              $target = substr($target, 1);
290          }          }
291          if ($target =~ m/^>[^>]/) {          if ($target =~ m/^>[^>]/) {
292                # We need to initialize the file (which clears it).
293              open TRACEFILE, $target;              open TRACEFILE, $target;
294              print TRACEFILE "[" . Now() . "] <Tracer>: Tracing initialized.\n";              print TRACEFILE "[" . Now() . "] [notice] [Tracer] Tracing initialized.\n";
295              close TRACEFILE;              close TRACEFILE;
296                # Set to append mode now that the file has been cleared.
297              $Destination = ">$target";              $Destination = ">$target";
298          } else {          } else {
299              $Destination = $target;              $Destination = $target;
# Line 368  Line 305 
305      $SetupCount++;      $SetupCount++;
306  }  }
307    
308  =head3 StandardSetup  =head3 SetLevel
309    
310  C<< my ($options, @parameters) = StandardSetup(\@categories, \%options, $parmHelp, @ARGV); >>      Tracer::SetLevel($newLevel);
311    
312  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.  
313    
314  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.  
315    
316  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  
317    
318      ["Sprout", "SproutLoad", "ERDB"]  Proposed new trace level.
319    
320  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.  
321    
322  =over 4  =cut
323    
324  =item SQL  sub SetLevel {
325        $TraceLevel = $_[0];
326    }
327    
328  Traces SQL commands and activity.  =head3 ParseDate
329    
330  =item Tracer      my $time = Tracer::ParseDate($dateString);
331    
332  Traces error messages and call stacks.  Convert a date into a PERL time number. This method expects a date-like string
333    and parses it into a number. The string must be vaguely date-like or it will
334    return an undefined value. Our requirement is that a month and day be
335    present and that three pieces of the date string (time of day, month and day,
336    year) be separated by likely delimiters, such as spaces, commas, and such-like.
337    
338  =back  If a time of day is present, it must be in military time with two digits for
339    everything but the hour.
340    
341  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.  
342    
343      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
344    equally innocuous. This means, however, that a sufficiently long sentence with date-like
345    parts in it may be interpreted as a date. Hopefully this will not be a problem.
346    
347  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  
348    
349  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.  
350    
351      TransactFeatures -trace=3 -sql -user=Bruce register ../xacts IDs.tbl  =over 4
352    
353  would send the trace output to C<traceBruce.log> in the temporary directory.  =item dateString
354    
355  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.  
356    
357  You can specify a different default trace level by setting C<$options->{trace}>  =item RETURN
 prior to calling this method.  
358    
359  An example at this point would help. Consider, for example, the command-line utility  Returns a PERL time, that is, a number of seconds since the epoch, or C<undef> if
360  C<TransactFeatures>. It accepts a list of positional parameters plus the options  the date string is invalid. A valid date string must contain a month and day.
 C<safe>, C<noAlias>, C<start>, and C<tblFiles>. To start up this command, we execute  
 the following code.  
361    
362      my ($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);  
363    
364    =cut
365    
366  The call to C<ParseCommand> specifies the default values for the options and  # Universal month conversion table.
367  stores the actual options in a hash that is returned as C<$options>. The  use constant MONTHS => {    Jan =>  0, January   =>  0, '01' =>  0,  '1' =>  0,
368  positional parameters are returned in C<@parameters>.                              Feb =>  1, February  =>  1, '02' =>  1,  '2' =>  1,
369                                Mar =>  2, March     =>  2, '03' =>  2,  '3' =>  2,
370                                Apr =>  3, April     =>  3, '04' =>  3,  '4' =>  3,
371                                May =>  4, May       =>  4, '05' =>  4,  '5' =>  4,
372                                Jun =>  5, June      =>  5, '06' =>  5,  '6' =>  5,
373                                Jul =>  6, July      =>  6, '07' =>  6,  '7' =>  6,
374                                Aug =>  7, August    =>  7, '08' =>  7,  '8' =>  7,
375                                Sep =>  8, September =>  8, '09' =>  8,  '9' =>  8,
376                                Oct =>  9, October  =>   9, '10' =>  9,
377                                Nov => 10, November =>  10, '11' => 10,
378                                Dec => 11, December =>  11, '12' => 11
379                            };
380    
381  The following is a sample command line for C<TransactFeatures>.  sub ParseDate {
382        # Get the parameters.
383        my ($dateString) = @_;
384        # Declare the return variable.
385        my $retVal;
386        # Find the month and day of month. There are two ways that can happen. We check for the
387        # numeric style first. That way, if the user's done something like "Sun 12/22", then we
388        # won't be fooled into thinking the month is Sunday.
389        if ($dateString =~ m#\b(\d{1,2})/(\d{1,2})\b# || $dateString =~ m#\b(\w+)\s(\d{1,2})\b#) {
390            my ($mon, $mday) = (MONTHS->{$1}, $2);
391            # Insist that the month and day are valid.
392            if (defined($mon) && $2 >= 1 && $2 <= 31) {
393                # Find the time.
394                my ($hour, $min, $sec) = (0, 0, 0);
395                if ($dateString =~ /\b(\d{1,2}):(\d{2}):(\d{2})\b/) {
396                    ($hour, $min, $sec) = ($1, $2, $3);
397                }
398                # Find the year.
399                my $year;
400                if ($dateString =~ /\b(\d{4})\b/) {
401                    $year = $1;
402                } else {
403                    # Get the default year, which is this one. Note we must convert it to
404                    # the four-digit value expected by "timelocal".
405                    (undef, undef, undef, undef, undef, $year) = localtime();
406                    $year += 1900;
407                }
408                $retVal = timelocal($sec, $min, $hour, $mday, $mon, $year);
409            }
410        }
411        # Return the result.
412        return $retVal;
413    }
414    
415      TransactFeatures -trace=2 -noAlias register ../xacts IDs.tbl  =head3 LogErrors
416    
417  In this case, C<register>, C<../xacts>, and C<IDs.tbl> are the positional      Tracer::LogErrors($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<$options> hash would be  
418    
419      { trace => 2, sql => 0, safe => 0,  Route the standard error output to a log file.
       noAlias => 1, start => ' ', tblFiles => 0 }  
420    
421  Use of C<StandardSetup> in this way provides a simple way of performing  =over 4
 standard tracing setup and command-line parsing. Note that the caller is  
 not even aware of the command-line switches C<-trace> and C<-sql>, which  
 are used by this method to control the tracing. If additional tracing features  
 need to be added in the future, they can be processed by this method without  
 upsetting the command-line utilities.  
422    
423  If the C<background> option is specified on the command line, then the  =item fileName
 standard and error outputs will be directed to files in the temporary  
 directory, using the same suffix as the trace file. So, if the command  
 line specified  
424    
425      -user=Bruce -background  Name of the file to receive the error output.
426    
427  then the trace output would go to C<traceBruce.log>, the standard output to  =back
 C<outBruce.log>, and the error output to C<errBruce.log>. This is designed to  
 simplify starting a command in the background.  
428    
429  The user name is also used as the tracing key for L</Emergency Tracing>.  =cut
 Specifying a value of C<E> for the trace level causes emergency tracing to  
 be used instead of custom tracing. If the user name is not specified,  
 the tracing key is taken from the C<Tracing> environment variable. If there  
 is no value for that variable, the tracing key will be computed from the PID.  
430    
431  Finally, if the special option C<-h> is specified, the option names will  sub LogErrors {
432  be traced at level 0 and the program will exit without processing.      # Get the file name.
433  This provides a limited help capability. For example, if the user enters      my ($fileName) = @_;
434        # Open the file as the standard error output.
435        open STDERR, '>', $fileName;
436    }
437    
438      TransactFeatures -h  =head3 Trace
439    
440  he would see the following output.      Trace($message);
441    
442      TransactFeatures [options] command transactionDirectory IDfile  Write a trace message to the target location specified in L</TSetup>. If there has not been
443          -trace    tracing level (default E)  any prior call to B<TSetup>.
         -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  
444    
445  The caller has the option of modifying the tracing scheme by placing a value  =over 4
 for C<trace> in the incoming options hash. The default value can be overridden,  
 or the tracing to the standard output can be turned off by suffixing a minus  
 sign to the trace level. So, for example,  
446    
447      { trace => [0, "tracing level (default 0)"],  =item message
        ...  
448    
449  would set the default trace level to 0 instead of E, while  Message to write.
450    
451      { trace => ["2-", "tracing level (default 2)"],  =back
        ...  
452    
453  would set the default to 2, but trace only to the log file, not to the  =cut
 standard output.  
454    
455  The parameters to this method are as follows.  sub Trace {
456        # Get the parameters.
457        my ($message) = @_;
458        # Strip off any line terminators at the end of the message. We will add
459        # new-line stuff ourselves.
460        my $stripped = Strip($message);
461        # Compute the caller information.
462        my ($callPackage, $callFile, $callLine) = caller();
463        my $callFileTitle = basename($callFile);
464        # Check the caller.
465        my $callerInfo = ($callFileTitle ne "Tracer.pm" ? " [$callFileTitle $callLine]" : "");
466        # Get the timestamp.
467        my $timeStamp = Now();
468        # Build the prefix.
469        my $level = $LevelNames[$LastLevel] || "($LastLevel)";
470        my $prefix = "[$timeStamp] [$level] [$LastCategory]$callerInfo";
471        # Format the message.
472        my $formatted = "$prefix $stripped";
473        # Process according to the destination.
474        if ($Destination eq "TEXT") {
475            # Write the message to the standard output.
476            print "$formatted\n";
477        } elsif ($Destination eq "ERROR") {
478            # Write the message to the error output. Here, we want our prefix fields.
479            print STDERR "$formatted\n";
480        } elsif ($Destination eq "WARN") {
481            # Emit the message to the standard error output. It is presumed that the
482            # error logger will add its own prefix fields, the notable exception being
483            # the caller info.
484            print STDERR "$callerInfo$stripped\n";
485        } elsif ($Destination eq "QUEUE") {
486            # Push the message into the queue.
487            push @Queue, "$formatted";
488        } elsif ($Destination eq "HTML") {
489            # Convert the message to HTML and write it to the standard output.
490            my $escapedMessage = CGI::escapeHTML($stripped);
491            print "<p>$timeStamp $LastCategory $LastLevel: $escapedMessage</p>\n";
492        } elsif ($Destination =~ m/^>>/) {
493            # Write the trace message to an output file.
494            open(TRACING, $Destination) || die "Tracing open for \"$Destination\" failed: $!";
495            print TRACING "$formatted\n";
496            close TRACING;
497            # If the Tee flag is on, echo it to the standard output.
498            if ($TeeFlag) {
499                print "$formatted\n";
500            }
501        }
502    }
503    
504  =over 4  =head3 T
505    
506  =item categories      my $switch = T($category, $traceLevel);
507    
508  Reference to a list of tracing category names. These should be names of      or
 packages whose internal workings will need to be debugged to get the  
 command working.  
509    
510  =item options      my $switch = T($traceLevel);
511    
512  Reference to a hash containing the legal options for the current command mapped  Return TRUE if the trace level is at or above a specified value and the specified category
513  to their default values and descriptions. The user can override the defaults  is active, else FALSE. If no category is specified, the caller's package name is used.
 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  =over 4
516    
517  A string that vaguely describes the positional parameters. This is used  =item category
 if the user specifies the C<-h> option.  
518    
519  =item argv  Category to which the message belongs. If not specified, the caller's package name is
520    used.
521    
522  List of command line parameters, including the option switches, which must  =item traceLevel
523  precede the positional parameters and be prefixed by a hyphen.  
524    Relevant tracing level.
525    
526  =item RETURN  =item RETURN
527    
528  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.  
529    
530  =back  =back
531    
532  =cut  =cut
533    
534  sub StandardSetup {  sub T {
535        # Declare the return variable.
536        my $retVal = 0;
537        # Only proceed if tracing is turned on.
538        if ($Destination ne "NONE") {
539      # Get the parameters.      # Get the parameters.
540      my ($categories, $options, $parmHelp, @argv) = @_;          my ($category, $traceLevel) = @_;
541      # Get the default tracing key.          if (!defined $traceLevel) {
542      my $tkey = EmergencyKey();              # Here we have no category, so we need to get the calling package.
543      # Add the tracing options.              # The calling package is normally the first parameter. If it is
544      if (! exists $options->{trace}) {              # omitted, the first parameter will be the tracelevel. So, the
545          $options->{trace} = ['E', "tracing level (E for emergency tracing)"];              # first thing we do is shift the so-called category into the
546      }              # $traceLevel variable where it belongs.
547      $options->{sql} = [0, "turn on SQL tracing"];              $traceLevel = $category;
548      $options->{h} = [0, "display command-line options"];              my ($package, $fileName, $line) = caller;
549      $options->{user} = [$tkey, "tracing key"];              # If there is no calling package, we default to "main".
550      $options->{background} = [0, "spool standard and error output"];              if (!$package) {
551      # Create a parsing hash from the options hash. The parsing hash                  $category = "main";
     # contains the default values rather than the default value  
     # and the description. While we're at it, we'll memorize the  
     # length of the longest option name.  
     my $longestName = 0;  
     my %parseOptions = ();  
     for my $key (keys %{$options}) {  
         if (length $key > $longestName) {  
             $longestName = length $key;  
         }  
         $parseOptions{$key} = $options->{$key}->[0];  
     }  
     # Parse the command line.  
     my ($retOptions, @retParameters) = ParseCommand(\%parseOptions, @argv);  
     # Get the logfile suffix.  
     my $suffix = $retOptions->{user};  
     # Check for background mode.  
     if ($retOptions->{background}) {  
         my $outFileName = "$FIG_Config::temp/out$suffix.log";  
         my $errFileName = "$FIG_Config::temp/err$suffix.log";  
         open STDOUT, ">$outFileName";  
         open STDERR, ">$errFileName";  
     }  
     # Now we want to set up tracing. First, we need to know if the user  
     # wants emergency tracing.  
     if ($retOptions->{trace} eq 'E') {  
         ETracing($retOptions->{user});  
     } else {  
         # Here the tracing is controlled from the command line.  
         my @cats = @{$categories};  
         if ($retOptions->{sql}) {  
             push @cats, "SQL";  
         }  
         # Add the default categories.  
         push @cats, "Tracer";  
         # Next, we create the category string by joining the categories.  
         my $cats = join(" ", @cats);  
         # Check to determine whether or not the caller wants to turn off tracing  
         # to the standard output.  
         my $traceLevel = $retOptions->{trace};  
         my $textOKFlag = 1;  
         if ($traceLevel =~ /^(.)-/) {  
             $traceLevel = $1;  
             $textOKFlag = 0;  
         }  
         # Now we set up the trace mode.  
         my $traceMode;  
         # Verify that we can open a file in the FIG temporary directory.  
         my $traceFileName = "$FIG_Config::temp/trace$suffix.log";  
         if (open TESTTRACE, ">$traceFileName") {  
             # Here we can trace to a file.  
             $traceMode = ">$traceFileName";  
             if ($textOKFlag) {  
                 # Echo to standard output if the text-OK flag is set.  
                 $traceMode = "+$traceMode";  
             }  
             # Close the test file.  
             close TESTTRACE;  
         } else {  
             # Here we can't trace to a file. We trace to the standard output if it's  
             # okay, and the error log otherwise.  
             if ($textOKFlag) {  
                 $traceMode = "TEXT";  
552              } else {              } else {
553                  $traceMode = "WARN";                  my @cats = split /::/, $package;
554              }                  $category = $cats[$#cats];
         }  
         # Now set up the tracing.  
         TSetup("$traceLevel $cats", $traceMode);  
555      }      }
     # Check for the "h" option. If it is specified, dump the command-line  
     # options and exit the program.  
     if ($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] . ")";  
556              }              }
557              print "  $name $desc\n";          # Save the category name and level.
558            $LastCategory = $category;
559            $LastLevel = $traceLevel;
560            # Convert it to lower case before we hash it.
561            $category = lc $category;
562            # Validate the trace level.
563            if (ref $traceLevel) {
564                Confess("Bad trace level.");
565            } elsif (ref $TraceLevel) {
566                Confess("Bad trace config.");
567          }          }
568          exit(0);          # Make the check. Note that level 0 shows even if the category is turned off.
569            $retVal = ($traceLevel <= $TraceLevel && ($traceLevel == 0 || $AllTrace || exists $Categories{$category}));
570      }      }
571      # Return the parsed parameters.      # Return the computed result.
572      return ($retOptions, @retParameters);      return $retVal;
573  }  }
574    
575  =head3 Setups  =head3 QTrace
   
 C<< my $count = Tracer::Setups(); >>  
   
 Return the number of times L</TSetup> has been called.  
   
 This method allows for the creation of conditional tracing setups where, for example, we  
 may want to set up tracing if nobody else has done it before us.  
   
 =cut  
576    
577  sub Setups {      my $data = QTrace($format);
     return $SetupCount;  
 }  
578    
579  =head3 Open  Return the queued trace data in the specified format.
580    
581  C<< my $handle = Open($fileHandle, $fileSpec, $message); >>  =over 4
582    
583  Open a file.  =item format
584    
585  The I<$fileSpec> is essentially the second argument of the PERL C<open>  C<html> to format the data as an HTML list, C<text> to format it as straight text.
 function. The mode is specified using Unix-like shell information. So, for  
 example,  
586    
587      Open(\*LOGFILE, '>>/usr/spool/news/twitlog', "Could not open twit log.");  =back
588    
589  would open for output appended to the specified file, and  =cut
590    
591      Open(\*DATASTREAM, "| sort -u >$outputFile", "Could not open $outputFile.");  sub QTrace {
592        # Get the parameter.
593        my ($format) = @_;
594        # Create the return variable.
595        my $retVal = "";
596        # Only proceed if there is an actual queue.
597        if (@Queue) {
598            # Process according to the format.
599            if ($format =~ m/^HTML$/i) {
600                # Convert the queue into an HTML list.
601                $retVal = "<ul>\n";
602                for my $line (@Queue) {
603                    my $escapedLine = CGI::escapeHTML($line);
604                    $retVal .= "<li>$escapedLine</li>\n";
605                }
606                $retVal .= "</ul>\n";
607            } elsif ($format =~ m/^TEXT$/i) {
608                # Convert the queue into a list of text lines.
609                $retVal = join("\n", @Queue) . "\n";
610            }
611            # Clear the queue.
612            @Queue = ();
613        }
614        # Return the formatted list.
615        return $retVal;
616    }
617    
618  would open a pipe that sorts the records written and removes duplicates. Note  =head3 Confess
 the use of file handle syntax in the Open call. To use anonymous file handles,  
 code as follows.  
619    
620      my $logFile = Open(undef, '>>/usr/spool/news/twitlog', "Could not open twit log.");      Confess($message);
621    
622  The I<$message> parameter is used if the open fails. If it is set to C<0>, then  Trace the call stack and abort the program with the specified message. When used with
623  the open returns TRUE if successful and FALSE if an error occurred. Otherwise, a  the OR operator and the L</Assert> method, B<Confess> can function as a debugging assert.
624  failed open will throw an exception and the third parameter will be used to construct  So, for example
 an error message. If the parameter is omitted, a standard message is constructed  
 using the file spec.  
625    
626      Could not open "/usr/spool/news/twitlog"      Assert($recNum >= 0) || Confess("Invalid record number $recNum.");
627    
628  Note that the mode characters are automatically cleaned from the file name.  Will abort the program with a stack trace if the value of C<$recNum> is negative.
 The actual error message from the file system will be captured and appended to the  
 message in any case.  
629    
630      Could not open "/usr/spool/news/twitlog": file not found.  =over 4
631    
632  In some versions of PERL the only error message we get is a number, which  =item message
 corresponds to the C++ C<errno> value.  
633    
634      Could not open "/usr/spool/news/twitlog": 6.  Message to include in the trace.
635    
636  =over 4  =back
637    
638  =item fileHandle  =cut
639    
640  File handle. If this parameter is C<undef>, a file handle will be generated  sub Confess {
641  and returned as the value of this method.      # Get the parameters.
642        my ($message) = @_;
643        # Set up the category and level.
644        $LastCategory = "(confess)";
645        $LastLevel = 0;
646        if (! defined($FIG_Config::no_tool_hdr)) {
647            # Here we have a tool header. Display its length so that the user can adjust the line numbers.
648            my $toolHeaderFile = "$FIG_Config::fig_disk/dist/releases/current/$FIG_Config::arch/tool_hdr";
649            # Only proceed if the tool header file is actually present.
650            if (-f $toolHeaderFile) {
651                my $fh;
652                if (open $fh, "<$toolHeaderFile") {
653                    my @lines = <$fh>;
654                    Trace("Tool header has " . scalar(@lines) . " lines.");
655                }
656            }
657        }
658        # Trace the call stack.
659        Cluck($message);
660        # Abort the program.
661        croak(">>> $message");
662    }
663    
664  =item fileSpec  =head3 Warn
665    
666  File name and mode, as per the PERL C<open> function.      Warn($message);
667    
668  =item message (optional)  This method traces an important message. If an RSS feed is configured
669    (via I<FIG_Config::error_feed>) and the tracing destination is C<WARN>,
670    then the message will be echoed to the feed. In general, a tracing
671    destination of C<WARN> indicates that the caller is running as a web
672    service in a production environment; however, this is not a requirement.
673    
674    To force warnings into the RSS feed even when the tracing destination
675    is not C<WARN>, simply specify the C<Feed> tracing module. This can be
676    configured automatically when L</StandardSetup> is used.
677    
678    The L</Cluck> method calls this one for its final message. Since
679    L</Confess> calls L</Cluck>, this means that any error which is caught
680    and confessed will put something in the feed. This insures that someone
681    will be alerted relatively quickly when a failure occurs.
682    
683  Error message to use if the open fails. If omitted, a standard error message  =over 4
 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>.  
684    
685  =item RETURN  =item message
686    
687  Returns the name of the file handle assigned to the file, or C<undef> if the  Message to be traced.
 open failed.  
688    
689  =back  =back
690    
691  =cut  =cut
692    
693  sub Open {  sub Warn {
694      # Get the parameters.      # Get the parameters.
695      my ($fileHandle, $fileSpec, $message) = @_;      my ($message) = @_;
696      # Attempt to open the file.      # Trace the message.
697      my $rv = open $fileHandle, $fileSpec;      Trace($message);
698      # If the open failed, generate an error message.      # Check for feed forcing.
699      if (! $rv) {      my $forceFeed = exists $Categories{feed};
700          # Save the system error message.      # An error here would be disastrous. Note, however, that we aren't too worried
701          my $sysMessage = $!;      # about losing events. The error log is always available for the occasions where
702          # See if we need a default message.      # we mess up. Note that if debug mode is specified, we do this stuff even in a
703          if (!$message) {      # test environment.
704              # Clean any obvious mode characters and leading spaces from the      eval {
705              # filename.          # Do we need to put this in the RSS feed?
706              my ($fileName) = FindNamePart($fileSpec);          if ($FIG_Config::error_feed && ($Destination eq 'WARN' || $forceFeed)) {
707              $message = "Could not open \"$fileName\"";              # Yes. We now need to compute the date, the link, and the title.
708                # First, the date, in a very specific format.
709                my $date = strftime("%a, %02e %b %H:%M:%S %Y ", localtime) .
710                    (tz_local_offset() / 30);
711                # Environment data goes in here. We start with the date.
712                my $environment = "$date.  ";
713                # If we need to recap the message (because it's too long to be a title), we'll
714                # put it in here.
715                my $recap;
716                # Copy the message and remove excess space.
717                my $title = $message;
718                $title =~ s/\s+/ /gs;
719                # If it's too long, we have to split it up.
720                if (length $title > 60) {
721                    # Put the full message in the environment string.
722                    $recap = $title;
723                    # Excerpt it as the title.
724                    $title = substr($title, 0, 50) . "...";
725                }
726                # If we have a CGI object, then this is a web error. Otherwise, it's
727                # command-line.
728                if (defined $SavedCGI) {
729                    # We're in a web service. The environment is the user's IP, and the link
730                    # is the URL that got us here.
731                    my $key = $ENV{HTTP_X_FORWARDED_FOR} || $ENV{REMOTE_ADDR};
732                    $environment .= "Event Reported at IP address $key.";
733                    my $url = $SavedCGI->url(-full => 1, -query => 1);
734                    # We need the user agent string and (if available) the referrer.
735                    # The referrer will be the link.
736                    $environment .= "User Agent $ENV{HTTP_USER_AGENT}";
737                    if ($ENV{HTTP_REFERER}) {
738                        my $link = $ENV{HTTP_REFERER};
739                        $environment .= " referred from <a href=\"$link\">$link</a>.";
740                    } else {
741                        $environment .= " referrer unknown.";
742                    }
743                    # Close off the sentence with the original link.
744                    $environment .= " URL of error is <a href=\"$url\">$url</a>.";
745                } else {
746                    # No CGI object, so we're a command-line tool. Use the tracing
747                    # key and the PID as the user identifier, and add the command.
748                    my $key = EmergencyKey();
749                    $environment .= "Event Reported by $key Process $$.";
750                    if ($CommandLine) {
751                        # We're in a StandardSetup script, so we have the real command line.
752                        $environment .= "\n<pre>" . CGI::escapeHTML($CommandLine) . "</pre>\n";
753                    } elsif ($ENV{_}) {
754                        # We're in a BASH script, so the command has been stored in the _ variable.
755                        $environment .= "  Command = " . CGI::escapeHTML($ENV{_}) . "\n";
756                    }
757                }
758                # Build a GUID. We use the current time, the title, and the process ID,
759                # then digest the result.
760                my $guid = Digest::MD5::md5_base64(gettimeofday(), $title, $$);
761                # Finally, the description. This is a stack trace plus various environmental stuff.
762                my $stackTrace = "";
763                my @trace = LongMess();
764                # Only proceed if we got something back.
765                if (scalar(@trace) > 0) {
766                    $trace[0] =~ s/Tracer::Warn.+?called/Event occurred/;
767                    $stackTrace = "Stack trace:<pre>" . join("\n", @trace, "</pre>");
768                }
769                # We got the stack trace. Now it's time to put it all together.
770                # We have a goofy thing here in that we need to HTML-escape some sections of the description
771                # twice. They will be escaped once here, and then once when written by XML::Simple. They are
772                # unescaped once when processed by the RSS reader, and stuff in the description is treated as
773                # HTML. So, anything escaped here is treated as a literal when viewed in the RSS reader, but
774                # our <br>s and <pre>s are used to format the description.
775                $recap = (defined $recap ? "<em>" . CGI::escapeHTML($recap) . "</em><br /><br />" : "");
776                my $description = "$recap$environment  $stackTrace";
777                # Okay, we have all the pieces. Create a hash of the new event.
778                my $newItem = { title => $title,
779                                description => $description,
780                                category => $LastCategory,
781                                pubDate => $date,
782                                guid => $guid,
783                               };
784                # We need XML capability for this.
785                require XML::Simple;
786                # The RSS document goes in here.
787                my $rss;
788                # Get the name of the RSS file. It's in the FIG temporary directory.
789                my $fileName = "$FIG_Config::temp/$FIG_Config::error_feed";
790                # Does it exist?
791                if (-s $fileName) {
792                    # Slurp it in.
793                    $rss = XML::Simple::XMLin($fileName, ForceArray => ['item']);
794                } else {
795                    my $size = -s $fileName;
796                    # Create an empty channel.
797                    $rss = {
798                        channel => {
799                            title => 'NMPDR Warning Feed',
800                            link => "$FIG_Config::temp_url/$FIG_Config::error_feed",
801                            description => "Important messages regarding the status of the NMPDR.",
802                            generator => "NMPDR Trace Facility",
803                            docs => "http://blogs.law.harvard.edu/tech/rss",
804                            item => []
805                        },
806                    };
807          }          }
808          # Terminate with an error using the supplied message and the              # Get the channel object.
809          # error message from the file system.              my $channel = $rss->{channel};
810          Confess("$message: $!");              # Update the last-build date.
811                $channel->{lastBuildDate} = $date;
812                # Get the item array.
813                my $items = $channel->{item};
814                # Insure it has only 100 entries.
815                while (scalar @{$items} > 100) {
816                    pop @{$items};
817                }
818                # Add our new item at the front.
819                unshift @{$items}, $newItem;
820                # Create the XML. Note we do not include the root or the declaration. XML Simple can't handle
821                # the requirements for those.
822                my $xml = XML::Simple::XMLout($rss, NoAttr => 1, RootName => undef, XmlDecl => '');
823                # Here we put in the root and declaration. The problem is that the root has to have the version attribute
824                # in it. So, we suppress the root and do it by hand, and that requires suppressing the declaration, too.
825                $xml = "<?xml version=\"1.0\" encoding=\"utf-8\"?>\n<rss version=\"2.0\">$xml\n</rss>";
826                # We don't use Open here because we can't afford an error.
827                if (open XMLOUT, ">$fileName") {
828                    print XMLOUT $xml;
829                    close XMLOUT;
830                }
831            }
832        };
833        if ($@) {
834            # If the feed failed, we need to know why. The error will be traced, but this method will not be involved
835            # (which is a good thing).
836            my $error = $@;
837            Trace("Feed Error: $error") if T(Feed => 0);
838      }      }
     # Return the file handle.  
     return $fileHandle;  
839  }  }
840    
841  =head3 FindNamePart  =head3 Assert
   
 C<< my ($fileName, $start, $len) = Tracer::FindNamePart($fileSpec); >>  
842    
843  Extract the portion of a file specification that contains the file name.      Assert($condition1, $condition2, ... $conditionN);
844    
845  A file specification is the string passed to an C<open> call. It specifies the file  Return TRUE if all the conditions are true. This method can be used in conjunction with
846  mode and name. In a truly complex situation, it can specify a pipe sequence. This  the OR operator and the L</Confess> method as a debugging assert.
847  method assumes that the file name is whatever follows the first angle bracket  So, for example
 sequence.  So, for example, in the following strings the file name is  
 C</usr/fig/myfile.txt>.  
848    
849      >>/usr/fig/myfile.txt      Assert($recNum >= 0) || Confess("Invalid record number $recNum.");
     </usr/fig/myfile.txt  
     | sort -u > /usr/fig/myfile.txt  
850    
851  If the method cannot find a file name using its normal methods, it will return the  Will abort the program with a stack trace if the value of C<$recNum> is negative.
 whole incoming string.  
852    
853  =over 4  =cut
854    sub Assert {
855        my $retVal = 1;
856        LOOP: for my $condition (@_) {
857            if (! $condition) {
858                $retVal = 0;
859                last LOOP;
860            }
861        }
862        return $retVal;
863    }
864    
865  =item fileSpec  =head3 Cluck
866    
867  File specification string from which the file name is to be extracted.      Cluck($message);
868    
869  =item RETURN  Trace the call stack. Note that for best results, you should qualify the call with a
870    trace condition. For example,
871    
872  Returns a three-element list. The first element contains the file name portion of      Cluck("Starting record parse.") if T(3);
873  the specified string, or the whole string if a file name cannot be found via normal  
874  methods. The second element contains the start position of the file name portion and  will only trace the stack if the trace level for the package is 3 or more.
875  the third element contains the length.  
876    =over 4
877    
878    =item message
879    
880    Message to include in the trace.
881    
882  =back  =back
883    
884  =cut  =cut
885  #: Return Type $;  
886  sub FindNamePart {  sub Cluck {
887      # Get the parameters.      # Get the parameters.
888      my ($fileSpec) = @_;      my ($message) = @_;
889      # Default to the whole input string.      # Trace what's happening.
890      my ($retVal, $pos, $len) = ($fileSpec, 0, length $fileSpec);      Trace("Stack trace for event: $message");
891      # Parse out the file name if we can.      # Get the stack trace.
892      if ($fileSpec =~ m/(<|>>?)(.+?)(\s*)$/) {      my @trace = LongMess();
893          $retVal = $2;      # Convert the trace to a series of messages.
894          $len = length $retVal;      for my $line (@trace) {
895          $pos = (length $fileSpec) - (length $3) - $len;          # Replace the tab at the beginning with spaces.
896            $line =~ s/^\t/    /;
897            # Trace the line.
898            Trace($line);
899      }      }
900      # Return the result.      # Issue a warning. This displays the event message and inserts it into the RSS error feed.
901      return ($retVal, $pos, $len);      Warn($message);
902  }  }
903    
904  =head3 OpenDir  =head3 LongMess
905    
906  C<< my @files = OpenDir($dirName, $filtered, $flag); >>      my @lines = Tracer::LongMess();
907    
908  Open a directory and return all the file names. This function essentially performs  Return a stack trace with all tracing methods removed. The return will be in the form of a list
909  the functions of an C<opendir> and C<readdir>. If the I<$filtered> parameter is  of message strings.
 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,  
910    
911      my @files = OpenDir("/Volumes/fig/contigs", 1);  =cut
912    
913  is effectively the same as  sub LongMess {
914        # Declare the return variable.
915        my @retVal = ();
916        my $confession = longmess("");
917        for my $line (split /\s*\n/, $confession) {
918            unless ($line =~ /Tracer\.pm/) {
919                # Here we have a line worth keeping. Push it onto the result list.
920                push @retVal, $line;
921            }
922        }
923        # Return the result.
924        return @retVal;
925    }
926    
927      opendir(TMP, "/Volumes/fig/contigs") || Confess("Could not open /Volumes/fig/contigs.");  =head3 ScriptSetup (deprecated)
     my @files = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir(TMP);  
928    
929  Similarly, the following code      my ($cgi, $varHash) = ScriptSetup($noTrace);
930    
931      my @files = grep { $_ =~ /^\d/ } OpenDir("/Volumes/fig/orgs", 0, 1);  Perform standard tracing and debugging setup for scripts. The value returned is
932    the CGI object followed by a pre-built variable hash. At the end of the script,
933    the client should call L</ScriptFinish> to output the web page.
934    
935  Returns the names of all files in C</Volumes/fig/orgs> that begin with digits and  This method calls L</ETracing> to configure tracing, which allows the tracing
936  automatically returns an empty list if the directory fails to open.  to be configured via the emergency tracing form on the debugging control panel.
937    Tracing will then be turned on automatically for all programs that use the L</ETracing>
938    method, which includes every program that uses this method or L</StandardSetup>.
939    
940  =over 4  =over 4
941    
942  =item dirName  =item noTrace (optional)
943    
944  Name of the directory to open.  If specified, tracing will be suppressed. This is useful if the script wants to set up
945    tracing manually.
946    
947  =item filtered  =item RETURN
948    
949  TRUE if files whose names begin with a period (C<.>) should be automatically removed  Returns a two-element list consisting of a CGI query object and a variable hash for
950  from the list, else FALSE.  the output page.
951    
952  =item flag  =back
953    
954  TRUE if a failure to open is okay, else FALSE  =cut
955    
956    sub ScriptSetup {
957        # Get the parameters.
958        my ($noTrace) = @_;
959        # Get the CGI query object.
960        my $cgi = CGI->new();
961        # Set up tracing if it's not suppressed.
962        ETracing($cgi) unless $noTrace;
963        # Create the variable hash.
964        my $varHash = { results => '' };
965        # Return the query object and variable hash.
966        return ($cgi, $varHash);
967    }
968    
969    =head3 ETracing
970    
971        ETracing($parameter);
972    
973    Set up emergency tracing. Emergency tracing is tracing that is turned
974    on automatically for any program that calls this method. The emergency
975    tracing parameters are stored in a a file identified by a tracing key.
976    If this method is called with a CGI object, then the tracing key is
977    taken from a cookie. If it is called with no parameters, then the tracing
978    key is taken from an environment variable. If it is called with a string,
979    the tracing key is that string.
980    
981    =over 4
982    
983    =item parameter
984    
985    A parameter from which the tracing key is computed. If it is a scalar,
986    that scalar is used as the tracing key. If it is a CGI object, the
987    tracing key is taken from the C<IP> cookie. If it is omitted, the
988    tracing key is taken from the C<TRACING> environment variable. If it
989    is a CGI object and emergency tracing is not on, the C<Trace> and
990    C<TF> parameters will be used to determine the type of tracing.
991    
992  =back  =back
993    
994  =cut  =cut
995  #: Return Type @;  
996  sub OpenDir {  sub ETracing {
997      # Get the parameters.      # Get the parameter.
998      my ($dirName, $filtered, $flag) = @_;      my ($parameter) = @_;
999      # Declare the return variable.      # Check for CGI mode.
1000      my @retVal = ();      if (defined $parameter && ref $parameter eq 'CGI') {
1001      # Open the directory.          $SavedCGI = $parameter;
     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;  
1002          } else {          } else {
1003              @retVal = readdir $dirHandle;          $SavedCGI = undef;
1004        }
1005        # Default to no tracing except errors.
1006        my ($tracing, $dest) = ("0", "WARN");
1007        # Check for emergency tracing.
1008        my $tkey = EmergencyKey($parameter);
1009        my $emergencyFile = EmergencyFileName($tkey);
1010        if (-e $emergencyFile) {
1011            # We have the file. Read in the data.
1012            my @tracing = GetFile($emergencyFile);
1013            # Pull off the time limit.
1014            my $expire = shift @tracing;
1015            # Convert it to seconds.
1016            $expire *= 3600;
1017            # Check the file data.
1018            my $stat = stat($emergencyFile);
1019            my ($now) = gettimeofday;
1020            if ($now - $stat->mtime > $expire) {
1021                # Delete the expired file.
1022                unlink $emergencyFile;
1023            } else {
1024                # Emergency tracing is on. Pull off the destination and
1025                # the trace level;
1026                $dest = shift @tracing;
1027                my $level = shift @tracing;
1028                # Convert the destination to a real tracing destination.
1029                # temp directory.
1030                $dest = EmergencyTracingDest($tkey, $dest);
1031                # Insure Tracer is specified.
1032                my %moduleHash = map { $_ => 1 } @tracing;
1033                $moduleHash{Tracer} = 1;
1034                # Set the trace parameter.
1035                $tracing = join(" ", $level, sort keys %moduleHash);
1036            }
1037        } elsif (defined $SavedCGI) {
1038            # There's no emergency tracing, but we have a CGI object, so check
1039            # for tracing from the form parameters.
1040            if ($SavedCGI->param('Trace')) {
1041                # Here the user has requested tracing via a form.
1042                $dest = ($SavedCGI->param('TF') ? ">$FIG_Config::temp/Trace$$.log" : "QUEUE");
1043                $tracing = $SavedCGI->param('Trace') . " Tracer";
1044            }
1045        }
1046        # Setup the tracing we've determined from all the stuff above.
1047        TSetup($tracing, $dest);
1048        # Check to see if we're a web script.
1049        if (defined $SavedCGI) {
1050            # Yes we are. Trace the form and environment data.
1051            TraceParms($SavedCGI);
1052            # Check for RAW mode. In raw mode, we print a fake header so that we see everything
1053            # emitted by the script in its raw form.
1054            if (T(Raw => 3)) {
1055                print CGI::header(-type => 'text/plain', -tracing => 'Raw');
1056          }          }
     } elsif (! $flag) {  
         # Here the directory would not open and it's considered an error.  
         Confess("Could not open directory $dirName.");  
1057      }      }
     # Return the result.  
     return @retVal;  
1058  }  }
1059    
1060  =head3 SetLevel  =head3 EmergencyFileName
1061    
1062  C<< Tracer::SetLevel($newLevel); >>      my $fileName = Tracer::EmergencyFileName($tkey);
1063    
1064  Modify the trace level. A higher trace level will cause more messages to appear.  Return the emergency tracing file name. This is the file that specifies
1065    the tracing information.
1066    
1067  =over 4  =over 4
1068    
1069  =item newLevel  =item tkey
1070    
1071  Proposed new trace level.  Tracing key for the current program.
1072    
1073    =item RETURN
1074    
1075    Returns the name of the file to contain the emergency tracing information.
1076    
1077  =back  =back
1078    
1079  =cut  =cut
1080    
1081  sub SetLevel {  sub EmergencyFileName {
1082      $TraceLevel = $_[0];      # Get the parameters.
1083        my ($tkey) = @_;
1084        # Compute the emergency tracing file name.
1085        return "$FIG_Config::temp/Emergency$tkey.txt";
1086  }  }
1087    
1088  =head3 Now  =head3 EmergencyFileTarget
1089    
1090  C<< my $string = Tracer::Now(); >>      my $fileName = Tracer::EmergencyFileTarget($tkey);
1091    
1092  Return a displayable time stamp containing the local time.  Return the emergency tracing target file name. This is the file that receives
1093    the tracing output for file-based tracing.
1094    
1095    =over 4
1096    
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 trace output.
1104    
1105    =back
1106    
1107  =cut  =cut
1108    
1109  sub Now {  sub EmergencyFileTarget {
1110      my ($sec,$min,$hour,$mday,$mon,$year,$wday,$yday,$isdst) = localtime(time);      # Get the parameters.
1111      my $retVal = _p2($mon+1) . "/" . _p2($mday) . "/" . ($year + 1900) . " " .      my ($tkey) = @_;
1112                   _p2($hour) . ":" . _p2($min) . ":" . _p2($sec);      # Compute the emergency tracing file name.
1113      return $retVal;      return "$FIG_Config::temp/trace$tkey.log";
1114    }
1115    
1116    =head3 EmergencyTracingDest
1117    
1118        my $dest = Tracer::EmergencyTracingDest($tkey, $myDest);
1119    
1120    This method converts an emergency tracing destination to a real
1121    tracing destination. The main difference is that if the
1122    destination is C<FILE> or C<APPEND>, we convert it to file
1123    output. If the destination is C<DUAL>, we convert it to file
1124    and standard output.
1125    
1126    =over 4
1127    
1128    =item tkey
1129    
1130    Tracing key for this environment.
1131    
1132    =item myDest
1133    
1134    Destination from the emergency tracing file.
1135    
1136    =item RETURN
1137    
1138    Returns a destination that can be passed into L</TSetup>.
1139    
1140    =back
1141    
1142    =cut
1143    
1144    sub EmergencyTracingDest {
1145        # Get the parameters.
1146        my ($tkey, $myDest) = @_;
1147        # Declare the return variable.
1148        my $retVal = $myDest;
1149        # Process according to the destination value.
1150        if ($myDest eq 'FILE') {
1151            $retVal = ">" . EmergencyFileTarget($tkey);
1152        } elsif ($myDest eq 'APPEND') {
1153            $retVal = ">>" . EmergencyFileTarget($tkey);
1154        } elsif ($myDest eq 'DUAL') {
1155            $retVal = "+>" . EmergencyFileTarget($tkey);
1156        } elsif ($myDest eq 'WARN') {
1157            $retVal = "WARN";
1158        }
1159        # Return the result.
1160        return $retVal;
1161    }
1162    
1163    =head3 Emergency
1164    
1165        Emergency($key, $hours, $dest, $level, @modules);
1166    
1167    Turn on emergency tracing. This method is normally invoked over the web from
1168    a debugging console, but it can also be called by the C<trace.pl> script.
1169    The caller specifies the duration of the emergency in hours, the desired tracing
1170    destination, the trace level, and a list of the trace modules to activate.
1171    For the length of the duration, when a program in an environment with the
1172    specified tracing key active invokes a Sprout CGI script, tracing will be
1173    turned on automatically. See L</TSetup> for more about tracing setup and
1174    L</ETracing> for more about emergency tracing.
1175    
1176    =over 4
1177    
1178    =item tkey
1179    
1180    The tracing key. This is used to identify the control file and the trace file.
1181    
1182    =item hours
1183    
1184    Number of hours to keep emergency tracing alive.
1185    
1186    =item dest
1187    
1188    Tracing destination. If no path information is specified for a file
1189    destination, it is put in the FIG temporary directory.
1190    
1191    =item level
1192    
1193    Tracing level. A higher level means more trace messages.
1194    
1195    =item modules
1196    
1197    A list of the tracing modules to activate.
1198    
1199    =back
1200    
1201    =cut
1202    
1203    sub Emergency {
1204        # Get the parameters.
1205        my ($tkey, $hours, $dest, $level, @modules) = @_;
1206        # Create the emergency file.
1207        my $specFile = EmergencyFileName($tkey);
1208        my $outHandle = Open(undef, ">$specFile");
1209        print $outHandle join("\n", $hours, $dest, $level, @modules, "");
1210    }
1211    
1212    =head3 EmergencyKey
1213    
1214        my $tkey = EmergencyKey($parameter);
1215    
1216    Return the Key to be used for emergency tracing. This could be an IP address,
1217     a session ID, or a user name, depending on the environment.
1218    
1219    =over 4
1220    
1221    =item parameter
1222    
1223    Parameter defining the method for finding the tracing key. If it is a scalar,
1224    then it is presumed to be the tracing key itself. If it is a CGI object, then
1225    the tracing key is taken from the C<IP> cookie. Otherwise, the tracing key is
1226    taken from the C<TRACING> environment variable.
1227    
1228    =item RETURN
1229    
1230    Returns the key to be used for labels in emergency tracing.
1231    
1232    =back
1233    
1234    =cut
1235    
1236    sub EmergencyKey {
1237        # Get the parameters.
1238        my ($parameter) = @_;
1239        # Declare the return variable.
1240        my $retVal;
1241        # Determine the parameter type.
1242        if (! defined $parameter) {
1243            # Here we're supposed to check the environment. If that fails, we
1244            # get the effective login ID.
1245            $retVal = $ENV{TRACING} || scalar getpwuid($<);
1246        } else {
1247            my $ptype = ref $parameter;
1248            if ($ptype eq 'CGI') {
1249                # Here we were invoked from a web page. Look for a cookie.
1250                $retVal = $parameter->cookie('IP');
1251            } elsif (! $ptype) {
1252                # Here the key was passed in.
1253                $retVal = $parameter;
1254            }
1255        }
1256        # If no luck finding a key, use the PID.
1257        if (! defined $retVal) {
1258            $retVal = $$;
1259        }
1260        # Return the result.
1261        return $retVal;
1262    }
1263    
1264    
1265    =head3 TraceParms
1266    
1267        Tracer::TraceParms($cgi);
1268    
1269    Trace the CGI parameters at trace level CGI => 3 and the environment variables
1270    at level CGI => 4. A self-referencing URL is traced at level CGI => 2.
1271    
1272    =over 4
1273    
1274    =item cgi
1275    
1276    CGI query object containing the parameters to trace.
1277    
1278    =back
1279    
1280    =cut
1281    
1282    sub TraceParms {
1283        # Get the parameters.
1284        my ($cgi) = @_;
1285        if (T(CGI => 2)) {
1286            # Here we trace the GET-style URL for the script.
1287            Trace("[URL] " . $cgi->url(-relative => 1, -query => 1));
1288        }
1289        if (T(CGI => 3)) {
1290            # Here we want to trace the parameter data.
1291            my @names = $cgi->param;
1292            for my $parmName (sort @names) {
1293                # Note we skip the Trace parameters, which are for our use only.
1294                if ($parmName ne 'Trace' && $parmName ne 'TF') {
1295                    my @values = $cgi->param($parmName);
1296                    Trace("[CGI] $parmName = " . join(", ", @values));
1297                }
1298            }
1299            # Display the request method.
1300            my $method = $cgi->request_method();
1301            Trace("Method: $method");
1302        }
1303        if (T(CGI => 4)) {
1304            # Here we want the environment data too.
1305            for my $envName (sort keys %ENV) {
1306                Trace("[ENV] $envName = $ENV{$envName}");
1307            }
1308        }
1309    }
1310    
1311    =head3 TraceImages
1312    
1313        Tracer::TraceImages($htmlString);
1314    
1315    Trace information about all of an html document's images. The tracing
1316    will be for type "IMG" at level 3. The image's source string
1317    will be displayed. This is generally either the URL of the image or
1318    raw data for the image itself. If the source is too long, only the first 300
1319    characters will be shown at trace level 3. The entire source will be shown,
1320    however, at trace level 4. This method is not very smart, and might catch
1321    Javascript code, but it is still useful when debugging the arcane
1322    behavior of images in multiple browser environments.
1323    
1324    =over 4
1325    
1326    =item htmlString
1327    
1328    HTML text for an outgoing web page.
1329    
1330    =back
1331    
1332    =cut
1333    
1334    sub TraceImages {
1335        # Only proceed if we're at the proper trace level.
1336        if (T(IMG => 3)) {
1337            # For performance reasons we're manipulating $_[0] instead of retrieving the string
1338            # into a variable called "$htmlString". This is because we expect html strings to be
1339            # long, and don't want to copy them any more than we have to.
1340            Trace(length($_[0]) . " characters in web page.");
1341            # Loop through the HTML, culling image tags.
1342            while ($_[0] =~ /<img\s+[^>]+?src="([^"]+)"/sgi) {
1343                # Extract the source string and determine whether or not it's too long.
1344                my $srcString = $1;
1345                my $pos = pos($_[0]) - length($srcString);
1346                my $excess = length($srcString) - 300;
1347                # We'll put the display string in here.
1348                my $srcDisplay = $srcString;
1349                # If it's a data string, split it at the comma.
1350                $srcDisplay =~ s/^(data[^,]+,)/$1\n/;
1351                # If there's no excess or we're at trace level 4, we're done. At level 3 with
1352                # a long string, however, we only show the first 300 characters.
1353                if ($excess > 0 && ! T(IMG => 4)) {
1354                    $srcDisplay = substr($srcDisplay,0,300) . "\nplus $excess characters.";
1355                }
1356                # Output the trace message.
1357                Trace("Image tag at position $pos:\n$srcDisplay");
1358            }
1359        }
1360    }
1361    
1362    
1363    =head3 ScriptFinish (deprecated)
1364    
1365        ScriptFinish($webData, $varHash);
1366    
1367    Output a web page at the end of a script. Either the string to be output or the
1368    name of a template file can be specified. If the second parameter is omitted,
1369    it is assumed we have a string to be output; otherwise, it is assumed we have the
1370    name of a template file. The template should have the variable C<DebugData>
1371    specified in any form that invokes a standard script. If debugging mode is turned
1372    on, a form field will be put in that allows the user to enter tracing data.
1373    Trace messages will be placed immediately before the terminal C<BODY> tag in
1374    the output, formatted as a list.
1375    
1376    A typical standard script would loook like the following.
1377    
1378        BEGIN {
1379            # Print the HTML header.
1380            print "CONTENT-TYPE: text/html\n\n";
1381        }
1382        use Tracer;
1383        use CGI;
1384        use FIG;
1385        # ... more uses ...
1386    
1387        my ($cgi, $varHash) = ScriptSetup();
1388        eval {
1389            # ... get data from $cgi, put it in $varHash ...
1390        };
1391        if ($@) {
1392            Trace("Script Error: $@") if T(0);
1393        }
1394        ScriptFinish("Html/MyTemplate.html", $varHash);
1395    
1396    The idea here is that even if the script fails, you'll see trace messages and
1397    useful output.
1398    
1399    =over 4
1400    
1401    =item webData
1402    
1403    A string containing either the full web page to be written to the output or the
1404    name of a template file from which the page is to be constructed. If the name
1405    of a template file is specified, then the second parameter must be present;
1406    otherwise, it must be absent.
1407    
1408    =item varHash (optional)
1409    
1410    If specified, then a reference to a hash mapping variable names for a template
1411    to their values. The template file will be read into memory, and variable markers
1412    will be replaced by data in this hash reference.
1413    
1414    =back
1415    
1416    =cut
1417    
1418    sub ScriptFinish {
1419        # Get the parameters.
1420        my ($webData, $varHash) = @_;
1421        # Check for a template file situation.
1422        my $outputString;
1423        if (defined $varHash) {
1424            # Here we have a template file. We need to determine the template type.
1425            my $template;
1426            if ($FIG_Config::template_url && $webData =~ /\.php$/) {
1427                $template = "$FIG_Config::template_url/$webData";
1428            } else {
1429                $template = "<<$webData";
1430            }
1431            $outputString = PageBuilder::Build($template, $varHash, "Html");
1432        } else {
1433            # Here the user gave us a raw string.
1434            $outputString = $webData;
1435        }
1436        # Check for trace messages.
1437        if ($Destination ne "NONE" && $TraceLevel > 0) {
1438            # We have trace messages, so we want to put them at the end of the body. This
1439            # is either at the end of the whole string or at the beginning of the BODY
1440            # end-tag.
1441            my $pos = length $outputString;
1442            if ($outputString =~ m#</body>#gi) {
1443                $pos = (pos $outputString) - 7;
1444            }
1445            # If the trace messages were queued, we unroll them. Otherwise, we display the
1446            # destination.
1447            my $traceHtml;
1448            if ($Destination eq "QUEUE") {
1449                $traceHtml = QTrace('Html');
1450            } elsif ($Destination =~ /^>>(.+)$/) {
1451                # Here the tracing output it to a file. We code it as a hyperlink so the user
1452                # can copy the file name into the clipboard easily.
1453                my $actualDest = $1;
1454                $traceHtml = "<p>Tracing output to $actualDest.</p>\n";
1455            } else {
1456                # Here we have one of the special destinations.
1457                $traceHtml = "<P>Tracing output type is $Destination.</p>\n";
1458            }
1459            substr $outputString, $pos, 0, $traceHtml;
1460        }
1461        # Write the output string.
1462        print $outputString;
1463    }
1464    
1465    =head2 Command-Line Utility Methods
1466    
1467    =head3 SendSMS
1468    
1469        my $msgID = Tracer::SendSMS($phoneNumber, $msg);
1470    
1471    Send a text message to a phone number using Clickatell. The FIG_Config file must contain the
1472    user name, password, and API ID for the relevant account in the hash reference variable
1473    I<$FIG_Config::phone>, using the keys C<user>, C<password>, and C<api_id>. For
1474    example, if the user name is C<BruceTheHumanPet>, the password is C<silly>, and the API ID
1475    is C<2561022>, then the FIG_Config file must contain
1476    
1477        $phone =  { user => 'BruceTheHumanPet',
1478                    password => 'silly',
1479                    api_id => '2561022' };
1480    
1481    The original purpose of this method was to insure Bruce would be notified immediately when the
1482    Sprout Load terminates. Care should be taken if you do not wish Bruce to be notified immediately
1483    when you call this method.
1484    
1485    The message ID will be returned if successful, and C<undef> if an error occurs.
1486    
1487    =over 4
1488    
1489    =item phoneNumber
1490    
1491    Phone number to receive the message, in international format. A United States phone number
1492    would be prefixed by "1". A British phone number would be prefixed by "44".
1493    
1494    =item msg
1495    
1496    Message to send to the specified phone.
1497    
1498    =item RETURN
1499    
1500    Returns the message ID if successful, and C<undef> if the message could not be sent.
1501    
1502    =back
1503    
1504    =cut
1505    
1506    sub SendSMS {
1507        # Get the parameters.
1508        my ($phoneNumber, $msg) = @_;
1509        # Declare the return variable. If we do not change it, C<undef> will be returned.
1510        my $retVal;
1511        # Only proceed if we have phone support.
1512        if (! defined $FIG_Config::phone) {
1513            Trace("Phone support not present in FIG_Config.") if T(1);
1514        } else {
1515            # Get the phone data.
1516            my $parms = $FIG_Config::phone;
1517            # Get the Clickatell URL.
1518            my $url = "http://api.clickatell.com/http/";
1519            # Create the user agent.
1520            my $ua = LWP::UserAgent->new;
1521            # Request a Clickatell session.
1522            my $resp = $ua->post("$url/sendmsg", { user => $parms->{user},
1523                                         password => $parms->{password},
1524                                         api_id => $parms->{api_id},
1525                                         to => $phoneNumber,
1526                                         text => $msg});
1527            # Check for an error.
1528            if (! $resp->is_success) {
1529                Trace("Alert failed.") if T(1);
1530            } else {
1531                # Get the message ID.
1532                my $rstring = $resp->content;
1533                if ($rstring =~ /^ID:\s+(.*)$/) {
1534                    $retVal = $1;
1535                } else {
1536                    Trace("Phone attempt failed with $rstring") if T(1);
1537                }
1538            }
1539        }
1540        # Return the result.
1541        return $retVal;
1542    }
1543    
1544    =head3 StandardSetup
1545    
1546        my ($options, @parameters) = StandardSetup(\@categories, \%options, $parmHelp, @ARGV);
1547    
1548    This method performs standard command-line parsing and tracing setup. The return
1549    values are a hash of the command-line options and a list of the positional
1550    parameters. Tracing is automatically set up and the command-line options are
1551    validated.
1552    
1553    This is a complex method that does a lot of grunt work. The parameters can
1554    be more easily understood, however, once they are examined individually.
1555    
1556    The I<categories> parameter is the most obtuse. It is a reference to a list of
1557    special-purpose tracing categories. Most tracing categories are PERL package
1558    names. So, for example, if you wanted to turn on tracing inside the B<Sprout>,
1559    B<ERDB>, and B<SproutLoad> packages, you would specify the categories
1560    
1561        ["Sprout", "SproutLoad", "ERDB"]
1562    
1563    This would cause trace messages in the specified three packages to appear in
1564    the output. There are two special tracing categories that are automatically
1565    handled by this method. In other words, if you used L</TSetup> you would need
1566    to include these categories manually, but if you use this method they are turned
1567    on automatically.
1568    
1569    =over 4
1570    
1571    =item SQL
1572    
1573    Traces SQL commands and activity.
1574    
1575    =item Tracer
1576    
1577    Traces error messages and call stacks.
1578    
1579    =back
1580    
1581    C<SQL> is only turned on if the C<-sql> option is specified in the command line.
1582    The trace level is specified using the C<-trace> command-line option. For example,
1583    the following command line for C<TransactFeatures> turns on SQL tracing and runs
1584    all tracing at level 3.
1585    
1586        TransactFeatures -trace=3 -sql register ../xacts IDs.tbl
1587    
1588    Standard tracing is output to the standard output and echoed to the file
1589    C<trace>I<$$>C<.log> in the FIG temporary directory, where I<$$> is the
1590    process ID. You can also specify the C<user> parameter to put a user ID
1591    instead of a process ID in the trace file name. So, for example
1592    
1593    The default trace level is 2. To get all messages, specify a trace level of 4.
1594    For a genome-by-genome update, use 3.
1595    
1596        TransactFeatures -trace=3 -sql -user=Bruce register ../xacts IDs.tbl
1597    
1598    would send the trace output to C<traceBruce.log> in the temporary directory.
1599    
1600    The I<options> parameter is a reference to a hash containing the command-line
1601    options, their default values, and an explanation of what they mean. Command-line
1602    options may be in the form of switches or keywords. In the case of a switch, the
1603    option value is 1 if it is specified and 0 if it is not specified. In the case
1604    of a keyword, the value is separated from the option name by an equal sign. You
1605    can see this last in the command-line example above.
1606    
1607    You can specify a different default trace level by setting C<$options->{trace}>
1608    prior to calling this method.
1609    
1610    An example at this point would help. Consider, for example, the command-line utility
1611    C<TransactFeatures>. It accepts a list of positional parameters plus the options
1612    C<safe>, C<noAlias>, C<start>, and C<tblFiles>. To start up this command, we execute
1613    the following code.
1614    
1615        my ($options, @parameters) = Tracer::StandardSetup(["DocUtils"],
1616                            { safe => [0, "use database transactions"],
1617                              noAlias => [0, "do not expect aliases in CHANGE transactions"],
1618                              start => [' ', "start with this genome"],
1619                              tblFiles => [0, "output TBL files containing the corrected IDs"] },
1620                            "<command> <transactionDirectory> <IDfile>",
1621                          @ARGV);
1622    
1623    
1624    The call to C<ParseCommand> specifies the default values for the options and
1625    stores the actual options in a hash that is returned as C<$options>. The
1626    positional parameters are returned in C<@parameters>.
1627    
1628    The following is a sample command line for C<TransactFeatures>.
1629    
1630        TransactFeatures -trace=2 -noAlias register ../xacts IDs.tbl
1631    
1632    Single and double hyphens are equivalent. So, you could also code the
1633    above command as
1634    
1635        TransactFeatures --trace=2 --noAlias register ../xacts IDs.tbl
1636    
1637    In this case, C<register>, C<../xacts>, and C<IDs.tbl> are the positional
1638    parameters, and would find themselves in I<@parameters> after executing the
1639    above code fragment. The tracing would be set to level 2, and the categories
1640    would be C<Tracer>, and <DocUtils>. C<Tracer> is standard,
1641    and C<DocUtils> was included because it came in within the first parameter
1642    to this method. The I<$options> hash would be
1643    
1644        { trace => 2, sql => 0, safe => 0,
1645          noAlias => 1, start => ' ', tblFiles => 0 }
1646    
1647    Use of C<StandardSetup> in this way provides a simple way of performing
1648    standard tracing setup and command-line parsing. Note that the caller is
1649    not even aware of the command-line switches C<-trace> and C<-sql>, which
1650    are used by this method to control the tracing. If additional tracing features
1651    need to be added in the future, they can be processed by this method without
1652    upsetting the command-line utilities.
1653    
1654    If the C<background> option is specified on the command line, then the
1655    standard and error outputs will be directed to files in the temporary
1656    directory, using the same suffix as the trace file. So, if the command
1657    line specified
1658    
1659        -user=Bruce -background
1660    
1661    then the trace output would go to C<traceBruce.log>, the standard output to
1662    C<outBruce.log>, and the error output to C<errBruce.log>. This is designed to
1663    simplify starting a command in the background.
1664    
1665    The user name is also used as the tracing key for L</Emergency Tracing>.
1666    Specifying a value of C<E> for the trace level causes emergency tracing to
1667    be used instead of custom tracing. If the user name is not specified,
1668    the tracing key is taken from the C<Tracing> environment variable. If there
1669    is no value for that variable, the tracing key will be computed from the active
1670    login ID.
1671    
1672    Since the default situation in StandardSetup is to trace to the standard
1673    output, errors that occur in command-line scripts will not generate
1674    RSS events. To force the events, use the C<warn> option.
1675    
1676        TransactFeatures -background -warn register ../xacts IDs.tbl
1677    
1678    Finally, if the special option C<-help> is specified, the option
1679    names will be traced at level 0 and the program will exit without processing.
1680    This provides a limited help capability. For example, if the user enters
1681    
1682        TransactFeatures -help
1683    
1684    he would see the following output.
1685    
1686        TransactFeatures [options] <command> <transactionDirectory> <IDfile>
1687            -trace    tracing level (default E)
1688            -sql      trace SQL commands
1689            -safe     use database transactions
1690            -noAlias  do not expect aliases in CHANGE transactions
1691            -start    start with this genome
1692            -tblFiles output TBL files containing the corrected IDs
1693    
1694    The caller has the option of modifying the tracing scheme by placing a value
1695    for C<trace> in the incoming options hash. The default value can be overridden,
1696    or the tracing to the standard output can be turned off by suffixing a minus
1697    sign to the trace level. So, for example,
1698    
1699        { trace => [0, "tracing level (default 0)"],
1700           ...
1701    
1702    would set the default trace level to 0 instead of E, while
1703    
1704        { trace => ["2-", "tracing level (default 2)"],
1705           ...
1706    
1707    would set the default to 2, but trace only to the log file, not to the
1708    standard output.
1709    
1710    The parameters to this method are as follows.
1711    
1712    =over 4
1713    
1714    =item categories
1715    
1716    Reference to a list of tracing category names. These should be names of
1717    packages whose internal workings will need to be debugged to get the
1718    command working.
1719    
1720    =item options
1721    
1722    Reference to a hash containing the legal options for the current command mapped
1723    to their default values and descriptions. The user can override the defaults
1724    by specifying the options as command-line switches prefixed by a hyphen.
1725    Tracing-related options may be added to this hash. If the C<-h> option is
1726    specified on the command line, the option descriptions will be used to
1727    explain the options. To turn off tracing to the standard output, add a
1728    minus sign to the value for C<trace> (see above).
1729    
1730    =item parmHelp
1731    
1732    A string that vaguely describes the positional parameters. This is used
1733    if the user specifies the C<-h> option.
1734    
1735    =item argv
1736    
1737    List of command line parameters, including the option switches, which must
1738    precede the positional parameters and be prefixed by a hyphen.
1739    
1740    =item RETURN
1741    
1742    Returns a list. The first element of the list is the reference to a hash that
1743    maps the command-line option switches to their values. These will either be the
1744    default values or overrides specified on the command line. The remaining
1745    elements of the list are the position parameters, in order.
1746    
1747    =back
1748    
1749    =cut
1750    
1751    sub StandardSetup {
1752        # Get the parameters.
1753        my ($categories, $options, $parmHelp, @argv) = @_;
1754        # Get the default tracing key.
1755        my $tkey = EmergencyKey();
1756        # Save the command line.
1757        $CommandLine = join(" ", $0, map { $_ =~ /\s/ ? "\"$_\"" : $_ } @argv);
1758        # Add the tracing options.
1759        if (! exists $options->{trace}) {
1760            $options->{trace} = ['2', "tracing level (E for emergency tracing)"];
1761        }
1762        $options->{sql} = [0, "turn on SQL tracing"];
1763        $options->{help} = [0, "display command-line options"];
1764        $options->{user} = [$tkey, "tracing key"];
1765        $options->{background} = [0, "spool standard and error output"];
1766        $options->{warn} = [0, "send errors to RSS feed"];
1767        # Create a parsing hash from the options hash. The parsing hash
1768        # contains the default values rather than the default value
1769        # and the description. While we're at it, we'll memorize the
1770        # length of the longest option name.
1771        my $longestName = 0;
1772        my %parseOptions = ();
1773        for my $key (keys %{$options}) {
1774            if (length $key > $longestName) {
1775                $longestName = length $key;
1776            }
1777            $parseOptions{$key} = $options->{$key}->[0];
1778        }
1779        # Parse the command line.
1780        my ($retOptions, @retParameters) = ParseCommand(\%parseOptions, @argv);
1781        # Get the logfile suffix.
1782        my $suffix = $retOptions->{user};
1783        # Check for background mode.
1784        if ($retOptions->{background}) {
1785            my $outFileName = "$FIG_Config::temp/out$suffix.log";
1786            my $errFileName = "$FIG_Config::temp/err$suffix.log";
1787            open STDOUT, ">$outFileName";
1788            open STDERR, ">$errFileName";
1789            # Check for phone support. If we have phone support and a phone number,
1790            # we want to turn it on.
1791            if ($ENV{PHONE} && defined($FIG_Config::phone)) {
1792                $retOptions->{phone} = $ENV{PHONE};
1793            }
1794        }
1795        # Now we want to set up tracing. First, we need to know if the user
1796        # wants emergency tracing.
1797        if ($retOptions->{trace} eq 'E') {
1798            ETracing($retOptions->{user});
1799        } else {
1800            # Here the tracing is controlled from the command line.
1801            my @cats = @{$categories};
1802            if ($retOptions->{sql}) {
1803                push @cats, "SQL";
1804            }
1805            if ($retOptions->{warn}) {
1806                push @cats, "Feed";
1807            }
1808            # Add the default categories.
1809            push @cats, "Tracer";
1810            # Next, we create the category string by joining the categories.
1811            my $cats = join(" ", @cats);
1812            # Check to determine whether or not the caller wants to turn off tracing
1813            # to the standard output.
1814            my $traceLevel = $retOptions->{trace};
1815            my $textOKFlag = 1;
1816            if ($traceLevel =~ /^(.)-/) {
1817                $traceLevel = $1;
1818                $textOKFlag = 0;
1819            }
1820            # Now we set up the trace mode.
1821            my $traceMode;
1822            # Verify that we can open a file in the FIG temporary directory.
1823            my $traceFileName = "$FIG_Config::temp/trace$suffix.log";
1824            if (open TESTTRACE, ">$traceFileName") {
1825                # Here we can trace to a file.
1826                $traceMode = ">$traceFileName";
1827                if ($textOKFlag) {
1828                    # Echo to standard output if the text-OK flag is set.
1829                    $traceMode = "+$traceMode";
1830                }
1831                # Close the test file.
1832                close TESTTRACE;
1833            } else {
1834                # Here we can't trace to a file. Complain about this.
1835                warn "Could not open trace file $traceFileName: $!\n";
1836                # We trace to the standard output if it's
1837                # okay, and the error log otherwise.
1838                if ($textOKFlag) {
1839                    $traceMode = "TEXT";
1840                } else {
1841                    $traceMode = "WARN";
1842                }
1843            }
1844            # Now set up the tracing.
1845            TSetup("$traceLevel $cats", $traceMode);
1846        }
1847        # Check for the "help" option. If it is specified, dump the command-line
1848        # options and exit the program.
1849        if ($retOptions->{help}) {
1850            $0 =~ m#[/\\](\w+)(\.pl)?$#i;
1851            print "$1 [options] $parmHelp\n";
1852            for my $key (sort keys %{$options}) {
1853                my $name = Pad($key, $longestName, 0, ' ');
1854                my $desc = $options->{$key}->[1];
1855                if ($options->{$key}->[0]) {
1856                    $desc .= " (default " . $options->{$key}->[0] . ")";
1857  }  }
1858                print "  $name $desc\n";
 # Pad a number to 2 digits.  
 sub _p2 {  
     my ($value) = @_;  
     $value = "0$value" if ($value < 10);  
     return $value;  
1859  }  }
1860            exit(0);
1861  =head3 LogErrors      }
1862        # Trace the options, if applicable.
1863  C<< Tracer::LogErrors($fileName); >>      if (T(3)) {
1864            my @parms = grep { $retOptions->{$_} } keys %{$retOptions};
1865  Route the standard error output to a log file.          Trace("Selected options: " . join(", ", sort @parms) . ".");
1866        }
1867  =over 4      # Return the parsed parameters.
1868        return ($retOptions, @retParameters);
 =item fileName  
   
 Name of the file to receive the error output.  
   
 =back  
   
 =cut  
   
 sub LogErrors {  
     # Get the file name.  
     my ($fileName) = @_;  
     # Open the file as the standard error output.  
     open STDERR, '>', $fileName;  
1869  }  }
1870    
1871  =head3 ReadOptions  =head3 ReadOptions
1872    
1873  C<< my %options = Tracer::ReadOptions($fileName); >>      my %options = Tracer::ReadOptions($fileName);
1874    
1875  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
1876  format  format
# Line 1017  Line 1931 
1931    
1932  =head3 GetOptions  =head3 GetOptions
1933    
1934  C<< Tracer::GetOptions(\%defaults, \%options); >>      Tracer::GetOptions(\%defaults, \%options);
1935    
1936  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
1937  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 1026  Line 1940 
1940    
1941  Consider the following example.  Consider the following example.
1942    
1943  C<< my $optionTable = GetOptions({ dbType => 'mySQL', trace => 0 }, $options); >>      my $optionTable = GetOptions({ dbType => 'mySQL', trace => 0 }, $options);
1944    
1945  In this example, the variable B<$options> is expected to contain at most two options-- B<dbType> and  In this example, the variable B<$options> is expected to contain at most two options-- B<dbType> and
1946  B<trace>. The default database type is C<mySQL> and the default trace level is C<0>. If the value of  B<trace>. The default database type is C<mySQL> and the default trace level is C<0>. If the value of
# Line 1034  Line 1948 
1948  the trace level will remain at 0. If B<$options> is undefined, then the database type and trace level  the trace level will remain at 0. If B<$options> is undefined, then the database type and trace level
1949  will remain C<mySQL> and C<0>. If, on the other hand, B<$options> is defined as  will remain C<mySQL> and C<0>. If, on the other hand, B<$options> is defined as
1950    
1951  C<< {databaseType => 'Oracle'} >>      {databaseType => 'Oracle'}
1952    
1953  an error will occur because the B<databaseType> option does not exist.  an error will occur because the B<databaseType> option does not exist.
1954    
# Line 1078  Line 1992 
1992    
1993  =head3 MergeOptions  =head3 MergeOptions
1994    
1995  C<< Tracer::MergeOptions(\%table, \%defaults); >>      Tracer::MergeOptions(\%table, \%defaults);
1996    
1997  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
1998  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 1110  Line 2024 
2024      }      }
2025  }  }
2026    
 =head3 Trace  
   
 C<< Trace($message); >>  
   
 Write a trace message to the target location specified in L</TSetup>. If there has not been  
 any prior call to B<TSetup>.  
   
 =over 4  
   
 =item message  
   
 Message to write.  
   
 =back  
   
 =cut  
   
 sub Trace {  
     # Get the parameters.  
     my ($message) = @_;  
     # Get the timestamp.  
     my $timeStamp = Now();  
     # Format the message. Note we strip off any line terminators at the end.  
     my $formatted = "[$timeStamp] <$LastCategory>: " . Strip($message);  
     # Process according to the destination.  
     if ($Destination eq "TEXT") {  
         # Write the message to the standard output.  
         print "$formatted\n";  
     } elsif ($Destination eq "ERROR") {  
         # Write the message to the error output.  
         print STDERR "$formatted\n";  
     } elsif ($Destination eq "QUEUE") {  
         # Push the message into the queue.  
         push @Queue, "$formatted";  
     } elsif ($Destination eq "HTML") {  
         # Convert the message to HTML and write it to the standard output.  
         my $escapedMessage = CGI::escapeHTML($message);  
         print "<p>$formatted</p>\n";  
     } elsif ($Destination eq "WARN") {  
        # Emit the message as a warning.  
        warn $message;  
     } elsif ($Destination =~ m/^>>/) {  
         # Write the trace message to an output file.  
         (open TRACING, $Destination) || die "Tracing open for \"$Destination\" failed: $!";  
         print TRACING "$formatted\n";  
         close TRACING;  
         # If the Tee flag is on, echo it to the standard output.  
         if ($TeeFlag) {  
             print "$formatted\n";  
         }  
     }  
 }  
   
 =head3 T  
   
 C<< my $switch = T($category, $traceLevel); >>  
   
     or  
   
 C<< my $switch = T($traceLevel); >>  
   
 Return TRUE if the trace level is at or above a specified value and the specified category  
 is active, else FALSE. If no category is specified, the caller's package name is used.  
   
 =over 4  
   
 =item category  
   
 Category to which the message belongs. If not specified, the caller's package name is  
 used.  
   
 =item traceLevel  
   
 Relevant tracing level.  
   
 =item RETURN  
   
 TRUE if a message at the specified trace level would appear in the trace, else FALSE.  
   
 =back  
   
 =cut  
   
 sub T {  
     # Declare the return variable.  
     my $retVal = 0;  
     # Only proceed if tracing is turned on.  
     if ($Destination ne "NONE") {  
         # Get the parameters.  
         my ($category, $traceLevel) = @_;  
         if (!defined $traceLevel) {  
             # Here we have no category, so we need to get the calling package.  
             # The calling package is normally the first parameter. If it is  
             # omitted, the first parameter will be the tracelevel. So, the  
             # first thing we do is shift the so-called category into the  
             # $traceLevel variable where it belongs.  
             $traceLevel = $category;  
             my ($package, $fileName, $line) = caller;  
             # If there is no calling package, we default to "main".  
             if (!$package) {  
                 $category = "main";  
             } else {  
                 $category = $package;  
             }  
         }  
         # Save the category name.  
         $LastCategory = $category;  
         # Convert it to lower case before we hash it.  
         $category = lc $category;  
         # Use the category and tracelevel to compute the result.  
         if (ref $traceLevel) {  
             Confess("Bad trace level.");  
         } elsif (ref $TraceLevel) {  
             Confess("Bad trace config.");  
         }  
         $retVal = ($traceLevel <= $TraceLevel && ($AllTrace || exists $Categories{$category}));  
     }  
     # Return the computed result.  
     return $retVal;  
 }  
   
2027  =head3 ParseCommand  =head3 ParseCommand
2028    
2029  C<< my ($options, @arguments) = Tracer::ParseCommand(\%optionTable, @inputList); >>      my ($options, @arguments) = Tracer::ParseCommand(\%optionTable, @inputList);
2030    
2031  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
2032  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
2033  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
2034  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.
2035    
2036  C<< my ($options, @arguments) = ParseCommand({ errors => 0, logFile => 'trace.log'}, @words); >>      my ($options, @arguments) = ParseCommand({ errors => 0, logFile => 'trace.log'}, @words);
2037    
2038  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,
2039  B<errors> and B<logFile>. If @words has the following format  B<errors> and B<logFile>. If @words has the following format
2040    
2041  C<< -logFile=error.log apple orange rutabaga >>      -logFile=error.log apple orange rutabaga
2042    
2043  then at the end of the invocation, C<$options> will be  then at the end of the invocation, C<$options> will be
2044    
2045  C<< { errors => 0, logFile => 'error.log' } >>      { errors => 0, logFile => 'error.log' }
2046    
2047  and C<@arguments> will contain  and C<@arguments> will contain
2048    
2049  C<< apple orange rutabaga >>      apple orange rutabaga
2050    
2051  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
2052  support for quote characters.  support for quote characters. Options can be specified with single or double hyphens.
2053    
2054  =over 4  =over 4
2055    
# Line 1281  Line 2074 
2074      my ($optionTable, @inputList) = @_;      my ($optionTable, @inputList) = @_;
2075      # Process any options in the input list.      # Process any options in the input list.
2076      my %overrides = ();      my %overrides = ();
2077      while ((@inputList > 0) && ($inputList[0] =~ /^-/)) {      while ((@inputList > 0) && ($inputList[0] =~ /^--?/)) {
2078          # Get the current option.          # Get the current option.
2079          my $arg = shift @inputList;          my $arg = shift @inputList;
2080          # Pull out the option name.          # Pull out the option name.
2081          $arg =~ /^-([^=]*)/g;          $arg =~ /^--?([^=]*)/g;
2082          my $name = $1;          my $name = $1;
2083          # Check for an option value.          # Check for an option value.
2084          if ($arg =~ /\G=(.*)$/g) {          if ($arg =~ /\G=(.*)$/g) {
# Line 1307  Line 2100 
2100      return ($optionTable, @retVal);      return ($optionTable, @retVal);
2101  }  }
2102    
 =head3 Escape  
2103    
2104  C<< my $codedString = Tracer::Escape($realString); >>  =head2 File Utility Methods
2105    
2106  Escape a string for use in a command length. Tabs will be replaced by C<\t>, new-lines  =head3 GetFile
2107  replaced by C<\n>, carriage returns will be deleted, and backslashes will be doubled. The  
2108  result is to reverse the effect of L</UnEscape>.      my @fileContents = Tracer::GetFile($fileName);
2109    
2110        or
2111    
2112        my $fileContents = Tracer::GetFile($fileName);
2113    
2114    Return the entire contents of a file. In list context, line-ends are removed and
2115    each line is a list element. In scalar context, line-ends are replaced by C<\n>.
2116    
2117  =over 4  =over 4
2118    
2119  =item realString  =item fileName
2120    
2121  String to escape.  Name of the file to read.
2122    
2123  =item RETURN  =item RETURN
2124    
2125  Escaped equivalent of the real string.  In a list context, returns the entire file as a list with the line terminators removed.
2126    In a scalar context, returns the entire file as a string. If an error occurs opening
2127    the file, an empty list will be returned.
2128    
2129  =back  =back
2130    
2131  =cut  =cut
2132    
2133  sub Escape {  sub GetFile {
2134      # Get the parameter.      # Get the parameters.
2135      my ($realString) = @_;      my ($fileName) = @_;
2136      # Initialize the return variable.      # Declare the return variable.
2137      my $retVal = "";      my @retVal = ();
2138      # Loop through the parameter string, looking for sequences to escape.      # Open the file for input.
2139      while (length $realString > 0) {      my $handle = Open(undef, "<$fileName");
2140          # Look for the first sequence to escape.      # Read the whole file into the return variable, stripping off any terminator
2141          if ($realString =~ /^(.*?)([\n\t\r\\])/) {      # characters.
2142              # Here we found it. The text preceding the sequence is in $1. The sequence      my $lineCount = 0;
2143              # itself is in $2. First, move the clear text to the return variable.      while (my $line = <$handle>) {
2144              $retVal .= $1;          $lineCount++;
2145              # Strip the processed section off the real string.          $line = Strip($line);
2146              $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;  
2147              }              }
2148        # Close it.
2149        close $handle;
2150        my $actualLines = @retVal;
2151        Trace("$actualLines lines read from file $fileName.") if T(File => 2);
2152        # Return the file's contents in the desired format.
2153        if (wantarray) {
2154            return @retVal;
2155          } else {          } else {
2156              # Here there are no more escape sequences. The rest of the string is          return join "\n", @retVal;
             # transferred unmodified.  
             $retVal .= $realString;  
             $realString = "";  
         }  
2157      }      }
     # Return the result.  
     return $retVal;  
2158  }  }
2159    
2160  =head3 UnEscape  =head3 PutFile
   
 C<< my $realString = Tracer::UnEscape($codedString); >>  
   
 Replace escape sequences with their actual equivalents. C<\t> will be replaced by  
 a tab, C<\n> by a new-line character, and C<\\> by a backslash. C<\r> codes will  
 be deleted.  
   
 =over 4  
   
 =item codedString  
   
 String to un-escape.  
   
 =item RETURN  
   
 Returns a copy of the original string with the escape sequences converted to their actual  
 values.  
2161    
2162  =back      Tracer::PutFile($fileName, \@lines);
2163    
2164  =cut  Write out a file from a list of lines of text.
2165    
2166  sub UnEscape {  =over 4
2167      # Get the parameter.  
2168      my ($codedString) = @_;  =item fileName
2169      # Initialize the return variable.  
2170      my $retVal = "";  Name of the output file.
2171      # Only proceed if the incoming string is nonempty.  
2172      if (defined $codedString) {  =item lines
2173          # Loop through the parameter string, looking for escape sequences. We can't do  
2174          # translating because it causes problems with the escaped slash. ("\\t" becomes  Reference to a list of text lines. The lines will be written to the file in order, with trailing
2175          # "\<tab>" no matter what we do.)  new-line characters. Alternatively, may be a string, in which case the string will be written without
2176          while (length $codedString > 0) {  modification.
2177              # Look for the first escape sequence.  
2178              if ($codedString =~ /^(.*?)\\(\\|n|t|r)/) {  =back
2179                  # Here we found it. The text preceding the sequence is in $1. The sequence  
2180                  # itself is in $2. First, move the clear text to the return variable.  =cut
2181                  $retVal .= $1;  
2182                  $codedString = substr $codedString, (2 + length $1);  sub PutFile {
2183                  # Get the escape value.      # Get the parameters.
2184                  my $char = $2;      my ($fileName, $lines) = @_;
2185                  # If we have a "\r", we are done.      # Open the output file.
2186                  if ($char ne 'r') {      my $handle = Open(undef, ">$fileName");
2187                      # Here it's not an 'r', so we convert it.      # Count the lines written.
2188                      $char =~ tr/\\tn/\\\t\n/;      if (ref $lines ne 'ARRAY') {
2189                      $retVal .= $char;          # Here we have a scalar, so we write it raw.
2190                  }          print $handle $lines;
2191            Trace("Scalar put to file $fileName.") if T(File => 3);
2192              } else {              } else {
2193                  # Here there are no more escape sequences. The rest of the string is          # Write the lines one at a time.
2194                  # transferred unmodified.          my $count = 0;
2195                  $retVal .= $codedString;          for my $line (@{$lines}) {
2196                  $codedString = "";              print $handle "$line\n";
2197              }              $count++;
2198          }          }
2199            Trace("$count lines put to file $fileName.") if T(File => 3);
2200      }      }
2201      # Return the result.      # Close the output file.
2202      return $retVal;      close $handle;
2203  }  }
2204    
2205  =head3 ParseRecord  =head3 ParseRecord
2206    
2207  C<< my @fields = Tracer::ParseRecord($line); >>      my @fields = Tracer::ParseRecord($line);
2208    
2209  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
2210  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 1469  Line 2249 
2249    
2250  =head3 Merge  =head3 Merge
2251    
2252  C<< my @mergedList = Tracer::Merge(@inputList); >>      my @mergedList = Tracer::Merge(@inputList);
2253    
2254  Sort a list of strings and remove duplicates.  Sort a list of strings and remove duplicates.
2255    
# Line 1515  Line 2295 
2295      return @inputList;      return @inputList;
2296  }  }
2297    
2298  =head3 Percent  =head3 Open
   
 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  
2299    
2300  =item number      my $handle = Open($fileHandle, $fileSpec, $message);
2301    
2302  Percent numerator.  Open a file.
2303    
2304  =item base  The I<$fileSpec> is essentially the second argument of the PERL C<open>
2305    function. The mode is specified using Unix-like shell information. So, for
2306    example,
2307    
2308  Percent base.      Open(\*LOGFILE, '>>/usr/spool/news/twitlog', "Could not open twit log.");
2309    
2310  =item RETURN  would open for output appended to the specified file, and
2311    
2312  Returns the percentage of the base represented by the numerator.      Open(\*DATASTREAM, "| sort -u >$outputFile", "Could not open $outputFile.");
2313    
2314  =back  would open a pipe that sorts the records written and removes duplicates. Note
2315    the use of file handle syntax in the Open call. To use anonymous file handles,
2316    code as follows.
2317    
2318  =cut      my $logFile = Open(undef, '>>/usr/spool/news/twitlog', "Could not open twit log.");
2319    
2320  sub Percent {  The I<$message> parameter is used if the open fails. If it is set to C<0>, then
2321      # Get the parameters.  the open returns TRUE if successful and FALSE if an error occurred. Otherwise, a
2322      my ($number, $base) = @_;  failed open will throw an exception and the third parameter will be used to construct
2323      # Declare the return variable.  an error message. If the parameter is omitted, a standard message is constructed
2324      my $retVal = 0;  using the file spec.
     # Compute the percent.  
     if ($base != 0) {  
         $retVal = $number * 100 / $base;  
     }  
     # Return the result.  
     return $retVal;  
 }  
2325    
2326  =head3 GetFile      Could not open "/usr/spool/news/twitlog"
2327    
2328  C<< my @fileContents = Tracer::GetFile($fileName); >>  Note that the mode characters are automatically cleaned from the file name.
2329    The actual error message from the file system will be captured and appended to the
2330    message in any case.
2331    
2332      or      Could not open "/usr/spool/news/twitlog": file not found.
2333    
2334  C<< my $fileContents = Tracer::GetFile($fileName); >>  In some versions of PERL the only error message we get is a number, which
2335    corresponds to the C++ C<errno> value.
2336    
2337  Return the entire contents of a file. In list context, line-ends are removed and      Could not open "/usr/spool/news/twitlog": 6.
 each line is a list element. In scalar context, line-ends are replaced by C<\n>.  
2338    
2339  =over 4  =over 4
2340    
2341  =item fileName  =item fileHandle
   
 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;  
     }  
     # 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;  
     }  
 }  
   
 =head3 PutFile  
2342    
2343  C<< Tracer::PutFile($fileName, \@lines); >>  File handle. If this parameter is C<undef>, a file handle will be generated
2344    and returned as the value of this method.
2345    
2346  Write out a file from a list of lines of text.  =item fileSpec
2347    
2348  =over 4  File name and mode, as per the PERL C<open> function.
2349    
2350  =item fileName  =item message (optional)
2351    
2352  Name of the output file.  Error message to use if the open fails. If omitted, a standard error message
2353    will be generated. In either case, the error information from the file system
2354    is appended to the message. To specify a conditional open that does not throw
2355    an error if it fails, use C<0>.
2356    
2357  =item lines  =item RETURN
2358    
2359  Reference to a list of text lines. The lines will be written to the file in order, with trailing  Returns the name of the file handle assigned to the file, or C<undef> if the
2360  new-line characters. Alternatively, may be a string, in which case the string will be written without  open failed.
 modification.  
2361    
2362  =back  =back
2363    
2364  =cut  =cut
2365    
2366  sub PutFile {  sub Open {
2367      # Get the parameters.      # Get the parameters.
2368      my ($fileName, $lines) = @_;      my ($fileHandle, $fileSpec, $message) = @_;
2369      # Open the output file.      # Attempt to open the file.
2370      my $handle = Open(undef, ">$fileName");      my $rv = open $fileHandle, $fileSpec;
2371      if (ref $lines ne 'ARRAY') {      # If the open failed, generate an error message.
2372          # Here we have a scalar, so we write it raw.      if (! $rv) {
2373          print $handle $lines;          # Save the system error message.
2374      } else {          my $sysMessage = $!;
2375          # Write the lines one at a time.          # See if we need a default message.
2376          for my $line (@{$lines}) {          if (!$message) {
2377              print $handle "$line\n";              # Clean any obvious mode characters and leading spaces from the
2378                # filename.
2379                my ($fileName) = FindNamePart($fileSpec);
2380                $message = "Could not open \"$fileName\"";
2381          }          }
2382            # Terminate with an error using the supplied message and the
2383            # error message from the file system.
2384            Confess("$message: $!");
2385      }      }
2386      # Close the output file.      # Return the file handle.
2387      close $handle;      return $fileHandle;
2388  }  }
2389    
2390  =head3 QTrace  =head3 FindNamePart
   
 C<< my $data = QTrace($format); >>  
   
 Return the queued trace data in the specified format.  
   
 =over 4  
   
 =item format  
   
 C<html> to format the data as an HTML list, C<text> to format it as straight text.  
   
 =back  
2391    
2392  =cut      my ($fileName, $start, $len) = Tracer::FindNamePart($fileSpec);
2393    
2394  sub QTrace {  Extract the portion of a file specification that contains the file name.
     # Get the parameter.  
     my ($format) = @_;  
     # Create the return variable.  
     my $retVal = "";  
     # Only proceed if there is an actual queue.  
     if (@Queue) {  
         # Process according to the format.  
         if ($format =~ m/^HTML$/i) {  
             # Convert the queue into an HTML list.  
             $retVal = "<ul>\n";  
             for my $line (@Queue) {  
                 my $escapedLine = CGI::escapeHTML($line);  
                 $retVal .= "<li>$escapedLine</li>\n";  
             }  
             $retVal .= "</ul>\n";  
         } elsif ($format =~ m/^TEXT$/i) {  
             # Convert the queue into a list of text lines.  
             $retVal = join("\n", @Queue) . "\n";  
         }  
         # Clear the queue.  
         @Queue = ();  
     }  
     # Return the formatted list.  
     return $retVal;  
 }  
2395    
2396  =head3 Confess  A file specification is the string passed to an C<open> call. It specifies the file
2397    mode and name. In a truly complex situation, it can specify a pipe sequence. This
2398    method assumes that the file name is whatever follows the first angle bracket
2399    sequence.  So, for example, in the following strings the file name is
2400    C</usr/fig/myfile.txt>.
2401    
2402  C<< Confess($message); >>      >>/usr/fig/myfile.txt
2403        </usr/fig/myfile.txt
2404        | sort -u > /usr/fig/myfile.txt
2405    
2406  Trace the call stack and abort the program with the specified message. When used with  If the method cannot find a file name using its normal methods, it will return the
2407  the OR operator and the L</Assert> method, B<Confess> can function as a debugging assert.  whole incoming string.
 So, for example  
2408    
2409  C<< Assert($recNum >= 0) || Confess("Invalid record number $recNum."); >>  =over 4
2410    
2411  Will abort the program with a stack trace if the value of C<$recNum> is negative.  =item fileSpec
2412    
2413  =over 4  File specification string from which the file name is to be extracted.
2414    
2415  =item message  =item RETURN
2416    
2417  Message to include in the trace.  Returns a three-element list. The first element contains the file name portion of
2418    the specified string, or the whole string if a file name cannot be found via normal
2419    methods. The second element contains the start position of the file name portion and
2420    the third element contains the length.
2421    
2422  =back  =back
2423    
2424  =cut  =cut
2425    #: Return Type $;
2426  sub Confess {  sub FindNamePart {
2427      # Get the parameters.      # Get the parameters.
2428      my ($message) = @_;      my ($fileSpec) = @_;
2429      # Trace the call stack.      # Default to the whole input string.
2430      Cluck($message);      my ($retVal, $pos, $len) = ($fileSpec, 0, length $fileSpec);
2431      # Abort the program.      # Parse out the file name if we can.
2432      croak(">>> $message");      if ($fileSpec =~ m/(<|>>?)(.+?)(\s*)$/) {
2433            $retVal = $2;
2434            $len = length $retVal;
2435            $pos = (length $fileSpec) - (length $3) - $len;
2436        }
2437        # Return the result.
2438        return ($retVal, $pos, $len);
2439  }  }
2440    
2441  =head3 Assert  =head3 OpenDir
2442    
2443  C<< Assert($condition1, $condition2, ... $conditionN); >>      my @files = OpenDir($dirName, $filtered, $flag);
2444    
2445  Return TRUE if all the conditions are true. This method can be used in conjunction with  Open a directory and return all the file names. This function essentially performs
2446  the OR operator and the L</Confess> method as a debugging assert.  the functions of an C<opendir> and C<readdir>. If the I<$filtered> parameter is
2447  So, for example  set to TRUE, all filenames beginning with a period (C<.>), dollar sign (C<$>),
2448    or pound sign (C<#>) and all filenames ending with a tilde C<~>) will be
2449    filtered out of the return list. If the directory does not open and I<$flag> is not
2450    set, an exception is thrown. So, for example,
2451    
2452  C<< Assert($recNum >= 0) || Confess("Invalid record number $recNum."); >>      my @files = OpenDir("/Volumes/fig/contigs", 1);
2453    
2454  Will abort the program with a stack trace if the value of C<$recNum> is negative.  is effectively the same as
2455    
2456  =cut      opendir(TMP, "/Volumes/fig/contigs") || Confess("Could not open /Volumes/fig/contigs.");
2457  sub Assert {      my @files = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir(TMP);
     my $retVal = 1;  
     LOOP: for my $condition (@_) {  
         if (! $condition) {  
             $retVal = 0;  
             last LOOP;  
         }  
     }  
     return $retVal;  
 }  
2458    
2459  =head3 Cluck  Similarly, the following code
2460    
2461  C<< Cluck($message); >>      my @files = grep { $_ =~ /^\d/ } OpenDir("/Volumes/fig/orgs", 0, 1);
2462    
2463  Trace the call stack. Note that for best results, you should qualify the call with a  Returns the names of all files in C</Volumes/fig/orgs> that begin with digits and
2464  trace condition. For example,  automatically returns an empty list if the directory fails to open.
2465    
2466  C<< Cluck("Starting record parse.") if T(3); >>  =over 4
2467    
2468  will only trace the stack if the trace level for the package is 3 or more.  =item dirName
2469    
2470  =over 4  Name of the directory to open.
2471    
2472  =item message  =item filtered
2473    
2474  Message to include in the trace.  TRUE if files whose names begin with a period (C<.>) should be automatically removed
2475    from the list, else FALSE.
2476    
2477    =item flag
2478    
2479    TRUE if a failure to open is okay, else FALSE
2480    
2481  =back  =back
2482    
2483  =cut  =cut
2484    #: Return Type @;
2485  sub Cluck {  sub OpenDir {
2486      # Get the parameters.      # Get the parameters.
2487      my ($message) = @_;      my ($dirName, $filtered, $flag) = @_;
2488      # Trace what's happening.      # Declare the return variable.
2489      Trace("Stack trace for event: $message");      my @retVal = ();
2490      my $confession = longmess($message);      # Open the directory.
2491      # Convert the confession to a series of trace messages. Note we skip any      if (opendir(my $dirHandle, $dirName)) {
2492      # messages relating to calls into Tracer.          # The directory opened successfully. Get the appropriate list according to the
2493      for my $line (split /\s*\n/, $confession) {          # strictures of the filter parameter.
2494          Trace($line) if ($line !~ /Tracer\.pm/);          if ($filtered) {
2495                @retVal = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir $dirHandle;
2496            } else {
2497                @retVal = readdir $dirHandle;
2498            }
2499        } elsif (! $flag) {
2500            # Here the directory would not open and it's considered an error.
2501            Confess("Could not open directory $dirName.");
2502      }      }
2503        # Return the result.
2504        return @retVal;
2505  }  }
2506    
 =head3 Min  
2507    
2508  C<< my $min = Min($value1, $value2, ... $valueN); >>  =head3 Insure
2509    
2510        Insure($dirName, $chmod);
2511    
2512  Return the minimum argument. The arguments are treated as numbers.  Insure a directory is present.
2513    
2514  =over 4  =over 4
2515    
2516  =item $value1, $value2, ... $valueN  =item dirName
2517    
2518  List of numbers to compare.  Name of the directory to check. If it does not exist, it will be created.
2519    
2520  =item RETURN  =item chmod (optional)
2521    
2522  Returns the lowest number in the list.  Security privileges to be given to the directory if it is created.
2523    
2524  =back  =back
2525    
2526  =cut  =cut
2527    
2528  sub Min {  sub Insure {
2529      # Get the parameters. Note that we prime the return value with the first parameter.      my ($dirName, $chmod) = @_;
2530      my ($retVal, @values) = @_;      if (! -d $dirName) {
2531      # Loop through the remaining parameters, looking for the lowest.          Trace("Creating $dirName directory.") if T(2);
2532      for my $value (@values) {          eval {
2533          if ($value < $retVal) {              mkpath $dirName;
2534              $retVal = $value;              # If we have permissions specified, set them here.
2535                if (defined($chmod)) {
2536                    chmod $chmod, $dirName;
2537                }
2538            };
2539            if ($@) {
2540                Confess("Error creating $dirName: $@");
2541          }          }
2542      }      }
     # Return the minimum found.  
     return $retVal;  
2543  }  }
2544    
2545  =head3 Max  =head3 ChDir
2546    
2547  C<< my $max = Max($value1, $value2, ... $valueN); >>      ChDir($dirName);
2548    
2549  Return the maximum argument. The arguments are treated as numbers.  Change to the specified directory.
2550    
2551  =over 4  =over 4
2552    
2553  =item $value1, $value2, ... $valueN  =item dirName
   
 List of numbers to compare.  
   
 =item RETURN  
2554    
2555  Returns the highest number in the list.  Name of the directory to which we want to change.
2556    
2557  =back  =back
2558    
2559  =cut  =cut
2560    
2561  sub Max {  sub ChDir {
2562      # Get the parameters. Note that we prime the return value with the first parameter.      my ($dirName) = @_;
2563      my ($retVal, @values) = @_;      if (! -d $dirName) {
2564      # Loop through the remaining parameters, looking for the highest.          Confess("Cannot change to directory $dirName: no such directory.");
2565      for my $value (@values) {      } else {
2566          if ($value > $retVal) {          Trace("Changing to directory $dirName.") if T(File => 4);
2567              $retVal = $value;          my $okFlag = chdir $dirName;
2568            if (! $okFlag) {
2569                Confess("Error switching to directory $dirName.");
2570          }          }
2571      }      }
     # Return the maximum found.  
     return $retVal;  
2572  }  }
2573    
2574  =head3 AddToListMap  =head3 SetPermissions
2575    
2576        Tracer::SetPermissions($dirName, $group, $mask, %otherMasks);
2577    
2578  C<< Tracer::AddToListMap(\%hash, $key, $value1, $value2, ... valueN); >>  Set the permissions for a directory and all the files and folders inside it.
2579    In addition, the group ownership will be changed to the specified value.
2580    
2581  Add a key-value pair to a hash of lists. If no value exists for the key, a singleton list  This method is more vulnerable than most to permission and compatability
2582  is created for the key. Otherwise, the new value is pushed onto the list.  problems, so it does internal error recovery.
2583    
2584  =over 4  =over 4
2585    
2586  =item hash  =item dirName
2587    
2588  Reference to the target hash.  Name of the directory to process.
2589    
2590  =item key  =item group
2591    
2592  Key for which the value is to be added.  Name of the group to be assigned.
2593    
2594  =item value1, value2, ... valueN  =item mask
2595    
2596  List of values to add to the key's value list.  Permission mask. Bits that are C<1> in this mask will be ORed into the
2597    permission bits of any file or directory that does not already have them
2598    set to 1.
2599    
2600  =back  =item otherMasks
2601    
2602  =cut  Map of search patterns to permission masks. If a directory name matches
2603    one of the patterns, that directory and all its members and subdirectories
2604    will be assigned the new pattern. For example, the following would
2605    assign 01664 to most files, but would use 01777 for directories named C<tmp>.
2606    
2607  sub AddToListMap {      Tracer::SetPermissions($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;  
     }  
 }  
2608    
2609  =head3 DebugMode  The list is ordered, so the following would use 0777 for C<tmp1> and
2610    0666 for C<tmp>, C<tmp2>, or C<tmp3>.
2611    
2612  C<< if (Tracer::DebugMode) { ...code... } >>      Tracer::SetPermissions($dirName, 'fig', 01664, '^tmp1' => 0777,
2613                                                       '^tmp' => 0666);
2614    
2615  Return TRUE if debug mode has been turned on, else abort.  Note that the pattern matches are all case-insensitive, and only directory
2616    names are matched, not file names.
2617    
2618  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.  
2619    
2620  =cut  =cut
2621    
2622  sub DebugMode {  sub SetPermissions {
2623      # Declare the return variable.      # Get the parameters.
2624      my $retVal = 0;      my ($dirName, $group, $mask, @otherMasks) = @_;
2625      # Check the debug configuration.      # Set up for error recovery.
2626      my $password = CGI::cookie("DebugMode");      eval {
2627      my $encrypted = Digest::MD5::md5_hex($password);          # Switch to the specified directory.
2628      if ($encrypted eq "252dec43280e0c0d6a75ffcec486e61d") {          ChDir($dirName);
2629          $retVal = 1;          # Get the group ID.
2630            my $gid = getgrnam($group);
2631            # Get the mask for tracing.
2632            my $traceMask = sprintf("%04o", $mask) . "($mask)";
2633            Trace("Fixing permissions for directory $dirName using group $group($gid) and mask $traceMask.") if T(File => 2);
2634            my $fixCount = 0;
2635            my $lookCount = 0;
2636            # @dirs will be a stack of directories to be processed.
2637            my @dirs = (getcwd());
2638            while (scalar(@dirs) > 0) {
2639                # Get the current directory.
2640                my $dir = pop @dirs;
2641                # Check for a match to one of the specified directory names. To do
2642                # that, we need to pull the individual part of the name off of the
2643                # whole path.
2644                my $simpleName = $dir;
2645                if ($dir =~ m!/([^/]+)$!) {
2646                    $simpleName = $1;
2647                }
2648                Trace("Simple directory name for $dir is $simpleName.") if T(File => 4);
2649                # Search for a match.
2650                my $match = 0;
2651                my $i;
2652                for ($i = 0; $i < $#otherMasks && ! $match; $i += 2) {
2653                    my $pattern = $otherMasks[$i];
2654                    if ($simpleName =~ /$pattern/i) {
2655                        $match = 1;
2656                    }
2657                }
2658                # Check for a match. Note we use $i-1 because the loop added 2
2659                # before terminating due to the match.
2660                if ($match && $otherMasks[$i-1] != $mask) {
2661                    # This directory matches one of the incoming patterns, and it's
2662                    # a different mask, so we process it recursively with that mask.
2663                    SetPermissions($dir, $group, $otherMasks[$i-1], @otherMasks);
2664      } else {      } else {
2665          # Here debug mode is off, so we generate an error.                  # Here we can process normally. Get all of the non-hidden members.
2666          Confess("Cannot use this facility without logging in.");                  my @submems = OpenDir($dir, 1);
2667                    for my $submem (@submems) {
2668                        # Get the full name.
2669                        my $thisMem = "$dir/$submem";
2670                        Trace("Checking member $thisMem.") if T(4);
2671                        $lookCount++;
2672                        if ($lookCount % 1000 == 0) {
2673                            Trace("$lookCount members examined. Current is $thisMem. Mask is $traceMask") if T(File => 3);
2674                        }
2675                        # Fix the group.
2676                        chown -1, $gid, $thisMem;
2677                        # Insure this member is not a symlink.
2678                        if (! -l $thisMem) {
2679                            # Get its info.
2680                            my $fileInfo = stat $thisMem;
2681                            # Only proceed if we got the info. Otherwise, it's a hard link
2682                            # and we want to skip it anyway.
2683                            if ($fileInfo) {
2684                                my $fileMode = $fileInfo->mode;
2685                                if (($fileMode & $mask) != $mask) {
2686                                    # Fix this member.
2687                                    $fileMode |= $mask;
2688                                    chmod $fileMode, $thisMem;
2689                                    $fixCount++;
2690                                }
2691                                # If it's a subdirectory, stack it.
2692                                if (-d $thisMem) {
2693                                    push @dirs, $thisMem;
2694                                }
2695                            }
2696                        }
2697                    }
2698                }
2699            }
2700            Trace("$lookCount files and directories processed, $fixCount fixed.") if T(File => 2);
2701        };
2702        # Check for an error.
2703        if ($@) {
2704            Confess("SetPermissions error: $@");
2705      }      }
     # Return the determination indicator.  
     return $retVal;  
2706  }  }
2707    
2708  =head3 Strip  =head3 GetLine
2709    
2710  C<< my $string = Tracer::Strip($line); >>      my @data = Tracer::GetLine($handle);
2711    
2712  Strip all line terminators off a string. This is necessary when dealing with files  Read a line of data from a tab-delimited file.
 that may have been transferred back and forth several times among different  
 operating environments.  
2713    
2714  =over 4  =over 4
2715    
2716  =item line  =item handle
2717    
2718  Line of text to be stripped.  Open file handle from which to read.
2719    
2720  =item RETURN  =item RETURN
2721    
2722  The same line of text with all the line-ending characters chopped from the end.  Returns a list of the fields in the record read. The fields are presumed to be
2723    tab-delimited. If we are at the end of the file, then an empty list will be
2724    returned. If an empty line is read, a single list item consisting of a null
2725    string will be returned.
2726    
2727  =back  =back
2728    
2729  =cut  =cut
2730    
2731  sub Strip {  sub GetLine {
2732      # Get a copy of the parameter string.      # Get the parameters.
2733      my ($string) = @_;      my ($handle) = @_;
2734      my $retVal = (defined $string ? $string : "");      # Declare the return variable.
2735      # Strip the line terminator characters.      my @retVal = ();
2736      $retVal =~ s/(\r|\n)+$//g;      Trace("File position is " . tell($handle) . ". EOF flag is " . eof($handle) . ".") if T(File => 4);
2737        # Read from the file.
2738        my $line = <$handle>;
2739        # Only proceed if we found something.
2740        if (defined $line) {
2741            # Remove the new-line. We are a bit over-cautious here because the file may be coming in via an
2742            # upload control and have a nonstandard EOL combination.
2743            $line =~ s/(\r|\n)+$//;
2744            # Here we do some fancy tracing to help in debugging complicated EOL marks.
2745            if (T(File => 4)) {
2746                my $escapedLine = $line;
2747                $escapedLine =~ s/\n/\\n/g;
2748                $escapedLine =~ s/\r/\\r/g;
2749                $escapedLine =~ s/\t/\\t/g;
2750                Trace("Line read: -->$escapedLine<--");
2751            }
2752            # If the line is empty, return a single empty string; otherwise, parse
2753            # it into fields.
2754            if ($line eq "") {
2755                push @retVal, "";
2756            } else {
2757                push @retVal, split /\t/,$line;
2758            }
2759        } else {
2760            # Trace the reason the read failed.
2761            Trace("End of file: $!") if T(File => 3);
2762        }
2763      # Return the result.      # Return the result.
2764      return $retVal;      return @retVal;
2765  }  }
2766    
2767  =head3 Pad  =head3 PutLine
2768    
2769  C<< my $paddedString = Tracer::Pad($string, $len, $left, $padChar); >>      Tracer::PutLine($handle, \@fields, $eol);
2770    
2771  Pad a string to a specified length. The pad character will be a  Write a line of data to a tab-delimited file. The specified field values will be
2772  space, and the padding will be on the right side unless specified  output in tab-separated form, with a trailing new-line.
 in the third parameter.  
2773    
2774  =over 4  =over 4
2775    
2776  =item string  =item handle
   
 String to be padded.  
   
 =item len  
   
 Desired length of the padded string.  
   
 =item left (optional)  
2777    
2778  TRUE if the string is to be left-padded; otherwise it will be padded on the right.  Output file handle.
2779    
2780  =item padChar (optional)  =item fields
2781    
2782  Character to use for padding. The default is a space.  List of field values.
2783    
2784  =item RETURN  =item eol (optional)
2785    
2786  Returns a copy of the original string with the pad character added to the  End-of-line character (default is "\n").
 specified end so that it achieves the desired length.  
2787    
2788  =back  =back
2789    
2790  =cut  =cut
2791    
2792  sub Pad {  sub PutLine {
2793      # Get the parameters.      # Get the parameters.
2794      my ($string, $len, $left, $padChar) = @_;      my ($handle, $fields, $eol) = @_;
2795      # Compute the padding character.      # Write the data.
2796      if (! defined $padChar) {      print $handle join("\t", @{$fields}) . ($eol || "\n");
         $padChar = " ";  
     }  
     # Compute the number of spaces needed.  
     my $needed = $len - length $string;  
     # Copy the string into the return variable.  
     my $retVal = $string;  
     # Only proceed if padding is needed.  
     if ($needed > 0) {  
         # Create the pad string.  
         my $pad = $padChar x $needed;  
         # Affix it to the return value.  
         if ($left) {  
             $retVal = $pad . $retVal;  
         } else {  
             $retVal .= $pad;  
         }  
     }  
     # Return the result.  
     return $retVal;  
 }  
   
 =head3 EOF  
   
 This is a constant that is lexically greater than any useful string.  
   
 =cut  
   
 sub EOF {  
     return "\xFF\xFF\xFF\xFF\xFF";  
2797  }  }
2798    
 =head3 TICK  
   
 C<< my @results = TICK($commandString); >>  
2799    
2800  Perform a back-tick operation on a command. If this is a Windows environment, any leading  =head3 PrintLine
 dot-slash (C<./> will be removed. So, for example, if you were doing  
   
     `./protein.cgi`  
2801    
2802  from inside a CGI script, it would work fine in Unix, but would issue an error message      Tracer::PrintLine($line);
 in Windows complaining that C<'.'> is not a valid command. If instead you code  
   
     TICK("./protein.cgi")  
2803    
2804  it will work correctly in both environments.  Print a line of text with a trailing new-line.
2805    
2806  =over 4  =over 4
2807    
2808  =item commandString  =item line
   
 The command string to pass to the system.  
   
 =item RETURN  
2809    
2810  Returns the standard output from the specified command, as a list.  Line of text to print.
2811    
2812  =back  =back
2813    
2814  =cut  =cut
2815  #: Return Type @;  
2816  sub TICK {  sub PrintLine {
2817      # Get the parameters.      # Get the parameters.
2818      my ($commandString) = @_;      my ($line) = @_;
2819      # Chop off the dot-slash if this is Windows.      # Print the line.
2820      if ($FIG_Config::win_mode) {      print "$line\n";
         $commandString =~ s!^\./!!;  
     }  
     # Activate the command and return the result.  
     return `$commandString`;  
2821  }  }
2822    
 =head3 ScriptSetup  
2823    
2824  C<< my ($cgi, $varHash) = ScriptSetup($noTrace); >>  =head2 Other Useful Methods
2825    
2826  Perform standard tracing and debugging setup for scripts. The value returned is  =head3 ParseParm
 the CGI object followed by a pre-built variable hash.  
2827    
2828  The C<Trace> form parameter is used to determine whether or not tracing is active and      my $listValue = Tracer::ParseParm($string);
 which trace modules (other than C<Tracer> itself) should be turned on. Specifying  
 the C<CGI> trace module will trace parameter and environment information. Parameters are  
 traced at level 3 and environment variables at level 4. To trace to a file instead of to  
 the web page, set C<TF> to 1. At the end of the script, the client should call  
 L</ScriptFinish> to output the web page.  
2829    
2830  In some situations, it is not practical to invoke tracing via form parameters. For this  Convert a parameter into a list reference. If the parameter is undefined,
2831  situation, you can turn on emergency tracing from the debugging control panel.  an undefined value will be returned. Otherwise, it will be parsed as a
2832  Tracing will then be turned on automatically for all programs that use the L</ETracing>  comma-separated list of values.
 method, which includes every program that uses this method or L</StandardSetup>.  
2833    
2834  =over 4  =over 4
2835    
2836  =item noTrace (optional)  =item string
2837    
2838  If specified, tracing will be suppressed. This is useful if the script wants to set up  Incoming string.
 tracing manually.  
2839    
2840  =item RETURN  =item RETURN
2841    
2842  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
2843  the output page.  was undefined.
2844    
2845  =back  =back
2846    
2847  =cut  =cut
2848    
2849  sub ScriptSetup {  sub ParseParm {
2850      # Get the parameters.      # Get the parameters.
2851      my ($noTrace) = @_;      my ($string) = @_;
2852      # Get the CGI query object.      # Declare the return variable.
2853      my $cgi = CGI->new();      my $retVal;
2854      # Set up tracing if it's not suppressed.      # Check for data.
2855      ETracing($cgi) unless $noTrace;      if (defined $string) {
2856      # Create the variable hash.          # We have some, so split it into a list.
2857      my $varHash = { results => '' };          $retVal = [ split /\s*,\s*/, $string];
     # Return the query object and variable hash.  
     return ($cgi, $varHash);  
 }  
   
 =head3 ETracing  
   
 C<< ETracing($parameter); >>  
   
 Set up emergency tracing. Emergency tracing is tracing that is turned  
 on automatically for any program that calls this method. The emergency  
 tracing parameters are stored in a a file identified by a tracing key.  
 If this method is called with a CGI object, then the tracing key is  
 taken from a cookie. If it is called with no parameters, then the tracing  
 key is taken from an environment variable. If it is called with a string,  
 the tracing key is that string.  
   
 =over 4  
   
 =item parameter  
   
 A parameter from which the tracing key is computed. If it is a scalar,  
 that scalar is used as the tracing key. If it is a CGI object, the  
 tracing key is taken from the C<IP> cookie. If it is omitted, the  
 tracing key is taken from the C<TRACING> environment variable. If it  
 is a CGI object and emergency tracing is not on, the C<Trace> and  
 C<TF> parameters will be used to determine the type of tracing.  
   
 =back  
   
 =cut  
   
 sub ETracing {  
     # Get the parameter.  
     my ($parameter) = @_;  
     # Check for CGI mode.  
     my $cgi = (ref $parameter eq 'CGI' ? $parameter : undef);  
     # Default to no tracing except errors.  
     my ($tracing, $dest) = ("0", "WARN");  
     # Check for emergency tracing.  
     my $tkey = EmergencyKey($parameter);  
     my $emergencyFile = EmergencyFileName($tkey);  
     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.  
             $dest = EmergencyTracingDest($tkey, $dest);  
             # Insure Tracer is specified.  
             my %moduleHash = map { $_ => 1 } @tracing;  
             $moduleHash{Tracer} = 1;  
             # Set the trace parameter.  
             $tracing = join(" ", $level, sort keys %moduleHash);  
         }  
     } elsif (defined $cgi) {  
         # There's no emergency tracing, but we have a CGI object, so check  
         # for tracing from the form parameters.  
         if ($cgi->param('Trace')) {  
             # Here the user has requested tracing via a form.  
             $dest = ($cgi->param('TF') ? ">$FIG_Config::temp/Trace$$.log" : "QUEUE");  
             $tracing = $cgi->param('Trace') . " Tracer";  
         }  
     }  
     # Setup the tracing we've determined from all the stuff above.  
     TSetup($tracing, $dest);  
     # If we're a web script, trace the parameter and environment data.  
     if (defined $cgi) {  
         TraceParms($cgi);  
2858      }      }
2859        # Return the result.
2860        return $retVal;
2861  }  }
2862    
2863  =head3 EmergencyFileName  =head3 Now
   
 C<< my $fileName = Tracer::EmergencyFileName($tkey); >>  
   
 Return the emergency tracing file name. This is the file that specifies  
 the tracing information.  
   
 =over 4  
   
 =item tkey  
   
 Tracing key for the current program.  
   
 =item RETURN  
2864    
2865  Returns the name of the file to contain the emergency tracing information.      my $string = Tracer::Now();
2866    
2867  =back  Return a displayable time stamp containing the local time. Whatever format this
2868    method produces must be parseable by L</ParseDate>.
2869    
2870  =cut  =cut
2871    
2872  sub EmergencyFileName {  sub Now {
2873      # Get the parameters.      return DisplayTime(time);
     my ($tkey) = @_;  
     # Compute the emergency tracing file name.  
     return "$FIG_Config::temp/Emergency$tkey.txt";  
2874  }  }
2875    
2876  =head3 EmergencyFileTarget  =head3 DisplayTime
2877    
2878  C<< my $fileName = Tracer::EmergencyFileTarget($tkey); >>      my $string = Tracer::DisplayTime($time);
2879    
2880  Return the emergency tracing target file name. This is the file that receives  Convert a time value to a displayable time stamp. Whatever format this
2881  the tracing output for file-based tracing.  method produces must be parseable by L</ParseDate>.
2882    
2883  =over 4  =over 4
2884    
2885  =item tkey  =item time
2886    
2887  Tracing key for the current program.  Time to display, in seconds since the epoch, or C<undef> if the time is unknown.
2888    
2889  =item RETURN  =item RETURN
2890    
2891  Returns the name of the file to contain the trace output.  Returns a displayable time, or C<(n/a)> if the incoming time is undefined.
2892    
2893  =back  =back
2894    
2895  =cut  =cut
2896    
2897  sub EmergencyFileTarget {  sub DisplayTime {
2898      # Get the parameters.      my ($time) = @_;
2899      my ($tkey) = @_;      my $retVal = "(n/a)";
2900      # Compute the emergency tracing file name.      if (defined $time) {
2901      return "$FIG_Config::temp/trace$tkey.log";          my ($sec,$min,$hour,$mday,$mon,$year,$wday,$yday,$isdst) = localtime($time);
2902            $retVal = _p2($mon+1) . "/" . _p2($mday) . "/" . ($year + 1900) . " " .
2903                      _p2($hour) . ":" . _p2($min) . ":" . _p2($sec);
2904        }
2905        return $retVal;
2906  }  }
2907    
2908  =head3 EmergencyTracingDest  # Pad a number to 2 digits.
2909    sub _p2 {
2910  C<< my $dest = Tracer::EmergencyTracingDest($tkey, $myDest); >>      my ($value) = @_;
2911        $value = "0$value" if ($value < 10);
2912        return $value;
2913    }
2914    
2915  This method converts an emergency tracing destination to a real  =head3 Escape
 tracing destination. The main difference is that if the  
 destination is C<FILE> or C<APPEND>, we convert it to file  
 output.  
2916    
2917  =over 4      my $codedString = Tracer::Escape($realString);
2918    
2919  =item tkey  Escape a string for use in a command. Tabs will be replaced by C<\t>, new-lines
2920    replaced by C<\n>, carriage returns will be deleted, and backslashes will be doubled. The
2921    result is to reverse the effect of L</UnEscape>.
2922    
2923  Tracing key for this environment.  =over 4
2924    
2925  =item myDest  =item realString
2926    
2927  Destination from the emergency tracing file.  String to escape.
2928    
2929  =item RETURN  =item RETURN
2930    
2931  Returns a destination that can be passed into L</TSetup>.  Escaped equivalent of the real string.
2932    
2933  =back  =back
2934    
2935  =cut  =cut
2936    
2937  sub EmergencyTracingDest {  sub Escape {
2938      # Get the parameters.      # Get the parameter.
2939      my ($tkey, $myDest) = @_;      my ($realString) = @_;
2940      # Declare the return variable.      # Initialize the return variable.
2941      my $retVal;      my $retVal = "";
2942      # Process according to the destination value.      # Loop through the parameter string, looking for sequences to escape.
2943      if ($myDest eq 'FILE') {      while (length $realString > 0) {
2944          $retVal = ">" . EmergencyFileTarget($tkey);          # Look for the first sequence to escape.
2945      } elsif ($myDest eq 'APPEND') {          if ($realString =~ /^(.*?)([\n\t\r\\])/) {
2946          $retVal = ">>" . EmergencyFileTarget($tkey);              # Here we found it. The text preceding the sequence is in $1. The sequence
2947                # itself is in $2. First, move the clear text to the return variable.
2948                $retVal .= $1;
2949                # Strip the processed section off the real string.
2950                $realString = substr $realString, (length $2) + (length $1);
2951                # Get the matched character.
2952                my $char = $2;
2953                # If we have a CR, we are done.
2954                if ($char ne "\r") {
2955                    # It's not a CR, so encode the escape sequence.
2956                    $char =~ tr/\t\n/tn/;
2957                    $retVal .= "\\" . $char;
2958                }
2959      } else {      } else {
2960          $retVal = $myDest;              # Here there are no more escape sequences. The rest of the string is
2961                # transferred unmodified.
2962                $retVal .= $realString;
2963                $realString = "";
2964            }
2965      }      }
2966      # Return the result.      # Return the result.
2967      return $retVal;      return $retVal;
2968  }  }
2969    
2970  =head3 Emergency  =head3 UnEscape
2971    
2972  C<< Emergency($key, $hours, $dest, $level, @modules); >>      my $realString = Tracer::UnEscape($codedString);
2973    
2974  Turn on emergency tracing. This method can only be invoked over the web and is  Replace escape sequences with their actual equivalents. C<\t> will be replaced by
2975  should not be called if debug mode is off. The caller specifies the duration of the  a tab, C<\n> by a new-line character, and C<\\> by a backslash. C<\r> codes will
2976  emergency in hours, the desired tracing destination, the trace level,  be deleted.
 and a list of the trace modules to activate. For the length of the duration, when a  
 program in an environment with the specified tracing key active invokes a Sprout  
 CGI script, tracing will be turned on automatically. See L</TSetup> for more  
 about tracing setup and L</ETracing> for more about emergency tracing.  
2977    
2978  =over 4  =over 4
2979    
2980  =item tkey  =item codedString
   
 The tracing key. This is used to identify the control file and the trace file.  
   
 =item hours  
   
 Number of hours to keep emergency tracing alive.  
   
 =item dest  
   
 Tracing destination. If no path information is specified for a file  
 destination, it is put in the FIG temporary directory.  
   
 =item level  
2981    
2982  Tracing level. A higher level means more trace messages.  String to un-escape.
2983    
2984  =item modules  =item RETURN
2985    
2986  A list of the tracing modules to activate.  Returns a copy of the original string with the escape sequences converted to their actual
2987    values.
2988    
2989  =back  =back
2990    
2991  =cut  =cut
2992    
2993  sub Emergency {  sub UnEscape {
2994      # Get the parameters.      # Get the parameter.
2995      my ($tkey, $hours, $dest, $level, @modules) = @_;      my ($codedString) = @_;
2996      # Create the emergency file.      # Initialize the return variable.
2997      my $specFile = EmergencyFileName($tkey);      my $retVal = "";
2998      my $outHandle = Open(undef, ">$specFile");      # Only proceed if the incoming string is nonempty.
2999      print $outHandle join("\n", $hours, $dest, $level, @modules, "");      if (defined $codedString) {
3000            # Loop through the parameter string, looking for escape sequences. We can't do
3001            # translating because it causes problems with the escaped slash. ("\\t" becomes
3002            # "\<tab>" no matter what we do.)
3003            while (length $codedString > 0) {
3004                # Look for the first escape sequence.
3005                if ($codedString =~ /^(.*?)\\(\\|n|t|r)/) {
3006                    # Here we found it. The text preceding the sequence is in $1. The sequence
3007                    # itself is in $2. First, move the clear text to the return variable.
3008                    $retVal .= $1;
3009                    $codedString = substr $codedString, (2 + length $1);
3010                    # Get the escape value.
3011                    my $char = $2;
3012                    # If we have a "\r", we are done.
3013                    if ($char ne 'r') {
3014                        # Here it's not an 'r', so we convert it.
3015                        $char =~ tr/\\tn/\\\t\n/;
3016                        $retVal .= $char;
3017                    }
3018                } else {
3019                    # Here there are no more escape sequences. The rest of the string is
3020                    # transferred unmodified.
3021                    $retVal .= $codedString;
3022                    $codedString = "";
3023                }
3024            }
3025        }
3026        # Return the result.
3027        return $retVal;
3028  }  }
3029    
3030  =head3 EmergencyKey  =head3 Percent
3031    
3032  C<< my $tkey = EmergencyKey($parameter); >>      my $percent = Tracer::Percent($number, $base);
3033    
3034  Return the Key to be used for emergency tracing. This could be an IP address,  Returns the percent of the base represented by the given number. If the base
3035   a session ID, or a user name, depending on the environment.  is zero, returns zero.
3036    
3037  =over 4  =over 4
3038    
3039  =item parameter  =item number
3040    
3041  Parameter defining the method for finding the tracing key. If it is a scalar,  Percent numerator.
3042  then it is presumed to be the tracing key itself. If it is a CGI object, then  
3043  the tracing key is taken from the C<IP> cookie. Otherwise, the tracing key is  =item base
3044  taken from the C<TRACING> environment variable.  
3045    Percent base.
3046    
3047  =item RETURN  =item RETURN
3048    
3049  Returns the key to be used for labels in emergency tracing.  Returns the percentage of the base represented by the numerator.
3050    
3051  =back  =back
3052    
3053  =cut  =cut
3054    
3055  sub EmergencyKey {  sub Percent {
3056      # Get the parameters.      # Get the parameters.
3057      my ($parameter) = @_;      my ($number, $base) = @_;
3058      # Declare the return variable.      # Declare the return variable.
3059      my $retVal;      my $retVal = 0;
3060      # Determine the parameter type.      # Compute the percent.
3061      if (! defined $parameter) {      if ($base != 0) {
3062          # Here we're supposed to check the environment.          $retVal = $number * 100 / $base;
         $retVal = $ENV{TRACING};  
     } else {  
         my $ptype = ref $parameter;  
         if ($ptype eq 'CGI') {  
             # Here we were invoked from a web page. Look for a cookie.  
             $retVal = $parameter->cookie('IP');  
         } elsif (! $ptype) {  
             # Here the key was passed in.  
             $retVal = $parameter;  
         }  
     }  
     # If no luck finding a key, use the PID.  
     if (! defined $retVal) {  
         $retVal = $$;  
3063      }      }
3064      # Return the result.      # Return the result.
3065      return $retVal;      return $retVal;
3066  }  }
3067    
3068    =head3 Constrain
3069    
3070  =head3 TraceParms      my $constrained = Constrain($value, $min, $max);
   
 C<< Tracer::TraceParms($cgi); >>  
3071    
3072  Trace the CGI parameters at trace level CGI => 3 and the environment variables  Modify a numeric value to bring it to a point in between a maximum and a minimum.
 at level CGI => 4.  
3073    
3074  =over 4  =over 4
3075    
3076  =item cgi  =item value
3077    
3078  CGI query object containing the parameters to trace.  Value to constrain.
3079    
3080  =back  =item min (optional)
3081    
3082  =cut  Minimum permissible value. If this parameter is undefined, no minimum constraint will be applied.
3083    
3084  sub TraceParms {  =item max (optional)
     # Get the parameters.  
     my ($cgi) = @_;  
     if (T(CGI => 3)) {  
         # Here we want to trace the parameter data.  
         my @names = $cgi->param;  
         for my $parmName (sort @names) {  
             # Note we skip the Trace parameters, which are for our use only.  
             if ($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}");  
         }  
     }  
 }  
3085    
3086  =head3 ScriptFinish  Maximum permissible value. If this parameter is undefined, no maximum constraint will be applied.
3087    
3088  C<< ScriptFinish($webData, $varHash); >>  =item RETURN
3089    
3090  Output a web page at the end of a script. Either the string to be output or the  Returns the incoming value, constrained according to the other parameters.
 name of a template file can be specified. If the second parameter is omitted,  
 it is assumed we have a string to be output; otherwise, it is assumed we have the  
 name of a template file. The template should have the variable C<DebugData>  
 specified in any form that invokes a standard script. If debugging mode is turned  
 on, a form field will be put in that allows the user to enter tracing data.  
 Trace messages will be placed immediately before the terminal C<BODY> tag in  
 the output, formatted as a list.  
3091    
3092  A typical standard script would loook like the following.  =back
3093    
3094      BEGIN {  =cut
         # Print the HTML header.  
         print "CONTENT-TYPE: text/html\n\n";  
     }  
     use Tracer;  
     use CGI;  
     use FIG;  
     # ... more uses ...  
3095    
3096      my ($cgi, $varHash) = ScriptSetup();  sub Constrain {
3097      eval {      # Get the parameters.
3098          # ... get data from $cgi, put it in $varHash ...      my ($value, $min, $max) = @_;
3099      };      # Declare the return variable.
3100      if ($@) {      my $retVal = $value;
3101          Trace("Script Error: $@") if T(0);      # Apply the minimum constraint.
3102        if (defined $min && $retVal < $min) {
3103            $retVal = $min;
3104        }
3105        # Apply the maximum constraint.
3106        if (defined $max && $retVal > $max) {
3107            $retVal = $max;
3108        }
3109        # Return the result.
3110        return $retVal;
3111      }      }
     ScriptFinish("Html/MyTemplate.html", $varHash);  
3112    
3113  The idea here is that even if the script fails, you'll see trace messages and  =head3 Min
3114  useful output.  
3115        my $min = Min($value1, $value2, ... $valueN);
3116    
3117    Return the minimum argument. The arguments are treated as numbers.
3118    
3119  =over 4  =over 4
3120    
3121  =item webData  =item $value1, $value2, ... $valueN
3122    
3123  A string containing either the full web page to be written to the output or the  List of numbers to compare.
 name of a template file from which the page is to be constructed. If the name  
 of a template file is specified, then the second parameter must be present;  
 otherwise, it must be absent.  
3124    
3125  =item varHash (optional)  =item RETURN
3126    
3127  If specified, then a reference to a hash mapping variable names for a template  Returns the lowest number in the list.
 to their values. The template file will be read into memory, and variable markers  
 will be replaced by data in this hash reference.  
3128    
3129  =back  =back
3130    
3131  =cut  =cut
3132    
3133  sub ScriptFinish {  sub Min {
3134      # Get the parameters.      # Get the parameters. Note that we prime the return value with the first parameter.
3135      my ($webData, $varHash) = @_;      my ($retVal, @values) = @_;
3136      # Check for a template file situation.      # Loop through the remaining parameters, looking for the lowest.
3137      my $outputString;      for my $value (@values) {
3138      if (defined $varHash) {          if ($value < $retVal) {
3139          # Here we have a template file. We need to determine the template type.              $retVal = $value;
         my $template;  
         if ($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 $actualDest.</p>\n";  
         } else {  
             # Here we have one of the special destinations.  
             $traceHtml = "<P>Tracing output type is $Destination.</p>\n";  
3140          }          }
         substr $outputString, $pos, 0, $traceHtml;  
3141      }      }
3142      # Write the output string.      # Return the minimum found.
3143      print $outputString;      return $retVal;
3144  }  }
3145    
3146  =head3 Insure  =head3 Max
3147    
3148  C<< Insure($dirName); >>      my $max = Max($value1, $value2, ... $valueN);
3149    
3150  Insure a directory is present.  Return the maximum argument. The arguments are treated as numbers.
3151    
3152  =over 4  =over 4
3153    
3154  =item dirName  =item $value1, $value2, ... $valueN
3155    
3156  Name of the directory to check. If it does not exist, it will be created.  List of numbers to compare.
3157    
3158    =item RETURN
3159    
3160    Returns the highest number in the list.
3161    
3162  =back  =back
3163    
3164  =cut  =cut
3165    
3166  sub Insure {  sub Max {
3167      my ($dirName) = @_;      # Get the parameters. Note that we prime the return value with the first parameter.
3168      if (! -d $dirName) {      my ($retVal, @values) = @_;
3169          Trace("Creating $dirName directory.") if T(2);      # Loop through the remaining parameters, looking for the highest.
3170          eval { mkpath $dirName; };      for my $value (@values) {
3171          if ($@) {          if ($value > $retVal) {
3172              Confess("Error creating $dirName: $@");              $retVal = $value;
3173          }          }
3174      }      }
3175        # Return the maximum found.
3176        return $retVal;
3177  }  }
3178    
 =head3 ChDir  
3179    
3180  C<< ChDir($dirName); >>  =head3 Strip
3181    
3182        my $string = Tracer::Strip($line);
3183    
3184  Change to the specified directory.  Strip all line terminators off a string. This is necessary when dealing with files
3185    that may have been transferred back and forth several times among different
3186    operating environments.
3187    
3188  =over 4  =over 4
3189    
3190  =item dirName  =item line
3191    
3192  Name of the directory to which we want to change.  Line of text to be stripped.
3193    
3194    =item RETURN
3195    
3196    The same line of text with all the line-ending characters chopped from the end.
3197    
3198  =back  =back
3199    
3200  =cut  =cut
3201    
3202  sub ChDir {  sub Strip {
3203      my ($dirName) = @_;      # Get a copy of the parameter string.
3204      if (! -d $dirName) {      my ($string) = @_;
3205          Confess("Cannot change to directory $dirName: no such directory.");      my $retVal = (defined $string ? $string : "");
3206      } else {      # Strip the line terminator characters.
3207          Trace("Changing to directory $dirName.") if T(4);      $retVal =~ s/(\r|\n)+$//g;
3208          my $okFlag = chdir $dirName;      # Return the result.
3209          if (! $okFlag) {      return $retVal;
             Confess("Error switching to directory $dirName.");  
         }  
     }  
3210  }  }
3211    
3212  =head3 SendSMS  =head3 Pad
3213    
3214  C<< my $msgID = Tracer::SendSMS($phoneNumber, $msg); >>      my $paddedString = Tracer::Pad($string, $len, $left, $padChar);
3215    
3216  Send a text message to a phone number using Clickatell. The FIG_Config file must contain the  Pad a string to a specified length. The pad character will be a
3217  user name, password, and API ID for the relevant account in the hash reference variable  space, and the padding will be on the right side unless specified
3218  I<$FIG_Config::phone>, using the keys C<user>, C<password>, and C<api_id>. For  in the third parameter.
 example, if the user name is C<BruceTheHumanPet>, the password is C<silly>, and the API ID  
 is C<2561022>, then the FIG_Config file must contain  
3219    
3220      $phone =  { user => 'BruceTheHumanPet',  =over 4
                 password => 'silly',  
                 api_id => '2561022' };  
3221    
3222  The original purpose of this method was to insure Bruce would be notified immediately when the  =item string
 Sprout Load terminates. Care should be taken if you do not wish Bruce to be notified immediately  
 when you call this method.  
3223    
3224  The message ID will be returned if successful, and C<undef> if an error occurs.  String to be padded.
3225    
3226  =over 4  =item len
3227    
3228  =item phoneNumber  Desired length of the padded string.
3229    
3230  Phone number to receive the message, in international format. A United States phone number  =item left (optional)
 would be prefixed by "1". A British phone number would be prefixed by "44".  
3231    
3232  =item msg  TRUE if the string is to be left-padded; otherwise it will be padded on the right.
3233    
3234  Message to send to the specified phone.  =item padChar (optional)
3235    
3236    Character to use for padding. The default is a space.
3237    
3238  =item RETURN  =item RETURN
3239    
3240  Returns the message ID if successful, and C<undef> if the message could not be sent.  Returns a copy of the original string with the pad character added to the
3241    specified end so that it achieves the desired length.
3242    
3243  =back  =back
3244    
3245  =cut  =cut
3246    
3247  sub SendSMS {  sub Pad {
3248      # Get the parameters.      # Get the parameters.
3249      my ($phoneNumber, $msg) = @_;      my ($string, $len, $left, $padChar) = @_;
3250      # Declare the return variable. If we do not change it, C<undef> will be returned.      # Compute the padding character.
3251      my $retVal;      if (! defined $padChar) {
3252      # Only proceed if we have phone support.          $padChar = " ";
3253      if (! defined $FIG_Config::phone) {      }
3254          Trace("Phone support not present in FIG_Config.") if T(1);      # Compute the number of spaces needed.
3255      } else {      my $needed = $len - length $string;
3256          # Get the phone data.      # Copy the string into the return variable.
3257          my $parms = $FIG_Config::phone;      my $retVal = $string;
3258          # Get the Clickatell URL.      # Only proceed if padding is needed.
3259          my $url = "http://api.clickatell.com/http/";      if ($needed > 0) {
3260          # Create the user agent.          # Create the pad string.
3261          my $ua = LWP::UserAgent->new;          my $pad = $padChar x $needed;
3262          # Request a Clickatell session.          # Affix it to the return value.
3263          my $resp = $ua->post("$url/sendmsg", { user => $parms->{user},          if ($left) {
3264                                       password => $parms->{password},              $retVal = $pad . $retVal;
                                      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;  
3265              } else {              } else {
3266                  Trace("Phone attempt failed with $rstring") if T(1);              $retVal .= $pad;
3267              }              }
3268          }          }
3269        # Return the result.
3270        return $retVal;
3271    }
3272    
3273    =head3 EOF
3274    
3275    This is a constant that is lexically greater than any useful string.
3276    
3277    =cut
3278    
3279    sub EOF {
3280        return "\xFF\xFF\xFF\xFF\xFF";
3281    }
3282    
3283    =head3 TICK
3284    
3285        my @results = TICK($commandString);
3286    
3287    Perform a back-tick operation on a command. If this is a Windows environment, any leading
3288    dot-slash (C<./> will be removed. So, for example, if you were doing
3289    
3290        `./protein.cgi`
3291    
3292    from inside a CGI script, it would work fine in Unix, but would issue an error message
3293    in Windows complaining that C<'.'> is not a valid command. If instead you code
3294    
3295        TICK("./protein.cgi")
3296    
3297    it will work correctly in both environments.
3298    
3299    =over 4
3300    
3301    =item commandString
3302    
3303    The command string to pass to the system.
3304    
3305    =item RETURN
3306    
3307    Returns the standard output from the specified command, as a list.
3308    
3309    =back
3310    
3311    =cut
3312    #: Return Type @;
3313    sub TICK {
3314        # Get the parameters.
3315        my ($commandString) = @_;
3316        # Chop off the dot-slash if this is Windows.
3317        if ($FIG_Config::win_mode) {
3318            $commandString =~ s!^\./!!;
3319      }      }
3320      # Return the result.      # Activate the command and return the result.
3321      return $retVal;      return `$commandString`;
3322  }  }
3323    
3324    
3325  =head3 CommaFormat  =head3 CommaFormat
3326    
3327  C<< my $formatted = Tracer::CommaFormat($number); >>      my $formatted = Tracer::CommaFormat($number);
3328    
3329  Insert commas into a number.  Insert commas into a number.
3330    
# Line 2695  Line 3357 
3357      # Return the result.      # Return the result.
3358      return $retVal;      return $retVal;
3359  }  }
 =head3 SetPermissions  
   
 C<< Tracer::SetPermissions($dirName, $group, $mask, %otherMasks); >>  
   
 Set the permissions for a directory and all the files and folders inside it.  
 In addition, the group ownership will be changed to the specified value.  
   
 This method is more vulnerable than most to permission and compatability  
 problems, so it does internal error recovery.  
   
 =over 4  
   
 =item dirName  
   
 Name of the directory to process.  
   
 =item group  
   
 Name of the group to be assigned.  
   
 =item mask  
   
 Permission mask. Bits that are C<1> in this mask will be ORed into the  
 permission bits of any file or directory that does not already have them  
 set to 1.  
   
 =item otherMasks  
3360    
 Map of search patterns to permission masks. If a directory name matches  
 one of the patterns, that directory and all its members and subdirectories  
 will be assigned the new pattern. For example, the following would  
 assign 01664 to most files, but would use 01777 for directories named C<tmp>.  
   
     Tracer::SetPermissions($dirName, 'fig', 01664, '^tmp$' => 01777);  
   
 The list is ordered, so the following would use 0777 for C<tmp1> and  
 0666 for C<tmp>, C<tmp2>, or C<tmp3>.  
   
     Tracer::SetPermissions($dirName, 'fig', 01664, '^tmp1' => 0777,  
                                                    '^tmp' => 0666);  
   
 Note that the pattern matches are all case-insensitive, and only directory  
 names are matched, not file names.  
   
 =back  
   
 =cut  
   
 sub SetPermissions {  
     # Get the parameters.  
     my ($dirName, $group, $mask, @otherMasks) = @_;  
     # Set up for error recovery.  
     eval {  
         # Switch to the specified directory.  
         ChDir($dirName);  
         # Get the group ID.  
         my $gid = getgrnam($group);  
         # Get the mask for tracing.  
         my $traceMask = sprintf("%04o", $mask) . "($mask)";  
         Trace("Fixing permissions for directory $dirName using group $group($gid) and mask $traceMask.") if T(2);  
         my $fixCount = 0;  
         my $lookCount = 0;  
         # @dirs will be a stack of directories to be processed.  
         my @dirs = (getcwd());  
         while (scalar(@dirs) > 0) {  
             # Get the current directory.  
             my $dir = pop @dirs;  
             # Check for a match to one of the specified directory names. To do  
             # that, we need to pull the individual part of the name off of the  
             # whole path.  
             my $simpleName = $dir;  
             if ($dir =~ m!/([^/]+)$!) {  
                 $simpleName = $1;  
             }  
             Trace("Simple directory name for $dir is $simpleName.") if T(4);  
             # Search for a match.  
             my $match = 0;  
             my $i;  
             for ($i = 0; $i < $#otherMasks && ! $match; $i += 2) {  
                 my $pattern = $otherMasks[$i];  
                 if ($simpleName =~ /$pattern/i) {  
                     $match = 1;  
                 }  
             }  
             # Check for a match. Note we use $i-1 because the loop added 2  
             # before terminating due to the match.  
             if ($match && $otherMasks[$i-1] != $mask) {  
                 # This directory matches one of the incoming patterns, and it's  
                 # a different mask, so we process it recursively with that mask.  
                 SetPermissions($dir, $group, $otherMasks[$i-1], @otherMasks);  
             } else {  
                 # Here we can process normally. Get all of the non-hidden members.  
                 my @submems = OpenDir($dir, 1);  
                 for my $submem (@submems) {  
                     # Get the full name.  
                     my $thisMem = "$dir/$submem";  
                     Trace("Checking member $thisMem.") if T(4);  
                     $lookCount++;  
                     if ($lookCount % 1000 == 0) {  
                         Trace("$lookCount members examined. Current is $thisMem. Mask is $traceMask") if T(3);  
                     }  
                     # Fix the group.  
                     chown -1, $gid, $thisMem;  
                     # Insure this member is not a symlink.  
                     if (! -l $thisMem) {  
                         # Get its info.  
                         my $fileInfo = stat $thisMem;  
                         # Only proceed if we got the info. Otherwise, it's a hard link  
                         # and we want to skip it anyway.  
                         if ($fileInfo) {  
                             my $fileMode = $fileInfo->mode;  
                             if (($fileMode & $mask) != $mask) {  
                                 # Fix this member.  
                                 $fileMode |= $mask;  
                                 chmod $fileMode, $thisMem;  
                                 $fixCount++;  
                             }  
                             # If it's a subdirectory, stack it.  
                             if (-d $thisMem) {  
                                 push @dirs, $thisMem;  
                             }  
                         }  
                     }  
                 }  
             }  
         }  
         Trace("$lookCount files and directories processed, $fixCount fixed.") if T(2);  
     };  
     # Check for an error.  
     if ($@) {  
         Confess("SetPermissions error: $@");  
     }  
 }  
3361    
3362  =head3 CompareLists  =head3 CompareLists
3363    
3364  C<< my ($inserted, $deleted) = Tracer::CompareLists(\@newList, \@oldList, $keyIndex); >>      my ($inserted, $deleted) = Tracer::CompareLists(\@newList, \@oldList, $keyIndex);
3365    
3366  Compare two lists of tuples, and return a hash analyzing the differences. The lists  Compare two lists of tuples, and return a hash analyzing the differences. The lists
3367  are presumed to be sorted alphabetically by the value in the $keyIndex column.  are presumed to be sorted alphabetically by the value in the $keyIndex column.
# Line 2896  Line 3426 
3426      return ($inserted, $deleted);      return ($inserted, $deleted);
3427  }  }
3428    
3429  =head3 GetLine  =head3 GenerateURL
3430    
3431  C<< my @data = Tracer::GetLine($handle); >>