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revision 1.73, Tue Oct 3 12:04:50 2006 UTC revision 1.103, Fri May 9 04:21:45 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    umask 2;                    # Fix the damn umask so everything is group-writable.
212    
213  =head2 Public Methods  =head2 Tracing Methods
214    
215    =head3 Setups
216    
217        my $count = Tracer::Setups();
218    
219    Return the number of times L</TSetup> has been called.
220    
221    This method allows for the creation of conditional tracing setups where, for example, we
222    may want to set up tracing if nobody else has done it before us.
223    
224    =cut
225    
226    sub Setups {
227        return $SetupCount;
228    }
229    
230  =head3 TSetup  =head3 TSetup
231    
232  C<< TSetup($categoryList, $target); >>      TSetup($categoryList, $target);
233    
234  This method is used to specify the trace options. The options are stored as package data  This method is used to specify the trace options. The options are stored as package data
235  and interrogated by the L</Trace> and L</T> methods.  and interrogated by the L</Trace> and L</T> methods.
# Line 346  Line 279 
279          }          }
280      }      }
281      # Now we need to process the destination information. The most important special      # Now we need to process the destination information. The most important special
282      # cases are the single ">", which requires we clear the file first, and the      # case is when we're writing to a file. This is indicated by ">" (overwrite) and
283      # "+" prefix which indicates a double echo.      # ">>" (append). A leading "+" for either indicates that we are also writing to
284        # the standard output (tee mode).
285      if ($target =~ m/^\+?>>?/) {      if ($target =~ m/^\+?>>?/) {
286          if ($target =~ m/^\+/) {          if ($target =~ m/^\+/) {
287              $TeeFlag = 1;              $TeeFlag = 1;
288              $target = substr($target, 1);              $target = substr($target, 1);
289          }          }
290          if ($target =~ m/^>[^>]/) {          if ($target =~ m/^>[^>]/) {
291                # We need to initialize the file (which clears it).
292              open TRACEFILE, $target;              open TRACEFILE, $target;
293              print TRACEFILE "[" . Now() . "] <Tracer>: Tracing initialized.\n";              print TRACEFILE "[" . Now() . "] [notice] [Tracer] Tracing initialized.\n";
294              close TRACEFILE;              close TRACEFILE;
295                # Set to append mode now that the file has been cleared.
296              $Destination = ">$target";              $Destination = ">$target";
297          } else {          } else {
298              $Destination = $target;              $Destination = $target;
# Line 368  Line 304 
304      $SetupCount++;      $SetupCount++;
305  }  }
306    
307  =head3 StandardSetup  =head3 SetLevel
308    
309  C<< my ($options, @parameters) = StandardSetup(\@categories, \%options, $parmHelp, @ARGV); >>      Tracer::SetLevel($newLevel);
310    
311  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.  
312    
313  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.  
314    
315  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  
316    
317      ["Sprout", "SproutLoad", "ERDB"]  Proposed new trace level.
318    
319  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.  
320    
321  =over 4  =cut
322    
323  =item SQL  sub SetLevel {
324        $TraceLevel = $_[0];
325    }
326    
327  Traces SQL commands and activity.  =head3 ParseDate
328    
329  =item Tracer      my $time = Tracer::ParseDate($dateString);
330    
331  Traces error messages and call stacks.  Convert a date into a PERL time number. This method expects a date-like string
332    and parses it into a number. The string must be vaguely date-like or it will
333    return an undefined value. Our requirement is that a month and day be
334    present and that three pieces of the date string (time of day, month and day,
335    year) be separated by likely delimiters, such as spaces, commas, and such-like.
336    
337  =back  If a time of day is present, it must be in military time with two digits for
338    everything but the hour.
339    
340  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.  
341    
342      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
343    equally innocuous. This means, however, that a sufficiently long sentence with date-like
344    parts in it may be interpreted as a date. Hopefully this will not be a problem.
345    
346  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  
347    
348  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.  
349    
350      TransactFeatures -trace=3 -sql -user=Bruce register ../xacts IDs.tbl  =over 4
351    
352  would send the trace output to C<traceBruce.log> in the temporary directory.  =item dateString
353    
354  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.  
355    
356  You can specify a different default trace level by setting C<$options->{trace}>  =item RETURN
 prior to calling this method.  
357    
358  An example at this point would help. Consider, for example, the command-line utility  Returns a PERL time, that is, a number of seconds since the epoch, or C<undef> if
359  C<TransactFeatures>. It accepts a list of positional parameters plus the options  the date string is invalid. A valid date string must contain a month and day.
 C<safe>, C<noAlias>, C<start>, and C<tblFiles>. To start up this command, we execute  
 the following code.  
360    
361      my ($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);  
362    
363    =cut
364    
365  The call to C<ParseCommand> specifies the default values for the options and  # Universal month conversion table.
366  stores the actual options in a hash that is returned as C<$options>. The  use constant MONTHS => {    Jan =>  0, January   =>  0, '01' =>  0,  '1' =>  0,
367  positional parameters are returned in C<@parameters>.                              Feb =>  1, February  =>  1, '02' =>  1,  '2' =>  1,
368                                Mar =>  2, March     =>  2, '03' =>  2,  '3' =>  2,
369                                Apr =>  3, April     =>  3, '04' =>  3,  '4' =>  3,
370                                May =>  4, May       =>  4, '05' =>  4,  '5' =>  4,
371                                Jun =>  5, June      =>  5, '06' =>  5,  '6' =>  5,
372                                Jul =>  6, July      =>  6, '07' =>  6,  '7' =>  6,
373                                Aug =>  7, August    =>  7, '08' =>  7,  '8' =>  7,
374                                Sep =>  8, September =>  8, '09' =>  8,  '9' =>  8,
375                                Oct =>  9, October  =>   9, '10' =>  9,
376                                Nov => 10, November =>  10, '11' => 10,
377                                Dec => 11, December =>  11, '12' => 11
378                            };
379    
380  The following is a sample command line for C<TransactFeatures>.  sub ParseDate {
381        # Get the parameters.
382        my ($dateString) = @_;
383        # Declare the return variable.
384        my $retVal;
385        # Find the month and day of month. There are two ways that can happen. We check for the
386        # numeric style first. That way, if the user's done something like "Sun 12/22", then we
387        # won't be fooled into thinking the month is Sunday.
388        if ($dateString =~ m#\b(\d{1,2})/(\d{1,2})\b# || $dateString =~ m#\b(\w+)\s(\d{1,2})\b#) {
389            my ($mon, $mday) = (MONTHS->{$1}, $2);
390            # Insist that the month and day are valid.
391            if (defined($mon) && $2 >= 1 && $2 <= 31) {
392                # Find the time.
393                my ($hour, $min, $sec) = (0, 0, 0);
394                if ($dateString =~ /\b(\d{1,2}):(\d{2}):(\d{2})\b/) {
395                    ($hour, $min, $sec) = ($1, $2, $3);
396                }
397                # Find the year.
398                my $year;
399                if ($dateString =~ /\b(\d{4})\b/) {
400                    $year = $1;
401                } else {
402                    # Get the default year, which is this one. Note we must convert it to
403                    # the four-digit value expected by "timelocal".
404                    (undef, undef, undef, undef, undef, $year) = localtime();
405                    $year += 1900;
406                }
407                $retVal = timelocal($sec, $min, $hour, $mday, $mon, $year);
408            }
409        }
410        # Return the result.
411        return $retVal;
412    }
413    
414      TransactFeatures -trace=2 -noAlias register ../xacts IDs.tbl  =head3 LogErrors
415    
416  In this case, C<register>, C<../xacts>, and C<IDs.tbl> are the positional      Tracer::LogErrors($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<$options> hash would be  
417    
418      { trace => 2, sql => 0, safe => 0,  Route the standard error output to a log file.
       noAlias => 1, start => ' ', tblFiles => 0 }  
419    
420  Use of C<StandardSetup> in this way provides a simple way of performing  =over 4
 standard tracing setup and command-line parsing. Note that the caller is  
 not even aware of the command-line switches C<-trace> and C<-sql>, which  
 are used by this method to control the tracing. If additional tracing features  
 need to be added in the future, they can be processed by this method without  
 upsetting the command-line utilities.  
421    
422  If the C<background> option is specified on the command line, then the  =item fileName
 standard and error outputs will be directed to files in the temporary  
 directory, using the same suffix as the trace file. So, if the command  
 line specified  
423    
424      -user=Bruce -background  Name of the file to receive the error output.
425    
426  then the trace output would go to C<traceBruce.log>, the standard output to  =back
 C<outBruce.log>, and the error output to C<errBruce.log>. This is designed to  
 simplify starting a command in the background.  
427    
428  The user name is also used as the tracing key for L</Emergency Tracing>.  =cut
 Specifying a value of C<E> for the trace level causes emergency tracing to  
 be used instead of custom tracing. If the user name is not specified,  
 the tracing key is taken from the C<Tracing> environment variable. If there  
 is no value for that variable, the tracing key will be computed from the PID.  
429    
430  Finally, if the special option C<-h> is specified, the option names will  sub LogErrors {
431  be traced at level 0 and the program will exit without processing.      # Get the file name.
432  This provides a limited help capability. For example, if the user enters      my ($fileName) = @_;
433        # Open the file as the standard error output.
434        open STDERR, '>', $fileName;
435    }
436    
437      TransactFeatures -h  =head3 Trace
438    
439  he would see the following output.      Trace($message);
440    
441      TransactFeatures [options] command transactionDirectory IDfile  Write a trace message to the target location specified in L</TSetup>. If there has not been
442          -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  
443    
444  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,  
445    
446      { trace => [0, "tracing level (default 0)"],  =item message
        ...  
447    
448  would set the default trace level to 0 instead of E, while  Message to write.
449    
450      { trace => ["2-", "tracing level (default 2)"],  =back
        ...  
451    
452  would set the default to 2, but trace only to the log file, not to the  =cut
 standard output.  
453    
454  The parameters to this method are as follows.  sub Trace {
455        # Get the parameters.
456        my ($message) = @_;
457        # Strip off any line terminators at the end of the message. We will add
458        # new-line stuff ourselves.
459        my $stripped = Strip($message);
460        # Compute the caller information.
461        my ($callPackage, $callFile, $callLine) = caller();
462        my $callFileTitle = basename($callFile);
463        # Check the caller.
464        my $callerInfo = ($callFileTitle ne "Tracer.pm" ? " [$callFileTitle $callLine]" : "");
465        # Get the timestamp.
466        my $timeStamp = Now();
467        # Build the prefix.
468        my $level = $LevelNames[$LastLevel] || "($LastLevel)";
469        my $prefix = "[$timeStamp] [$level] [$LastCategory]$callerInfo";
470        # Format the message.
471        my $formatted = "$prefix $stripped";
472        # Process according to the destination.
473        if ($Destination eq "TEXT") {
474            # Write the message to the standard output.
475            print "$formatted\n";
476        } elsif ($Destination eq "ERROR") {
477            # Write the message to the error output. Here, we want our prefix fields.
478            print STDERR "$formatted\n";
479        } elsif ($Destination eq "WARN") {
480            # Emit the message to the standard error output. It is presumed that the
481            # error logger will add its own prefix fields, the notable exception being
482            # the caller info.
483            print STDERR "$callerInfo$stripped\n";
484        } elsif ($Destination eq "QUEUE") {
485            # Push the message into the queue.
486            push @Queue, "$formatted";
487        } elsif ($Destination eq "HTML") {
488            # Convert the message to HTML and write it to the standard output.
489            my $escapedMessage = CGI::escapeHTML($stripped);
490            print "<p>$timeStamp $LastCategory $LastLevel: $escapedMessage</p>\n";
491        } elsif ($Destination =~ m/^>>/) {
492            # Write the trace message to an output file.
493            open(TRACING, $Destination) || die "Tracing open for \"$Destination\" failed: $!";
494            print TRACING "$formatted\n";
495            close TRACING;
496            # If the Tee flag is on, echo it to the standard output.
497            if ($TeeFlag) {
498                print "$formatted\n";
499            }
500        }
501    }
502    
503  =over 4  =head3 T
504    
505  =item categories      my $switch = T($category, $traceLevel);
506    
507  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.  
508    
509  =item options      my $switch = T($traceLevel);
510    
511  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
512  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).  
513    
514  =item parmHelp  =over 4
515    
516  A string that vaguely describes the positional parameters. This is used  =item category
 if the user specifies the C<-h> option.  
517    
518  =item argv  Category to which the message belongs. If not specified, the caller's package name is
519    used.
520    
521  List of command line parameters, including the option switches, which must  =item traceLevel
522  precede the positional parameters and be prefixed by a hyphen.  
523    Relevant tracing level.
524    
525  =item RETURN  =item RETURN
526    
527  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.  
528    
529  =back  =back
530    
531  =cut  =cut
532    
533  sub StandardSetup {  sub T {
534        # Declare the return variable.
535        my $retVal = 0;
536        # Only proceed if tracing is turned on.
537        if ($Destination ne "NONE") {
538      # Get the parameters.      # Get the parameters.
539      my ($categories, $options, $parmHelp, @argv) = @_;          my ($category, $traceLevel) = @_;
540      # Get the default tracing key.          if (!defined $traceLevel) {
541      my $tkey = EmergencyKey();              # Here we have no category, so we need to get the calling package.
542      # Add the tracing options.              # The calling package is normally the first parameter. If it is
543      if (! exists $options->{trace}) {              # omitted, the first parameter will be the tracelevel. So, the
544          $options->{trace} = ['E', "tracing level (E for emergency tracing)"];              # first thing we do is shift the so-called category into the
545      }              # $traceLevel variable where it belongs.
546      $options->{sql} = [0, "turn on SQL tracing"];              $traceLevel = $category;
547      $options->{h} = [0, "display command-line options"];              my ($package, $fileName, $line) = caller;
548      $options->{user} = [$tkey, "tracing key"];              # If there is no calling package, we default to "main".
549      $options->{background} = [0, "spool standard and error output"];              if (!$package) {
550      # 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";  
551              } else {              } else {
552                  $traceMode = "WARN";                  my @cats = split /::/, $package;
553              }                  $category = $cats[$#cats];
         }  
         # Now set up the tracing.  
         TSetup("$traceLevel $cats", $traceMode);  
554      }      }
     # Check for the "h" option. If it is specified, dump the command-line  
     # options and exit the program.  
     if ($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] . ")";  
555              }              }
556              print "  $name $desc\n";          # Save the category name and level.
557            $LastCategory = $category;
558            $LastLevel = $traceLevel;
559            # Convert it to lower case before we hash it.
560            $category = lc $category;
561            # Validate the trace level.
562            if (ref $traceLevel) {
563                Confess("Bad trace level.");
564            } elsif (ref $TraceLevel) {
565                Confess("Bad trace config.");
566          }          }
567          exit(0);          # Make the check. Note that level 0 shows even if the category is turned off.
568            $retVal = ($traceLevel <= $TraceLevel && ($traceLevel == 0 || $AllTrace || exists $Categories{$category}));
569      }      }
570      # Return the parsed parameters.      # Return the computed result.
571      return ($retOptions, @retParameters);      return $retVal;
572  }  }
573    
574  =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  
575    
576  sub Setups {      my $data = QTrace($format);
     return $SetupCount;  
 }  
577    
578  =head3 Open  Return the queued trace data in the specified format.
579    
580  C<< my $handle = Open($fileHandle, $fileSpec, $message); >>  =over 4
581    
582  Open a file.  =item format
583    
584  The I<$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,  
585    
586      Open(\*LOGFILE, '>>/usr/spool/news/twitlog', "Could not open twit log.");  =back
587    
588  would open for output appended to the specified file, and  =cut
589    
590      Open(\*DATASTREAM, "| sort -u >$outputFile", "Could not open $outputFile.");  sub QTrace {
591        # Get the parameter.
592        my ($format) = @_;
593        # Create the return variable.
594        my $retVal = "";
595        # Only proceed if there is an actual queue.
596        if (@Queue) {
597            # Process according to the format.
598            if ($format =~ m/^HTML$/i) {
599                # Convert the queue into an HTML list.
600                $retVal = "<ul>\n";
601                for my $line (@Queue) {
602                    my $escapedLine = CGI::escapeHTML($line);
603                    $retVal .= "<li>$escapedLine</li>\n";
604                }
605                $retVal .= "</ul>\n";
606            } elsif ($format =~ m/^TEXT$/i) {
607                # Convert the queue into a list of text lines.
608                $retVal = join("\n", @Queue) . "\n";
609            }
610            # Clear the queue.
611            @Queue = ();
612        }
613        # Return the formatted list.
614        return $retVal;
615    }
616    
617  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.  
618    
619      my $logFile = Open(undef, '>>/usr/spool/news/twitlog', "Could not open twit log.");      Confess($message);
620    
621  The I<$message> parameter is used if the open fails. If it is set to C<0>, then  Trace the call stack and abort the program with the specified message. When used with
622  the open returns TRUE if successful and FALSE if an error occurred. Otherwise, a  the OR operator and the L</Assert> method, B<Confess> can function as a debugging assert.
623  failed open will throw an exception and the third parameter will be used to construct  So, for example
 an error message. If the parameter is omitted, a standard message is constructed  
 using the file spec.  
624    
625      Could not open "/usr/spool/news/twitlog"      Assert($recNum >= 0) || Confess("Invalid record number $recNum.");
626    
627  Note that the mode characters are automatically cleaned from the file name.  Will abort the program with a stack trace if the value of C<$recNum> is negative.
 The actual error message from the file system will be captured and appended to the  
 message in any case.  
628    
629      Could not open "/usr/spool/news/twitlog": file not found.  =over 4
630    
631  In some versions of PERL the only error message we get is a number, which  =item message
 corresponds to the C++ C<errno> value.  
632    
633      Could not open "/usr/spool/news/twitlog": 6.  Message to include in the trace.
634    
635  =over 4  =back
636    
637  =item fileHandle  =cut
638    
639  File handle. If this parameter is C<undef>, a file handle will be generated  sub Confess {
640  and returned as the value of this method.      # Get the parameters.
641        my ($message) = @_;
642        # Set up the category and level.
643        $LastCategory = "(confess)";
644        $LastLevel = 0;
645        if (! defined($FIG_Config::no_tool_hdr)) {
646            # Here we have a tool header. Display its length so that the user can adjust the line numbers.
647            my $toolHeaderFile = "$FIG_Config::fig_disk/dist/releases/current/$FIG_Config::arch/tool_hdr";
648            # Only proceed if the tool header file is actually present.
649            if (-f $toolHeaderFile) {
650                my $fh;
651                if (open $fh, "<$toolHeaderFile") {
652                    my @lines = <$fh>;
653                    Trace("Tool header has " . scalar(@lines) . " lines.");
654                }
655            }
656        }
657        # Trace the call stack.
658        Cluck($message);
659        # Abort the program.
660        croak(">>> $message");
661    }
662    
663  =item fileSpec  =head3 Warn
664    
665  File name and mode, as per the PERL C<open> function.      Warn($message);
666    
667  =item message (optional)  This method traces an important message. If an RSS feed is configured
668    (via I<FIG_Config::error_feed>) and the tracing destination is C<WARN>,
669    then the message will be echoed to the feed. In general, a tracing
670    destination of C<WARN> indicates that the caller is running as a web
671    service in a production environment; however, this is not a requirement.
672    
673    To force warnings into the RSS feed even when the tracing destination
674    is not C<WARN>, simply specify the C<Feed> tracing module. This can be
675    configured automatically when L</StandardSetup> is used.
676    
677    The L</Cluck> method calls this one for its final message. Since
678    L</Confess> calls L</Cluck>, this means that any error which is caught
679    and confessed will put something in the feed. This insures that someone
680    will be alerted relatively quickly when a failure occurs.
681    
682  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>.  
683    
684  =item RETURN  =item message
685    
686  Returns the name of the file handle assigned to the file, or C<undef> if the  Message to be traced.
 open failed.  
687    
688  =back  =back
689    
690  =cut  =cut
691    
692  sub Open {  sub Warn {
693      # Get the parameters.      # Get the parameters.
694      my ($fileHandle, $fileSpec, $message) = @_;      my ($message) = @_;
695      # Attempt to open the file.      # Trace the message.
696      my $rv = open $fileHandle, $fileSpec;      Trace($message);
697      # If the open failed, generate an error message.      # Check for feed forcing.
698      if (! $rv) {      my $forceFeed = exists $Categories{feed};
699          # Save the system error message.      # An error here would be disastrous. Note, however, that we aren't too worried
700          my $sysMessage = $!;      # about losing events. The error log is always available for the occasions where
701          # See if we need a default message.      # we mess up. Note that if debug mode is specified, we do this stuff even in a
702          if (!$message) {      # test environment.
703              # Clean any obvious mode characters and leading spaces from the      eval {
704              # filename.          # Do we need to put this in the RSS feed?
705              my ($fileName) = FindNamePart($fileSpec);          if ($FIG_Config::error_feed && ($Destination eq 'WARN' || $forceFeed)) {
706              $message = "Could not open \"$fileName\"";              # Yes. We now need to compute the date, the link, and the title.
707                # First, the date, in a very specific format.
708                my $date = strftime("%a, %02e %b %H:%M:%S %Y ", localtime) .
709                    (tz_local_offset() / 30);
710                # Environment data goes in here. We start with the date.
711                my $environment = "$date.  ";
712                # If we need to recap the message (because it's too long to be a title), we'll
713                # put it in here.
714                my $recap;
715                # Copy the message and remove excess space.
716                my $title = $message;
717                $title =~ s/\s+/ /gs;
718                # If it's too long, we have to split it up.
719                if (length $title > 60) {
720                    # Put the full message in the environment string.
721                    $recap = $title;
722                    # Excerpt it as the title.
723                    $title = substr($title, 0, 50) . "...";
724                }
725                # If we have a CGI object, then this is a web error. Otherwise, it's
726                # command-line.
727                if (defined $SavedCGI) {
728                    # We're in a web service. The environment is the user's IP, and the link
729                    # is the URL that got us here.
730                    my $key = $ENV{HTTP_X_FORWARDED_FOR} || $ENV{REMOTE_ADDR};
731                    $environment .= "Event Reported at IP address $key.";
732                    my $url = $SavedCGI->url(-full => 1, -query => 1);
733                    # We need the user agent string and (if available) the referrer.
734                    # The referrer will be the link.
735                    $environment .= "User Agent $ENV{HTTP_USER_AGENT}";
736                    if ($ENV{HTTP_REFERER}) {
737                        my $link = $ENV{HTTP_REFERER};
738                        $environment .= " referred from <a href=\"$link\">$link</a>.";
739                    } else {
740                        $environment .= " referrer unknown.";
741                    }
742                    # Close off the sentence with the original link.
743                    $environment .= " URL of error is <a href=\"$url\">$url</a>.";
744                } else {
745                    # No CGI object, so we're a command-line tool. Use the tracing
746                    # key and the PID as the user identifier, and add the command.
747                    my $key = EmergencyKey();
748                    $environment .= "Event Reported by $key Process $$. Command $ENV{_}.";
749                }
750                # Build a GUID. We use the current time, the title, and the process ID,
751                # then digest the result.
752                my $guid = Digest::MD5::md5_base64(gettimeofday(), $title, $$);
753                # Finally, the description. This is a stack trace plus various environmental stuff.
754                my $stackTrace = "";
755                my @trace = LongMess();
756                # Only proceed if we got something back.
757                if (scalar(@trace) > 0) {
758                    $trace[0] =~ s/Tracer::Warn.+?called/Event occurred/;
759                    $stackTrace = "Stack trace:<pre>" . join("\n", @trace, "</pre>");
760                }
761                # We got the stack trace. Now it's time to put it all together.
762                # We have a goofy thing here in that we need to HTML-escape some sections of the description
763                # twice. They will be escaped once here, and then once when written by XML::Simple. They are
764                # unescaped once when processed by the RSS reader, and stuff in the description is treated as
765                # HTML. So, anything escaped here is treated as a literal when viewed in the RSS reader, but
766                # our <br>s and <pre>s are used to format the description.
767                $recap = (defined $recap ? "<em>" . CGI::escapeHTML($recap) . "</em><br /><br />" : "");
768                my $description = "$recap$environment  $stackTrace";
769                # Okay, we have all the pieces. Create a hash of the new event.
770                my $newItem = { title => $title,
771                                description => $description,
772                                category => $LastCategory,
773                                pubDate => $date,
774                                guid => $guid,
775                               };
776                # We need XML capability for this.
777                require XML::Simple;
778                # The RSS document goes in here.
779                my $rss;
780                # Get the name of the RSS file. It's in the FIG temporary directory.
781                my $fileName = "$FIG_Config::temp/$FIG_Config::error_feed";
782                # Does it exist?
783                if (-s $fileName) {
784                    # Slurp it in.
785                    $rss = XML::Simple::XMLin($fileName, ForceArray => ['item']);
786                } else {
787                    my $size = -s $fileName;
788                    # Create an empty channel.
789                    $rss = {
790                        channel => {
791                            title => 'NMPDR Warning Feed',
792                            link => "$FIG_Config::temp_url/$FIG_Config::error_feed",
793                            description => "Important messages regarding the status of the NMPDR.",
794                            generator => "NMPDR Trace Facility",
795                            docs => "http://blogs.law.harvard.edu/tech/rss",
796                            item => []
797                        },
798                    };
799          }          }
800          # Terminate with an error using the supplied message and the              # Get the channel object.
801          # error message from the file system.              my $channel = $rss->{channel};
802          Confess("$message: $!");              # Update the last-build date.
803                $channel->{lastBuildDate} = $date;
804                # Get the item array.
805                my $items = $channel->{item};
806                # Insure it has only 100 entries.
807                while (scalar @{$items} > 100) {
808                    pop @{$items};
809                }
810                # Add our new item at the front.
811                unshift @{$items}, $newItem;
812                # Create the XML. Note we do not include the root or the declaration. XML Simple can't handle
813                # the requirements for those.
814                my $xml = XML::Simple::XMLout($rss, NoAttr => 1, RootName => undef, XmlDecl => '');
815                # Here we put in the root and declaration. The problem is that the root has to have the version attribute
816                # in it. So, we suppress the root and do it by hand, and that requires suppressing the declaration, too.
817                $xml = "<?xml version=\"1.0\" encoding=\"utf-8\"?>\n<rss version=\"2.0\">$xml\n</rss>";
818                # We don't use Open here because we can't afford an error.
819                if (open XMLOUT, ">$fileName") {
820                    print XMLOUT $xml;
821                    close XMLOUT;
822                }
823            }
824        };
825        if ($@) {
826            # If the feed failed, we need to know why. The error will be traced, but this method will not be involved
827            # (which is a good thing).
828            my $error = $@;
829            Trace("Feed Error: $error") if T(Feed => 0);
830      }      }
     # Return the file handle.  
     return $fileHandle;  
831  }  }
832    
833  =head3 FindNamePart  =head3 Assert
   
 C<< my ($fileName, $start, $len) = Tracer::FindNamePart($fileSpec); >>  
834    
835  Extract the portion of a file specification that contains the file name.      Assert($condition1, $condition2, ... $conditionN);
836    
837  A file specification is the string passed to an C<open> call. It specifies the file  Return TRUE if all the conditions are true. This method can be used in conjunction with
838  mode and name. In a truly complex situation, it can specify a pipe sequence. This  the OR operator and the L</Confess> method as a debugging assert.
839  method assumes that the file name is whatever follows the first angle bracket  So, for example
 sequence.  So, for example, in the following strings the file name is  
 C</usr/fig/myfile.txt>.  
840    
841      >>/usr/fig/myfile.txt      Assert($recNum >= 0) || Confess("Invalid record number $recNum.");
     </usr/fig/myfile.txt  
     | sort -u > /usr/fig/myfile.txt  
842    
843  If the method cannot find a file name using its normal methods, it will return the  Will abort the program with a stack trace if the value of C<$recNum> is negative.
 whole incoming string.  
844    
845  =over 4  =cut
846    sub Assert {
847        my $retVal = 1;
848        LOOP: for my $condition (@_) {
849            if (! $condition) {
850                $retVal = 0;
851                last LOOP;
852            }
853        }
854        return $retVal;
855    }
856    
857  =item fileSpec  =head3 Cluck
858    
859  File specification string from which the file name is to be extracted.      Cluck($message);
860    
861  =item RETURN  Trace the call stack. Note that for best results, you should qualify the call with a
862    trace condition. For example,
863    
864  Returns a three-element list. The first element contains the file name portion of      Cluck("Starting record parse.") if T(3);
865  the specified string, or the whole string if a file name cannot be found via normal  
866  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.
867  the third element contains the length.  
868    =over 4
869    
870    =item message
871    
872    Message to include in the trace.
873    
874  =back  =back
875    
876  =cut  =cut
877  #: Return Type $;  
878  sub FindNamePart {  sub Cluck {
879      # Get the parameters.      # Get the parameters.
880      my ($fileSpec) = @_;      my ($message) = @_;
881      # Default to the whole input string.      # Trace what's happening.
882      my ($retVal, $pos, $len) = ($fileSpec, 0, length $fileSpec);      Trace("Stack trace for event: $message");
883      # Parse out the file name if we can.      # Get the stack trace.
884      if ($fileSpec =~ m/(<|>>?)(.+?)(\s*)$/) {      my @trace = LongMess();
885          $retVal = $2;      # Convert the trace to a series of messages.
886          $len = length $retVal;      for my $line (@trace) {
887          $pos = (length $fileSpec) - (length $3) - $len;          # Replace the tab at the beginning with spaces.
888            $line =~ s/^\t/    /;
889            # Trace the line.
890            Trace($line);
891      }      }
892      # Return the result.      # Issue a warning. This displays the event message and inserts it into the RSS error feed.
893      return ($retVal, $pos, $len);      Warn($message);
894  }  }
895    
896  =head3 OpenDir  =head3 LongMess
897    
898  C<< my @files = OpenDir($dirName, $filtered, $flag); >>      my @lines = Tracer::LongMess();
899    
900  Open a directory and return all the file names. This function essentially performs  Return a stack trace with all tracing methods removed. The return will be in the form of a list
901  the functions of an C<opendir> and C<readdir>. If the I<$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,  
902    
903      my @files = OpenDir("/Volumes/fig/contigs", 1);  =cut
904    
905  is effectively the same as  sub LongMess {
906        # Declare the return variable.
907        my @retVal = ();
908        my $confession = longmess("");
909        for my $line (split /\s*\n/, $confession) {
910            unless ($line =~ /Tracer\.pm/) {
911                # Here we have a line worth keeping. Push it onto the result list.
912                push @retVal, $line;
913            }
914        }
915        # Return the result.
916        return @retVal;
917    }
918    
919      opendir(TMP, "/Volumes/fig/contigs") || Confess("Could not open /Volumes/fig/contigs.");  =head3 ScriptSetup (deprecated)
     my @files = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir(TMP);  
920    
921  Similarly, the following code      my ($cgi, $varHash) = ScriptSetup($noTrace);
922    
923      my @files = grep { $_ =~ /^\d/ } OpenDir("/Volumes/fig/orgs", 0, 1);  Perform standard tracing and debugging setup for scripts. The value returned is
924    the CGI object followed by a pre-built variable hash. At the end of the script,
925    the client should call L</ScriptFinish> to output the web page.
926    
927  Returns the names of all files in C</Volumes/fig/orgs> that begin with digits and  This method calls L</ETracing> to configure tracing, which allows the tracing
928  automatically returns an empty list if the directory fails to open.  to be configured via the emergency tracing form on the debugging control panel.
929    Tracing will then be turned on automatically for all programs that use the L</ETracing>
930    method, which includes every program that uses this method or L</StandardSetup>.
931    
932  =over 4  =over 4
933    
934  =item dirName  =item noTrace (optional)
935    
936  Name of the directory to open.  If specified, tracing will be suppressed. This is useful if the script wants to set up
937    tracing manually.
938    
939  =item filtered  =item RETURN
940    
941  TRUE if files whose names begin with a period (C<.>) should be automatically removed  Returns a two-element list consisting of a CGI query object and a variable hash for
942  from the list, else FALSE.  the output page.
943    
944  =item flag  =back
945    
946  TRUE if a failure to open is okay, else FALSE  =cut
947    
948    sub ScriptSetup {
949        # Get the parameters.
950        my ($noTrace) = @_;
951        # Get the CGI query object.
952        my $cgi = CGI->new();
953        # Set up tracing if it's not suppressed.
954        ETracing($cgi) unless $noTrace;
955        # Create the variable hash.
956        my $varHash = { results => '' };
957        # Return the query object and variable hash.
958        return ($cgi, $varHash);
959    }
960    
961    =head3 ETracing
962    
963        ETracing($parameter);
964    
965    Set up emergency tracing. Emergency tracing is tracing that is turned
966    on automatically for any program that calls this method. The emergency
967    tracing parameters are stored in a a file identified by a tracing key.
968    If this method is called with a CGI object, then the tracing key is
969    taken from a cookie. If it is called with no parameters, then the tracing
970    key is taken from an environment variable. If it is called with a string,
971    the tracing key is that string.
972    
973    =over 4
974    
975    =item parameter
976    
977    A parameter from which the tracing key is computed. If it is a scalar,
978    that scalar is used as the tracing key. If it is a CGI object, the
979    tracing key is taken from the C<IP> cookie. If it is omitted, the
980    tracing key is taken from the C<TRACING> environment variable. If it
981    is a CGI object and emergency tracing is not on, the C<Trace> and
982    C<TF> parameters will be used to determine the type of tracing.
983    
984  =back  =back
985    
986  =cut  =cut
987  #: Return Type @;  
988  sub OpenDir {  sub ETracing {
989      # Get the parameters.      # Get the parameter.
990      my ($dirName, $filtered, $flag) = @_;      my ($parameter) = @_;
991      # Declare the return variable.      # Check for CGI mode.
992      my @retVal = ();      if (defined $parameter && ref $parameter eq 'CGI') {
993      # 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;  
994          } else {          } else {
995              @retVal = readdir $dirHandle;          $SavedCGI = undef;
996        }
997        # Default to no tracing except errors.
998        my ($tracing, $dest) = ("0", "WARN");
999        # Check for emergency tracing.
1000        my $tkey = EmergencyKey($parameter);
1001        my $emergencyFile = EmergencyFileName($tkey);
1002        if (-e $emergencyFile) {
1003            # We have the file. Read in the data.
1004            my @tracing = GetFile($emergencyFile);
1005            # Pull off the time limit.
1006            my $expire = shift @tracing;
1007            # Convert it to seconds.
1008            $expire *= 3600;
1009            # Check the file data.
1010            my $stat = stat($emergencyFile);
1011            my ($now) = gettimeofday;
1012            if ($now - $stat->mtime > $expire) {
1013                # Delete the expired file.
1014                unlink $emergencyFile;
1015            } else {
1016                # Emergency tracing is on. Pull off the destination and
1017                # the trace level;
1018                $dest = shift @tracing;
1019                my $level = shift @tracing;
1020                # Convert the destination to a real tracing destination.
1021                # temp directory.
1022                $dest = EmergencyTracingDest($tkey, $dest);
1023                # Insure Tracer is specified.
1024                my %moduleHash = map { $_ => 1 } @tracing;
1025                $moduleHash{Tracer} = 1;
1026                # Set the trace parameter.
1027                $tracing = join(" ", $level, sort keys %moduleHash);
1028            }
1029        } elsif (defined $SavedCGI) {
1030            # There's no emergency tracing, but we have a CGI object, so check
1031            # for tracing from the form parameters.
1032            if ($SavedCGI->param('Trace')) {
1033                # Here the user has requested tracing via a form.
1034                $dest = ($SavedCGI->param('TF') ? ">$FIG_Config::temp/Trace$$.log" : "QUEUE");
1035                $tracing = $SavedCGI->param('Trace') . " Tracer";
1036            }
1037        }
1038        # Setup the tracing we've determined from all the stuff above.
1039        TSetup($tracing, $dest);
1040        # Check to see if we're a web script.
1041        if (defined $SavedCGI) {
1042            # Yes we are. Trace the form and environment data.
1043            TraceParms($SavedCGI);
1044            # Check for RAW mode. In raw mode, we print a fake header so that we see everything
1045            # emitted by the script in its raw form.
1046            if (T(Raw => 3)) {
1047                print CGI::header(-type => 'text/plain', -tracing => 'Raw');
1048          }          }
     } elsif (! $flag) {  
         # Here the directory would not open and it's considered an error.  
         Confess("Could not open directory $dirName.");  
1049      }      }
     # Return the result.  
     return @retVal;  
1050  }  }
1051    
1052  =head3 SetLevel  =head3 EmergencyFileName
1053    
1054  C<< Tracer::SetLevel($newLevel); >>      my $fileName = Tracer::EmergencyFileName($tkey);
1055    
1056  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
1057    the tracing information.
1058    
1059  =over 4  =over 4
1060    
1061  =item newLevel  =item tkey
1062    
1063  Proposed new trace level.  Tracing key for the current program.
1064    
1065    =item RETURN
1066    
1067    Returns the name of the file to contain the emergency tracing information.
1068    
1069  =back  =back
1070    
1071  =cut  =cut
1072    
1073  sub SetLevel {  sub EmergencyFileName {
1074      $TraceLevel = $_[0];      # Get the parameters.
1075        my ($tkey) = @_;
1076        # Compute the emergency tracing file name.
1077        return "$FIG_Config::temp/Emergency$tkey.txt";
1078  }  }
1079    
1080  =head3 Now  =head3 EmergencyFileTarget
1081    
1082  C<< my $string = Tracer::Now(); >>      my $fileName = Tracer::EmergencyFileTarget($tkey);
1083    
1084  Return a displayable time stamp containing the local time.  Return the emergency tracing target file name. This is the file that receives
1085    the tracing output for file-based tracing.
1086    
1087    =over 4
1088    
1089    =item tkey
1090    
1091    Tracing key for the current program.
1092    
1093    =item RETURN
1094    
1095    Returns the name of the file to contain the trace output.
1096    
1097    =back
1098    
1099  =cut  =cut
1100    
1101  sub Now {  sub EmergencyFileTarget {
1102      my ($sec,$min,$hour,$mday,$mon,$year,$wday,$yday,$isdst) = localtime(time);      # Get the parameters.
1103      my $retVal = _p2($mon+1) . "/" . _p2($mday) . "/" . ($year + 1900) . " " .      my ($tkey) = @_;
1104                   _p2($hour) . ":" . _p2($min) . ":" . _p2($sec);      # Compute the emergency tracing file name.
1105      return $retVal;      return "$FIG_Config::temp/trace$tkey.log";
1106    }
1107    
1108    =head3 EmergencyTracingDest
1109    
1110        my $dest = Tracer::EmergencyTracingDest($tkey, $myDest);
1111    
1112    This method converts an emergency tracing destination to a real
1113    tracing destination. The main difference is that if the
1114    destination is C<FILE> or C<APPEND>, we convert it to file
1115    output. If the destination is C<DUAL>, we convert it to file
1116    and standard output.
1117    
1118    =over 4
1119    
1120    =item tkey
1121    
1122    Tracing key for this environment.
1123    
1124    =item myDest
1125    
1126    Destination from the emergency tracing file.
1127    
1128    =item RETURN
1129    
1130    Returns a destination that can be passed into L</TSetup>.
1131    
1132    =back
1133    
1134    =cut
1135    
1136    sub EmergencyTracingDest {
1137        # Get the parameters.
1138        my ($tkey, $myDest) = @_;
1139        # Declare the return variable.
1140        my $retVal = $myDest;
1141        # Process according to the destination value.
1142        if ($myDest eq 'FILE') {
1143            $retVal = ">" . EmergencyFileTarget($tkey);
1144        } elsif ($myDest eq 'APPEND') {
1145            $retVal = ">>" . EmergencyFileTarget($tkey);
1146        } elsif ($myDest eq 'DUAL') {
1147            $retVal = "+>" . EmergencyFileTarget($tkey);
1148        } elsif ($myDest eq 'WARN') {
1149            $retVal = "WARN";
1150        }
1151        # Return the result.
1152        return $retVal;
1153    }
1154    
1155    =head3 Emergency
1156    
1157        Emergency($key, $hours, $dest, $level, @modules);
1158    
1159    Turn on emergency tracing. This method is normally invoked over the web from
1160    a debugging console, but it can also be called by the C<trace.pl> script.
1161    The caller specifies the duration of the emergency in hours, the desired tracing
1162    destination, the trace level, and a list of the trace modules to activate.
1163    For the length of the duration, when a program in an environment with the
1164    specified tracing key active invokes a Sprout CGI script, tracing will be
1165    turned on automatically. See L</TSetup> for more about tracing setup and
1166    L</ETracing> for more about emergency tracing.
1167    
1168    =over 4
1169    
1170    =item tkey
1171    
1172    The tracing key. This is used to identify the control file and the trace file.
1173    
1174    =item hours
1175    
1176    Number of hours to keep emergency tracing alive.
1177    
1178    =item dest
1179    
1180    Tracing destination. If no path information is specified for a file
1181    destination, it is put in the FIG temporary directory.
1182    
1183    =item level
1184    
1185    Tracing level. A higher level means more trace messages.
1186    
1187    =item modules
1188    
1189    A list of the tracing modules to activate.
1190    
1191    =back
1192    
1193    =cut
1194    
1195    sub Emergency {
1196        # Get the parameters.
1197        my ($tkey, $hours, $dest, $level, @modules) = @_;
1198        # Create the emergency file.
1199        my $specFile = EmergencyFileName($tkey);
1200        my $outHandle = Open(undef, ">$specFile");
1201        print $outHandle join("\n", $hours, $dest, $level, @modules, "");
1202    }
1203    
1204    =head3 EmergencyKey
1205    
1206        my $tkey = EmergencyKey($parameter);
1207    
1208    Return the Key to be used for emergency tracing. This could be an IP address,
1209     a session ID, or a user name, depending on the environment.
1210    
1211    =over 4
1212    
1213    =item parameter
1214    
1215    Parameter defining the method for finding the tracing key. If it is a scalar,
1216    then it is presumed to be the tracing key itself. If it is a CGI object, then
1217    the tracing key is taken from the C<IP> cookie. Otherwise, the tracing key is
1218    taken from the C<TRACING> environment variable.
1219    
1220    =item RETURN
1221    
1222    Returns the key to be used for labels in emergency tracing.
1223    
1224    =back
1225    
1226    =cut
1227    
1228    sub EmergencyKey {
1229        # Get the parameters.
1230        my ($parameter) = @_;
1231        # Declare the return variable.
1232        my $retVal;
1233        # Determine the parameter type.
1234        if (! defined $parameter) {
1235            # Here we're supposed to check the environment. If that fails, we
1236            # get the effective login ID.
1237            $retVal = $ENV{TRACING} || scalar getpwuid($<);
1238        } else {
1239            my $ptype = ref $parameter;
1240            if ($ptype eq 'CGI') {
1241                # Here we were invoked from a web page. Look for a cookie.
1242                $retVal = $parameter->cookie('IP');
1243            } elsif (! $ptype) {
1244                # Here the key was passed in.
1245                $retVal = $parameter;
1246            }
1247        }
1248        # If no luck finding a key, use the PID.
1249        if (! defined $retVal) {
1250            $retVal = $$;
1251        }
1252        # Return the result.
1253        return $retVal;
1254    }
1255    
1256    
1257    =head3 TraceParms
1258    
1259        Tracer::TraceParms($cgi);
1260    
1261    Trace the CGI parameters at trace level CGI => 3 and the environment variables
1262    at level CGI => 4. A self-referencing URL is traced at level CGI => 2.
1263    
1264    =over 4
1265    
1266    =item cgi
1267    
1268    CGI query object containing the parameters to trace.
1269    
1270    =back
1271    
1272    =cut
1273    
1274    sub TraceParms {
1275        # Get the parameters.
1276        my ($cgi) = @_;
1277        if (T(CGI => 2)) {
1278            # Here we trace the GET-style URL for the script.
1279            Trace("[URL] " . $cgi->url(-relative => 1, -query => 1));
1280        }
1281        if (T(CGI => 3)) {
1282            # Here we want to trace the parameter data.
1283            my @names = $cgi->param;
1284            for my $parmName (sort @names) {
1285                # Note we skip the Trace parameters, which are for our use only.
1286                if ($parmName ne 'Trace' && $parmName ne 'TF') {
1287                    my @values = $cgi->param($parmName);
1288                    Trace("[CGI] $parmName = " . join(", ", @values));
1289                }
1290            }
1291            # Display the request method.
1292            my $method = $cgi->request_method();
1293            Trace("Method: $method");
1294        }
1295        if (T(CGI => 4)) {
1296            # Here we want the environment data too.
1297            for my $envName (sort keys %ENV) {
1298                Trace("[ENV] $envName = $ENV{$envName}");
1299            }
1300        }
1301    }
1302    
1303    =head3 TraceImages
1304    
1305        Tracer::TraceImages($htmlString);
1306    
1307    Trace information about all of an html document's images. The tracing
1308    will be for type "IMG" at level 3. The image's source string
1309    will be displayed. This is generally either the URL of the image or
1310    raw data for the image itself. If the source is too long, only the first 300
1311    characters will be shown at trace level 3. The entire source will be shown,
1312    however, at trace level 4. This method is not very smart, and might catch
1313    Javascript code, but it is still useful when debugging the arcane
1314    behavior of images in multiple browser environments.
1315    
1316    =over 4
1317    
1318    =item htmlString
1319    
1320    HTML text for an outgoing web page.
1321    
1322    =back
1323    
1324    =cut
1325    
1326    sub TraceImages {
1327        # Only proceed if we're at the proper trace level.
1328        if (T(IMG => 3)) {
1329            # For performance reasons we're manipulating $_[0] instead of retrieving the string
1330            # into a variable called "$htmlString". This is because we expect html strings to be
1331            # long, and don't want to copy them any more than we have to.
1332            Trace(length($_[0]) . " characters in web page.");
1333            # Loop through the HTML, culling image tags.
1334            while ($_[0] =~ /<img\s+[^>]+?src="([^"]+)"/sgi) {
1335                # Extract the source string and determine whether or not it's too long.
1336                my $srcString = $1;
1337                my $pos = pos($_[0]) - length($srcString);
1338                my $excess = length($srcString) - 300;
1339                # We'll put the display string in here.
1340                my $srcDisplay = $srcString;
1341                # If it's a data string, split it at the comma.
1342                $srcDisplay =~ s/^(data[^,]+,)/$1\n/;
1343                # If there's no excess or we're at trace level 4, we're done. At level 3 with
1344                # a long string, however, we only show the first 300 characters.
1345                if ($excess > 0 && ! T(IMG => 4)) {
1346                    $srcDisplay = substr($srcDisplay,0,300) . "\nplus $excess characters.";
1347                }
1348                # Output the trace message.
1349                Trace("Image tag at position $pos:\n$srcDisplay");
1350            }
1351        }
1352    }
1353    
1354    
1355    =head3 ScriptFinish (deprecated)
1356    
1357        ScriptFinish($webData, $varHash);
1358    
1359    Output a web page at the end of a script. Either the string to be output or the
1360    name of a template file can be specified. If the second parameter is omitted,
1361    it is assumed we have a string to be output; otherwise, it is assumed we have the
1362    name of a template file. The template should have the variable C<DebugData>
1363    specified in any form that invokes a standard script. If debugging mode is turned
1364    on, a form field will be put in that allows the user to enter tracing data.
1365    Trace messages will be placed immediately before the terminal C<BODY> tag in
1366    the output, formatted as a list.
1367    
1368    A typical standard script would loook like the following.
1369    
1370        BEGIN {
1371            # Print the HTML header.
1372            print "CONTENT-TYPE: text/html\n\n";
1373        }
1374        use Tracer;
1375        use CGI;
1376        use FIG;
1377        # ... more uses ...
1378    
1379        my ($cgi, $varHash) = ScriptSetup();
1380        eval {
1381            # ... get data from $cgi, put it in $varHash ...
1382        };
1383        if ($@) {
1384            Trace("Script Error: $@") if T(0);
1385        }
1386        ScriptFinish("Html/MyTemplate.html", $varHash);
1387    
1388    The idea here is that even if the script fails, you'll see trace messages and
1389    useful output.
1390    
1391    =over 4
1392    
1393    =item webData
1394    
1395    A string containing either the full web page to be written to the output or the
1396    name of a template file from which the page is to be constructed. If the name
1397    of a template file is specified, then the second parameter must be present;
1398    otherwise, it must be absent.
1399    
1400    =item varHash (optional)
1401    
1402    If specified, then a reference to a hash mapping variable names for a template
1403    to their values. The template file will be read into memory, and variable markers
1404    will be replaced by data in this hash reference.
1405    
1406    =back
1407    
1408    =cut
1409    
1410    sub ScriptFinish {
1411        # Get the parameters.
1412        my ($webData, $varHash) = @_;
1413        # Check for a template file situation.
1414        my $outputString;
1415        if (defined $varHash) {
1416            # Here we have a template file. We need to determine the template type.
1417            my $template;
1418            if ($FIG_Config::template_url && $webData =~ /\.php$/) {
1419                $template = "$FIG_Config::template_url/$webData";
1420            } else {
1421                $template = "<<$webData";
1422            }
1423            $outputString = PageBuilder::Build($template, $varHash, "Html");
1424        } else {
1425            # Here the user gave us a raw string.
1426            $outputString = $webData;
1427        }
1428        # Check for trace messages.
1429        if ($Destination ne "NONE" && $TraceLevel > 0) {
1430            # We have trace messages, so we want to put them at the end of the body. This
1431            # is either at the end of the whole string or at the beginning of the BODY
1432            # end-tag.
1433            my $pos = length $outputString;
1434            if ($outputString =~ m#</body>#gi) {
1435                $pos = (pos $outputString) - 7;
1436            }
1437            # If the trace messages were queued, we unroll them. Otherwise, we display the
1438            # destination.
1439            my $traceHtml;
1440            if ($Destination eq "QUEUE") {
1441                $traceHtml = QTrace('Html');
1442            } elsif ($Destination =~ /^>>(.+)$/) {
1443                # Here the tracing output it to a file. We code it as a hyperlink so the user
1444                # can copy the file name into the clipboard easily.
1445                my $actualDest = $1;
1446                $traceHtml = "<p>Tracing output to $actualDest.</p>\n";
1447            } else {
1448                # Here we have one of the special destinations.
1449                $traceHtml = "<P>Tracing output type is $Destination.</p>\n";
1450            }
1451            substr $outputString, $pos, 0, $traceHtml;
1452        }
1453        # Write the output string.
1454        print $outputString;
1455    }
1456    
1457    =head2 Command-Line Utility Methods
1458    
1459    =head3 SendSMS
1460    
1461        my $msgID = Tracer::SendSMS($phoneNumber, $msg);
1462    
1463    Send a text message to a phone number using Clickatell. The FIG_Config file must contain the
1464    user name, password, and API ID for the relevant account in the hash reference variable
1465    I<$FIG_Config::phone>, using the keys C<user>, C<password>, and C<api_id>. For
1466    example, if the user name is C<BruceTheHumanPet>, the password is C<silly>, and the API ID
1467    is C<2561022>, then the FIG_Config file must contain
1468    
1469        $phone =  { user => 'BruceTheHumanPet',
1470                    password => 'silly',
1471                    api_id => '2561022' };
1472    
1473    The original purpose of this method was to insure Bruce would be notified immediately when the
1474    Sprout Load terminates. Care should be taken if you do not wish Bruce to be notified immediately
1475    when you call this method.
1476    
1477    The message ID will be returned if successful, and C<undef> if an error occurs.
1478    
1479    =over 4
1480    
1481    =item phoneNumber
1482    
1483    Phone number to receive the message, in international format. A United States phone number
1484    would be prefixed by "1". A British phone number would be prefixed by "44".
1485    
1486    =item msg
1487    
1488    Message to send to the specified phone.
1489    
1490    =item RETURN
1491    
1492    Returns the message ID if successful, and C<undef> if the message could not be sent.
1493    
1494    =back
1495    
1496    =cut
1497    
1498    sub SendSMS {
1499        # Get the parameters.
1500        my ($phoneNumber, $msg) = @_;
1501        # Declare the return variable. If we do not change it, C<undef> will be returned.
1502        my $retVal;
1503        # Only proceed if we have phone support.
1504        if (! defined $FIG_Config::phone) {
1505            Trace("Phone support not present in FIG_Config.") if T(1);
1506        } else {
1507            # Get the phone data.
1508            my $parms = $FIG_Config::phone;
1509            # Get the Clickatell URL.
1510            my $url = "http://api.clickatell.com/http/";
1511            # Create the user agent.
1512            my $ua = LWP::UserAgent->new;
1513            # Request a Clickatell session.
1514            my $resp = $ua->post("$url/sendmsg", { user => $parms->{user},
1515                                         password => $parms->{password},
1516                                         api_id => $parms->{api_id},
1517                                         to => $phoneNumber,
1518                                         text => $msg});
1519            # Check for an error.
1520            if (! $resp->is_success) {
1521                Trace("Alert failed.") if T(1);
1522            } else {
1523                # Get the message ID.
1524                my $rstring = $resp->content;
1525                if ($rstring =~ /^ID:\s+(.*)$/) {
1526                    $retVal = $1;
1527                } else {
1528                    Trace("Phone attempt failed with $rstring") if T(1);
1529                }
1530            }
1531        }
1532        # Return the result.
1533        return $retVal;
1534    }
1535    
1536    =head3 StandardSetup
1537    
1538        my ($options, @parameters) = StandardSetup(\@categories, \%options, $parmHelp, @ARGV);
1539    
1540    This method performs standard command-line parsing and tracing setup. The return
1541    values are a hash of the command-line options and a list of the positional
1542    parameters. Tracing is automatically set up and the command-line options are
1543    validated.
1544    
1545    This is a complex method that does a lot of grunt work. The parameters can
1546    be more easily understood, however, once they are examined individually.
1547    
1548    The I<categories> parameter is the most obtuse. It is a reference to a list of
1549    special-purpose tracing categories. Most tracing categories are PERL package
1550    names. So, for example, if you wanted to turn on tracing inside the B<Sprout>,
1551    B<ERDB>, and B<SproutLoad> packages, you would specify the categories
1552    
1553        ["Sprout", "SproutLoad", "ERDB"]
1554    
1555    This would cause trace messages in the specified three packages to appear in
1556    the output. There are two special tracing categories that are automatically
1557    handled by this method. In other words, if you used L</TSetup> you would need
1558    to include these categories manually, but if you use this method they are turned
1559    on automatically.
1560    
1561    =over 4
1562    
1563    =item SQL
1564    
1565    Traces SQL commands and activity.
1566    
1567    =item Tracer
1568    
1569    Traces error messages and call stacks.
1570    
1571    =back
1572    
1573    C<SQL> is only turned on if the C<-sql> option is specified in the command line.
1574    The trace level is specified using the C<-trace> command-line option. For example,
1575    the following command line for C<TransactFeatures> turns on SQL tracing and runs
1576    all tracing at level 3.
1577    
1578        TransactFeatures -trace=3 -sql register ../xacts IDs.tbl
1579    
1580    Standard tracing is output to the standard output and echoed to the file
1581    C<trace>I<$$>C<.log> in the FIG temporary directory, where I<$$> is the
1582    process ID. You can also specify the C<user> parameter to put a user ID
1583    instead of a process ID in the trace file name. So, for example
1584    
1585    The default trace level is 2. To get all messages, specify a trace level of 4.
1586    For a genome-by-genome update, use 3.
1587    
1588        TransactFeatures -trace=3 -sql -user=Bruce register ../xacts IDs.tbl
1589    
1590    would send the trace output to C<traceBruce.log> in the temporary directory.
1591    
1592    The I<options> parameter is a reference to a hash containing the command-line
1593    options, their default values, and an explanation of what they mean. Command-line
1594    options may be in the form of switches or keywords. In the case of a switch, the
1595    option value is 1 if it is specified and 0 if it is not specified. In the case
1596    of a keyword, the value is separated from the option name by an equal sign. You
1597    can see this last in the command-line example above.
1598    
1599    You can specify a different default trace level by setting C<$options->{trace}>
1600    prior to calling this method.
1601    
1602    An example at this point would help. Consider, for example, the command-line utility
1603    C<TransactFeatures>. It accepts a list of positional parameters plus the options
1604    C<safe>, C<noAlias>, C<start>, and C<tblFiles>. To start up this command, we execute
1605    the following code.
1606    
1607        my ($options, @parameters) = Tracer::StandardSetup(["DocUtils"],
1608                            { safe => [0, "use database transactions"],
1609                              noAlias => [0, "do not expect aliases in CHANGE transactions"],
1610                              start => [' ', "start with this genome"],
1611                              tblFiles => [0, "output TBL files containing the corrected IDs"] },
1612                            "<command> <transactionDirectory> <IDfile>",
1613                          @ARGV);
1614    
1615    
1616    The call to C<ParseCommand> specifies the default values for the options and
1617    stores the actual options in a hash that is returned as C<$options>. The
1618    positional parameters are returned in C<@parameters>.
1619    
1620    The following is a sample command line for C<TransactFeatures>.
1621    
1622        TransactFeatures -trace=2 -noAlias register ../xacts IDs.tbl
1623    
1624    Single and double hyphens are equivalent. So, you could also code the
1625    above command as
1626    
1627        TransactFeatures --trace=2 --noAlias register ../xacts IDs.tbl
1628    
1629    In this case, C<register>, C<../xacts>, and C<IDs.tbl> are the positional
1630    parameters, and would find themselves in I<@parameters> after executing the
1631    above code fragment. The tracing would be set to level 2, and the categories
1632    would be C<Tracer>, and <DocUtils>. C<Tracer> is standard,
1633    and C<DocUtils> was included because it came in within the first parameter
1634    to this method. The I<$options> hash would be
1635    
1636        { trace => 2, sql => 0, safe => 0,
1637          noAlias => 1, start => ' ', tblFiles => 0 }
1638    
1639    Use of C<StandardSetup> in this way provides a simple way of performing
1640    standard tracing setup and command-line parsing. Note that the caller is
1641    not even aware of the command-line switches C<-trace> and C<-sql>, which
1642    are used by this method to control the tracing. If additional tracing features
1643    need to be added in the future, they can be processed by this method without
1644    upsetting the command-line utilities.
1645    
1646    If the C<background> option is specified on the command line, then the
1647    standard and error outputs will be directed to files in the temporary
1648    directory, using the same suffix as the trace file. So, if the command
1649    line specified
1650    
1651        -user=Bruce -background
1652    
1653    then the trace output would go to C<traceBruce.log>, the standard output to
1654    C<outBruce.log>, and the error output to C<errBruce.log>. This is designed to
1655    simplify starting a command in the background.
1656    
1657    The user name is also used as the tracing key for L</Emergency Tracing>.
1658    Specifying a value of C<E> for the trace level causes emergency tracing to
1659    be used instead of custom tracing. If the user name is not specified,
1660    the tracing key is taken from the C<Tracing> environment variable. If there
1661    is no value for that variable, the tracing key will be computed from the active
1662    login ID.
1663    
1664    Since the default situation in StandardSetup is to trace to the standard
1665    output, errors that occur in command-line scripts will not generate
1666    RSS events. To force the events, use the C<warn> option.
1667    
1668        TransactFeatures -background -warn register ../xacts IDs.tbl
1669    
1670    Finally, if the special option C<-help> is specified, the option
1671    names will be traced at level 0 and the program will exit without processing.
1672    This provides a limited help capability. For example, if the user enters
1673    
1674        TransactFeatures -help
1675    
1676    he would see the following output.
1677    
1678        TransactFeatures [options] <command> <transactionDirectory> <IDfile>
1679            -trace    tracing level (default E)
1680            -sql      trace SQL commands
1681            -safe     use database transactions
1682            -noAlias  do not expect aliases in CHANGE transactions
1683            -start    start with this genome
1684            -tblFiles output TBL files containing the corrected IDs
1685    
1686    The caller has the option of modifying the tracing scheme by placing a value
1687    for C<trace> in the incoming options hash. The default value can be overridden,
1688    or the tracing to the standard output can be turned off by suffixing a minus
1689    sign to the trace level. So, for example,
1690    
1691        { trace => [0, "tracing level (default 0)"],
1692           ...
1693    
1694    would set the default trace level to 0 instead of E, while
1695    
1696        { trace => ["2-", "tracing level (default 2)"],
1697           ...
1698    
1699    would set the default to 2, but trace only to the log file, not to the
1700    standard output.
1701    
1702    The parameters to this method are as follows.
1703    
1704    =over 4
1705    
1706    =item categories
1707    
1708    Reference to a list of tracing category names. These should be names of
1709    packages whose internal workings will need to be debugged to get the
1710    command working.
1711    
1712    =item options
1713    
1714    Reference to a hash containing the legal options for the current command mapped
1715    to their default values and descriptions. The user can override the defaults
1716    by specifying the options as command-line switches prefixed by a hyphen.
1717    Tracing-related options may be added to this hash. If the C<-h> option is
1718    specified on the command line, the option descriptions will be used to
1719    explain the options. To turn off tracing to the standard output, add a
1720    minus sign to the value for C<trace> (see above).
1721    
1722    =item parmHelp
1723    
1724    A string that vaguely describes the positional parameters. This is used
1725    if the user specifies the C<-h> option.
1726    
1727    =item argv
1728    
1729    List of command line parameters, including the option switches, which must
1730    precede the positional parameters and be prefixed by a hyphen.
1731    
1732    =item RETURN
1733    
1734    Returns a list. The first element of the list is the reference to a hash that
1735    maps the command-line option switches to their values. These will either be the
1736    default values or overrides specified on the command line. The remaining
1737    elements of the list are the position parameters, in order.
1738    
1739    =back
1740    
1741    =cut
1742    
1743    sub StandardSetup {
1744        # Get the parameters.
1745        my ($categories, $options, $parmHelp, @argv) = @_;
1746        # Get the default tracing key.
1747        my $tkey = EmergencyKey();
1748        # Add the tracing options.
1749        if (! exists $options->{trace}) {
1750            $options->{trace} = ['2', "tracing level (E for emergency tracing)"];
1751        }
1752        $options->{sql} = [0, "turn on SQL tracing"];
1753        $options->{help} = [0, "display command-line options"];
1754        $options->{user} = [$tkey, "tracing key"];
1755        $options->{background} = [0, "spool standard and error output"];
1756        $options->{warn} = [0, "send errors to RSS feed"];
1757        # Create a parsing hash from the options hash. The parsing hash
1758        # contains the default values rather than the default value
1759        # and the description. While we're at it, we'll memorize the
1760        # length of the longest option name.
1761        my $longestName = 0;
1762        my %parseOptions = ();
1763        for my $key (keys %{$options}) {
1764            if (length $key > $longestName) {
1765                $longestName = length $key;
1766            }
1767            $parseOptions{$key} = $options->{$key}->[0];
1768        }
1769        # Parse the command line.
1770        my ($retOptions, @retParameters) = ParseCommand(\%parseOptions, @argv);
1771        # Get the logfile suffix.
1772        my $suffix = $retOptions->{user};
1773        # Check for background mode.
1774        if ($retOptions->{background}) {
1775            my $outFileName = "$FIG_Config::temp/out$suffix.log";
1776            my $errFileName = "$FIG_Config::temp/err$suffix.log";
1777            open STDOUT, ">$outFileName";
1778            open STDERR, ">$errFileName";
1779            # Check for phone support. If we have phone support and a phone number,
1780            # we want to turn it on.
1781            if ($ENV{PHONE} && defined($FIG_Config::phone)) {
1782                $retOptions->{phone} = $ENV{PHONE};
1783            }
1784        }
1785        # Now we want to set up tracing. First, we need to know if the user
1786        # wants emergency tracing.
1787        if ($retOptions->{trace} eq 'E') {
1788            ETracing($retOptions->{user});
1789        } else {
1790            # Here the tracing is controlled from the command line.
1791            my @cats = @{$categories};
1792            if ($retOptions->{sql}) {
1793                push @cats, "SQL";
1794            }
1795            if ($retOptions->{warn}) {
1796                push @cats, "Feed";
1797            }
1798            # Add the default categories.
1799            push @cats, "Tracer";
1800            # Next, we create the category string by joining the categories.
1801            my $cats = join(" ", @cats);
1802            # Check to determine whether or not the caller wants to turn off tracing
1803            # to the standard output.
1804            my $traceLevel = $retOptions->{trace};
1805            my $textOKFlag = 1;
1806            if ($traceLevel =~ /^(.)-/) {
1807                $traceLevel = $1;
1808                $textOKFlag = 0;
1809            }
1810            # Now we set up the trace mode.
1811            my $traceMode;
1812            # Verify that we can open a file in the FIG temporary directory.
1813            my $traceFileName = "$FIG_Config::temp/trace$suffix.log";
1814            if (open TESTTRACE, ">$traceFileName") {
1815                # Here we can trace to a file.
1816                $traceMode = ">$traceFileName";
1817                if ($textOKFlag) {
1818                    # Echo to standard output if the text-OK flag is set.
1819                    $traceMode = "+$traceMode";
1820                }
1821                # Close the test file.
1822                close TESTTRACE;
1823            } else {
1824                # Here we can't trace to a file. Complain about this.
1825                warn "Could not open trace file $traceFileName: $!\n";
1826                # We trace to the standard output if it's
1827                # okay, and the error log otherwise.
1828                if ($textOKFlag) {
1829                    $traceMode = "TEXT";
1830                } else {
1831                    $traceMode = "WARN";
1832                }
1833            }
1834            # Now set up the tracing.
1835            TSetup("$traceLevel $cats", $traceMode);
1836        }
1837        # Check for the "help" option. If it is specified, dump the command-line
1838        # options and exit the program.
1839        if ($retOptions->{help}) {
1840            $0 =~ m#[/\\](\w+)(\.pl)?$#i;
1841            print "$1 [options] $parmHelp\n";
1842            for my $key (sort keys %{$options}) {
1843                my $name = Pad($key, $longestName, 0, ' ');
1844                my $desc = $options->{$key}->[1];
1845                if ($options->{$key}->[0]) {
1846                    $desc .= " (default " . $options->{$key}->[0] . ")";
1847  }  }
1848                print "  $name $desc\n";
 # Pad a number to 2 digits.  
 sub _p2 {  
     my ($value) = @_;  
     $value = "0$value" if ($value < 10);  
     return $value;  
1849  }  }
1850            exit(0);
1851  =head3 LogErrors      }
1852        # Trace the options, if applicable.
1853  C<< Tracer::LogErrors($fileName); >>      if (T(3)) {
1854            my @parms = grep { $retOptions->{$_} } keys %{$retOptions};
1855  Route the standard error output to a log file.          Trace("Selected options: " . join(", ", sort @parms) . ".");
1856        }
1857  =over 4      # Return the parsed parameters.
1858        return ($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, '>', $fileName;  
1859  }  }
1860    
1861  =head3 ReadOptions  =head3 ReadOptions
1862    
1863  C<< my %options = Tracer::ReadOptions($fileName); >>      my %options = Tracer::ReadOptions($fileName);
1864    
1865  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
1866  format  format
# Line 1017  Line 1921 
1921    
1922  =head3 GetOptions  =head3 GetOptions
1923    
1924  C<< Tracer::GetOptions(\%defaults, \%options); >>      Tracer::GetOptions(\%defaults, \%options);
1925    
1926  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
1927  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 1930 
1930    
1931  Consider the following example.  Consider the following example.
1932    
1933  C<< my $optionTable = GetOptions({ dbType => 'mySQL', trace => 0 }, $options); >>      my $optionTable = GetOptions({ dbType => 'mySQL', trace => 0 }, $options);
1934    
1935  In this example, the variable B<$options> is expected to contain at most two options-- B<dbType> and  In this example, the variable B<$options> is expected to contain at most two options-- B<dbType> and
1936  B<trace>. The default database type is C<mySQL> and the default trace level is C<0>. If the value of  B<trace>. The default database type is C<mySQL> and the default trace level is C<0>. If the value of
# Line 1034  Line 1938 
1938  the trace level will remain at 0. If B<$options> is undefined, then the database type and trace level  the trace level will remain at 0. If B<$options> is undefined, then the database type and trace level
1939  will remain C<mySQL> and C<0>. If, on the other hand, B<$options> is defined as  will remain C<mySQL> and C<0>. If, on the other hand, B<$options> is defined as
1940    
1941  C<< {databaseType => 'Oracle'} >>      {databaseType => 'Oracle'}
1942    
1943  an error will occur because the B<databaseType> option does not exist.  an error will occur because the B<databaseType> option does not exist.
1944    
# Line 1078  Line 1982 
1982    
1983  =head3 MergeOptions  =head3 MergeOptions
1984    
1985  C<< Tracer::MergeOptions(\%table, \%defaults); >>      Tracer::MergeOptions(\%table, \%defaults);
1986    
1987  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
1988  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 2014 
2014      }      }
2015  }  }
2016    
 =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;  
 }  
   
2017  =head3 ParseCommand  =head3 ParseCommand
2018    
2019  C<< my ($options, @arguments) = Tracer::ParseCommand(\%optionTable, @inputList); >>      my ($options, @arguments) = Tracer::ParseCommand(\%optionTable, @inputList);
2020    
2021  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
2022  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
2023  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
2024  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.
2025    
2026  C<< my ($options, @arguments) = ParseCommand({ errors => 0, logFile => 'trace.log'}, @words); >>      my ($options, @arguments) = ParseCommand({ errors => 0, logFile => 'trace.log'}, @words);
2027    
2028  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,
2029  B<errors> and B<logFile>. If @words has the following format  B<errors> and B<logFile>. If @words has the following format
2030    
2031  C<< -logFile=error.log apple orange rutabaga >>      -logFile=error.log apple orange rutabaga
2032    
2033  then at the end of the invocation, C<$options> will be  then at the end of the invocation, C<$options> will be
2034    
2035  C<< { errors => 0, logFile => 'error.log' } >>      { errors => 0, logFile => 'error.log' }
2036    
2037  and C<@arguments> will contain  and C<@arguments> will contain
2038    
2039  C<< apple orange rutabaga >>      apple orange rutabaga
2040    
2041  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
2042  support for quote characters.  support for quote characters. Options can be specified with single or double hyphens.
2043    
2044  =over 4  =over 4
2045    
# Line 1281  Line 2064 
2064      my ($optionTable, @inputList) = @_;      my ($optionTable, @inputList) = @_;
2065      # Process any options in the input list.      # Process any options in the input list.
2066      my %overrides = ();      my %overrides = ();
2067      while ((@inputList > 0) && ($inputList[0] =~ /^-/)) {      while ((@inputList > 0) && ($inputList[0] =~ /^--?/)) {
2068          # Get the current option.          # Get the current option.
2069          my $arg = shift @inputList;          my $arg = shift @inputList;
2070          # Pull out the option name.          # Pull out the option name.
2071          $arg =~ /^-([^=]*)/g;          $arg =~ /^--?([^=]*)/g;
2072          my $name = $1;          my $name = $1;
2073          # Check for an option value.          # Check for an option value.
2074          if ($arg =~ /\G=(.*)$/g) {          if ($arg =~ /\G=(.*)$/g) {
# Line 1307  Line 2090 
2090      return ($optionTable, @retVal);      return ($optionTable, @retVal);
2091  }  }
2092    
 =head3 Escape  
2093    
2094  C<< my $codedString = Tracer::Escape($realString); >>  =head2 File Utility Methods
2095    
2096  Escape a string for use in a command length. Tabs will be replaced by C<\t>, new-lines  =head3 GetFile
2097  replaced by C<\n>, carriage returns will be deleted, and backslashes will be doubled. The  
2098  result is to reverse the effect of L</UnEscape>.      my @fileContents = Tracer::GetFile($fileName);
2099    
2100        or
2101    
2102        my $fileContents = Tracer::GetFile($fileName);
2103    
2104    Return the entire contents of a file. In list context, line-ends are removed and
2105    each line is a list element. In scalar context, line-ends are replaced by C<\n>.
2106    
2107  =over 4  =over 4
2108    
2109  =item realString  =item fileName
2110    
2111  String to escape.  Name of the file to read.
2112    
2113  =item RETURN  =item RETURN
2114    
2115  Escaped equivalent of the real string.  In a list context, returns the entire file as a list with the line terminators removed.
2116    In a scalar context, returns the entire file as a string. If an error occurs opening
2117    the file, an empty list will be returned.
2118    
2119  =back  =back
2120    
2121  =cut  =cut
2122    
2123  sub Escape {  sub GetFile {
2124      # Get the parameter.      # Get the parameters.
2125      my ($realString) = @_;      my ($fileName) = @_;
2126      # Initialize the return variable.      # Declare the return variable.
2127      my $retVal = "";      my @retVal = ();
2128      # Loop through the parameter string, looking for sequences to escape.      # Open the file for input.
2129      while (length $realString > 0) {      my $handle = Open(undef, "<$fileName");
2130          # Look for the first sequence to escape.      # Read the whole file into the return variable, stripping off any terminator
2131          if ($realString =~ /^(.*?)([\n\t\r\\])/) {      # characters.
2132              # Here we found it. The text preceding the sequence is in $1. The sequence      my $lineCount = 0;
2133              # itself is in $2. First, move the clear text to the return variable.      while (my $line = <$handle>) {
2134              $retVal .= $1;          $lineCount++;
2135              # Strip the processed section off the real string.          $line = Strip($line);
2136              $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;  
2137              }              }
2138        # Close it.
2139        close $handle;
2140        my $actualLines = @retVal;
2141        Trace("$actualLines lines read from file $fileName.") if T(File => 2);
2142        # Return the file's contents in the desired format.
2143        if (wantarray) {
2144            return @retVal;
2145          } else {          } else {
2146              # Here there are no more escape sequences. The rest of the string is          return join "\n", @retVal;
             # transferred unmodified.  
             $retVal .= $realString;  
             $realString = "";  
         }  
2147      }      }
     # Return the result.  
     return $retVal;  
2148  }  }
2149    
2150  =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.  
2151    
2152  =back      Tracer::PutFile($fileName, \@lines);
2153    
2154  =cut  Write out a file from a list of lines of text.
2155    
2156  sub UnEscape {  =over 4
2157      # Get the parameter.  
2158      my ($codedString) = @_;  =item fileName
2159      # Initialize the return variable.  
2160      my $retVal = "";  Name of the output file.
2161      # Only proceed if the incoming string is nonempty.  
2162      if (defined $codedString) {  =item lines
2163          # Loop through the parameter string, looking for escape sequences. We can't do  
2164          # 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
2165          # "\<tab>" no matter what we do.)  new-line characters. Alternatively, may be a string, in which case the string will be written without
2166          while (length $codedString > 0) {  modification.
2167              # Look for the first escape sequence.  
2168              if ($codedString =~ /^(.*?)\\(\\|n|t|r)/) {  =back
2169                  # Here we found it. The text preceding the sequence is in $1. The sequence  
2170                  # itself is in $2. First, move the clear text to the return variable.  =cut
2171                  $retVal .= $1;  
2172                  $codedString = substr $codedString, (2 + length $1);  sub PutFile {
2173                  # Get the escape value.      # Get the parameters.
2174                  my $char = $2;      my ($fileName, $lines) = @_;
2175                  # If we have a "\r", we are done.      # Open the output file.
2176                  if ($char ne 'r') {      my $handle = Open(undef, ">$fileName");
2177                      # Here it's not an 'r', so we convert it.      # Count the lines written.
2178                      $char =~ tr/\\tn/\\\t\n/;      if (ref $lines ne 'ARRAY') {
2179                      $retVal .= $char;          # Here we have a scalar, so we write it raw.
2180                  }          print $handle $lines;
2181            Trace("Scalar put to file $fileName.") if T(File => 3);
2182              } else {              } else {
2183                  # Here there are no more escape sequences. The rest of the string is          # Write the lines one at a time.
2184                  # transferred unmodified.          my $count = 0;
2185                  $retVal .= $codedString;          for my $line (@{$lines}) {
2186                  $codedString = "";              print $handle "$line\n";
2187              }              $count++;
2188          }          }
2189            Trace("$count lines put to file $fileName.") if T(File => 3);
2190      }      }
2191      # Return the result.      # Close the output file.
2192      return $retVal;      close $handle;
2193  }  }
2194    
2195  =head3 ParseRecord  =head3 ParseRecord
2196    
2197  C<< my @fields = Tracer::ParseRecord($line); >>      my @fields = Tracer::ParseRecord($line);
2198    
2199  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
2200  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 2239 
2239    
2240  =head3 Merge  =head3 Merge
2241    
2242  C<< my @mergedList = Tracer::Merge(@inputList); >>      my @mergedList = Tracer::Merge(@inputList);
2243    
2244  Sort a list of strings and remove duplicates.  Sort a list of strings and remove duplicates.
2245    
# Line 1515  Line 2285 
2285      return @inputList;      return @inputList;
2286  }  }
2287    
2288  =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  
2289    
2290  =item number      my $handle = Open($fileHandle, $fileSpec, $message);
2291    
2292  Percent numerator.  Open a file.
2293    
2294  =item base  The I<$fileSpec> is essentially the second argument of the PERL C<open>
2295    function. The mode is specified using Unix-like shell information. So, for
2296    example,
2297    
2298  Percent base.      Open(\*LOGFILE, '>>/usr/spool/news/twitlog', "Could not open twit log.");
2299    
2300  =item RETURN  would open for output appended to the specified file, and
2301    
2302  Returns the percentage of the base represented by the numerator.      Open(\*DATASTREAM, "| sort -u >$outputFile", "Could not open $outputFile.");
2303    
2304  =back  would open a pipe that sorts the records written and removes duplicates. Note
2305    the use of file handle syntax in the Open call. To use anonymous file handles,
2306    code as follows.
2307    
2308  =cut      my $logFile = Open(undef, '>>/usr/spool/news/twitlog', "Could not open twit log.");
2309    
2310  sub Percent {  The I<$message> parameter is used if the open fails. If it is set to C<0>, then
2311      # Get the parameters.  the open returns TRUE if successful and FALSE if an error occurred. Otherwise, a
2312      my ($number, $base) = @_;  failed open will throw an exception and the third parameter will be used to construct
2313      # Declare the return variable.  an error message. If the parameter is omitted, a standard message is constructed
2314      my $retVal = 0;  using the file spec.
     # Compute the percent.  
     if ($base != 0) {  
         $retVal = $number * 100 / $base;  
     }  
     # Return the result.  
     return $retVal;  
 }  
2315    
2316  =head3 GetFile      Could not open "/usr/spool/news/twitlog"
2317    
2318  C<< my @fileContents = Tracer::GetFile($fileName); >>  Note that the mode characters are automatically cleaned from the file name.
2319    The actual error message from the file system will be captured and appended to the
2320    message in any case.
2321    
2322      or      Could not open "/usr/spool/news/twitlog": file not found.
2323    
2324  C<< my $fileContents = Tracer::GetFile($fileName); >>  In some versions of PERL the only error message we get is a number, which
2325    corresponds to the C++ C<errno> value.
2326    
2327  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>.  
2328    
2329  =over 4  =over 4
2330    
2331  =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  
2332    
2333  C<< Tracer::PutFile($fileName, \@lines); >>  File handle. If this parameter is C<undef>, a file handle will be generated
2334    and returned as the value of this method.
2335    
2336  Write out a file from a list of lines of text.  =item fileSpec
2337    
2338  =over 4  File name and mode, as per the PERL C<open> function.
2339    
2340  =item fileName  =item message (optional)
2341    
2342  Name of the output file.  Error message to use if the open fails. If omitted, a standard error message
2343    will be generated. In either case, the error information from the file system
2344    is appended to the message. To specify a conditional open that does not throw
2345    an error if it fails, use C<0>.
2346    
2347  =item lines  =item RETURN
2348    
2349  Reference to a list of text lines. The lines will be written to the file in order, with trailing  Returns the name of the file handle assigned to the file, or C<undef> if the
2350  new-line characters. Alternatively, may be a string, in which case the string will be written without  open failed.
 modification.  
2351    
2352  =back  =back
2353    
2354  =cut  =cut
2355    
2356  sub PutFile {  sub Open {
2357      # Get the parameters.      # Get the parameters.
2358      my ($fileName, $lines) = @_;      my ($fileHandle, $fileSpec, $message) = @_;
2359      # Open the output file.      # Attempt to open the file.
2360      my $handle = Open(undef, ">$fileName");      my $rv = open $fileHandle, $fileSpec;
2361      if (ref $lines ne 'ARRAY') {      # If the open failed, generate an error message.
2362          # Here we have a scalar, so we write it raw.      if (! $rv) {
2363          print $handle $lines;          # Save the system error message.
2364      } else {          my $sysMessage = $!;
2365          # Write the lines one at a time.          # See if we need a default message.
2366          for my $line (@{$lines}) {          if (!$message) {
2367              print $handle "$line\n";              # Clean any obvious mode characters and leading spaces from the
2368                # filename.
2369                my ($fileName) = FindNamePart($fileSpec);
2370                $message = "Could not open \"$fileName\"";
2371          }          }
2372            # Terminate with an error using the supplied message and the
2373            # error message from the file system.
2374            Confess("$message: $!");
2375      }      }
2376      # Close the output file.      # Return the file handle.
2377      close $handle;      return $fileHandle;
2378  }  }
2379    
2380  =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  
2381    
2382  =cut      my ($fileName, $start, $len) = Tracer::FindNamePart($fileSpec);
2383    
2384  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 $retVal;  
 }  
2385    
2386  =head3 Confess  A file specification is the string passed to an C<open> call. It specifies the file
2387    mode and name. In a truly complex situation, it can specify a pipe sequence. This
2388    method assumes that the file name is whatever follows the first angle bracket
2389    sequence.  So, for example, in the following strings the file name is
2390    C</usr/fig/myfile.txt>.
2391    
2392  C<< Confess($message); >>      >>/usr/fig/myfile.txt
2393        </usr/fig/myfile.txt
2394        | sort -u > /usr/fig/myfile.txt
2395    
2396  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
2397  the OR operator and the L</Assert> method, B<Confess> can function as a debugging assert.  whole incoming string.
 So, for example  
2398    
2399  C<< Assert($recNum >= 0) || Confess("Invalid record number $recNum."); >>  =over 4
2400    
2401  Will abort the program with a stack trace if the value of C<$recNum> is negative.  =item fileSpec
2402    
2403  =over 4  File specification string from which the file name is to be extracted.
2404    
2405  =item message  =item RETURN
2406    
2407  Message to include in the trace.  Returns a three-element list. The first element contains the file name portion of
2408    the specified string, or the whole string if a file name cannot be found via normal
2409    methods. The second element contains the start position of the file name portion and
2410    the third element contains the length.
2411    
2412  =back  =back
2413    
2414  =cut  =cut
2415    #: Return Type $;
2416  sub Confess {  sub FindNamePart {
2417      # Get the parameters.      # Get the parameters.
2418      my ($message) = @_;      my ($fileSpec) = @_;
2419      # Trace the call stack.      # Default to the whole input string.
2420      Cluck($message);      my ($retVal, $pos, $len) = ($fileSpec, 0, length $fileSpec);
2421      # Abort the program.      # Parse out the file name if we can.
2422      croak(">>> $message");      if ($fileSpec =~ m/(<|>>?)(.+?)(\s*)$/) {
2423            $retVal = $2;
2424            $len = length $retVal;
2425            $pos = (length $fileSpec) - (length $3) - $len;
2426        }
2427        # Return the result.
2428        return ($retVal, $pos, $len);
2429  }  }
2430    
2431  =head3 Assert  =head3 OpenDir
2432    
2433  C<< Assert($condition1, $condition2, ... $conditionN); >>      my @files = OpenDir($dirName, $filtered, $flag);
2434    
2435  Return TRUE if all the conditions are true. This method can be used in conjunction with  Open a directory and return all the file names. This function essentially performs
2436  the OR operator and the L</Confess> method as a debugging assert.  the functions of an C<opendir> and C<readdir>. If the I<$filtered> parameter is
2437  So, for example  set to TRUE, all filenames beginning with a period (C<.>), dollar sign (C<$>),
2438    or pound sign (C<#>) and all filenames ending with a tilde C<~>) will be
2439    filtered out of the return list. If the directory does not open and I<$flag> is not
2440    set, an exception is thrown. So, for example,
2441    
2442  C<< Assert($recNum >= 0) || Confess("Invalid record number $recNum."); >>      my @files = OpenDir("/Volumes/fig/contigs", 1);
2443    
2444  Will abort the program with a stack trace if the value of C<$recNum> is negative.  is effectively the same as
2445    
2446  =cut      opendir(TMP, "/Volumes/fig/contigs") || Confess("Could not open /Volumes/fig/contigs.");
2447  sub Assert {      my @files = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir(TMP);
     my $retVal = 1;  
     LOOP: for my $condition (@_) {  
         if (! $condition) {  
             $retVal = 0;  
             last LOOP;  
         }  
     }  
     return $retVal;  
 }  
2448    
2449  =head3 Cluck  Similarly, the following code
2450    
2451  C<< Cluck($message); >>      my @files = grep { $_ =~ /^\d/ } OpenDir("/Volumes/fig/orgs", 0, 1);
2452    
2453  Trace the call stack. Note that for best results, you should qualify the call with a  Returns the names of all files in C</Volumes/fig/orgs> that begin with digits and
2454  trace condition. For example,  automatically returns an empty list if the directory fails to open.
2455    
2456  C<< Cluck("Starting record parse.") if T(3); >>  =over 4
2457    
2458  will only trace the stack if the trace level for the package is 3 or more.  =item dirName
2459    
2460  =over 4  Name of the directory to open.
2461    
2462  =item message  =item filtered
2463    
2464  Message to include in the trace.  TRUE if files whose names begin with a period (C<.>) should be automatically removed
2465    from the list, else FALSE.
2466    
2467    =item flag
2468    
2469    TRUE if a failure to open is okay, else FALSE
2470    
2471  =back  =back
2472    
2473  =cut  =cut
2474    #: Return Type @;
2475  sub Cluck {  sub OpenDir {
2476      # Get the parameters.      # Get the parameters.
2477      my ($message) = @_;      my ($dirName, $filtered, $flag) = @_;
2478      # Trace what's happening.      # Declare the return variable.
2479      Trace("Stack trace for event: $message");      my @retVal = ();
2480      my $confession = longmess($message);      # Open the directory.
2481      # Convert the confession to a series of trace messages. Note we skip any      if (opendir(my $dirHandle, $dirName)) {
2482      # messages relating to calls into Tracer.          # The directory opened successfully. Get the appropriate list according to the
2483      for my $line (split /\s*\n/, $confession) {          # strictures of the filter parameter.
2484          Trace($line) if ($line !~ /Tracer\.pm/);          if ($filtered) {
2485                @retVal = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir $dirHandle;
2486            } else {
2487                @retVal = readdir $dirHandle;
2488            }
2489        } elsif (! $flag) {
2490            # Here the directory would not open and it's considered an error.
2491            Confess("Could not open directory $dirName.");
2492      }      }
2493        # Return the result.
2494        return @retVal;
2495  }  }
2496    
 =head3 Min  
2497    
2498  C<< my $min = Min($value1, $value2, ... $valueN); >>  =head3 Insure
2499    
2500        Insure($dirName, $chmod);
2501    
2502  Return the minimum argument. The arguments are treated as numbers.  Insure a directory is present.
2503    
2504  =over 4  =over 4
2505    
2506  =item $value1, $value2, ... $valueN  =item dirName
2507    
2508  List of numbers to compare.  Name of the directory to check. If it does not exist, it will be created.
2509    
2510  =item RETURN  =item chmod (optional)
2511    
2512  Returns the lowest number in the list.  Security privileges to be given to the directory if it is created.
2513    
2514  =back  =back
2515    
2516  =cut  =cut
2517    
2518  sub Min {  sub Insure {
2519      # Get the parameters. Note that we prime the return value with the first parameter.      my ($dirName, $chmod) = @_;
2520      my ($retVal, @values) = @_;      if (! -d $dirName) {
2521      # Loop through the remaining parameters, looking for the lowest.          Trace("Creating $dirName directory.") if T(2);
2522      for my $value (@values) {          eval {
2523          if ($value < $retVal) {              mkpath $dirName;
2524              $retVal = $value;              # If we have permissions specified, set them here.
2525                if (defined($chmod)) {
2526                    chmod $chmod, $dirName;
2527                }
2528            };
2529            if ($@) {
2530                Confess("Error creating $dirName: $@");
2531          }          }
2532      }      }
     # Return the minimum found.  
     return $retVal;  
2533  }  }
2534    
2535  =head3 Max  =head3 ChDir
2536    
2537  C<< my $max = Max($value1, $value2, ... $valueN); >>      ChDir($dirName);
2538    
2539  Return the maximum argument. The arguments are treated as numbers.  Change to the specified directory.
2540    
2541  =over 4  =over 4
2542    
2543  =item $value1, $value2, ... $valueN  =item dirName
   
 List of numbers to compare.  
   
 =item RETURN  
2544    
2545  Returns the highest number in the list.  Name of the directory to which we want to change.
2546    
2547  =back  =back
2548    
2549  =cut  =cut
2550    
2551  sub Max {  sub ChDir {
2552      # Get the parameters. Note that we prime the return value with the first parameter.      my ($dirName) = @_;
2553      my ($retVal, @values) = @_;      if (! -d $dirName) {
2554      # Loop through the remaining parameters, looking for the highest.          Confess("Cannot change to directory $dirName: no such directory.");
2555      for my $value (@values) {      } else {
2556          if ($value > $retVal) {          Trace("Changing to directory $dirName.") if T(File => 4);
2557              $retVal = $value;          my $okFlag = chdir $dirName;
2558            if (! $okFlag) {
2559                Confess("Error switching to directory $dirName.");
2560          }          }
2561      }      }
     # Return the maximum found.  
     return $retVal;  
2562  }  }
2563    
2564  =head3 AddToListMap  =head3 SetPermissions
2565    
2566        Tracer::SetPermissions($dirName, $group, $mask, %otherMasks);
2567    
2568  C<< Tracer::AddToListMap(\%hash, $key, $value1, $value2, ... valueN); >>  Set the permissions for a directory and all the files and folders inside it.
2569    In addition, the group ownership will be changed to the specified value.
2570    
2571  Add a key-value pair to a hash of lists. If no value exists for the key, a singleton list  This method is more vulnerable than most to permission and compatability
2572  is created for the key. Otherwise, the new value is pushed onto the list.  problems, so it does internal error recovery.
2573    
2574  =over 4  =over 4
2575    
2576  =item hash  =item dirName
2577    
2578  Reference to the target hash.  Name of the directory to process.
2579    
2580  =item key  =item group
2581    
2582  Key for which the value is to be added.  Name of the group to be assigned.
2583    
2584  =item value1, value2, ... valueN  =item mask
2585    
2586  List of values to add to the key's value list.  Permission mask. Bits that are C<1> in this mask will be ORed into the
2587    permission bits of any file or directory that does not already have them
2588    set to 1.
2589    
2590  =back  =item otherMasks
2591    
2592  =cut  Map of search patterns to permission masks. If a directory name matches
2593    one of the patterns, that directory and all its members and subdirectories
2594    will be assigned the new pattern. For example, the following would
2595    assign 01664 to most files, but would use 01777 for directories named C<tmp>.
2596    
2597  sub AddToListMap {      Tracer::SetPermissions($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;  
     }  
 }  
2598    
2599  =head3 DebugMode  The list is ordered, so the following would use 0777 for C<tmp1> and
2600    0666 for C<tmp>, C<tmp2>, or C<tmp3>.
2601    
2602  C<< if (Tracer::DebugMode) { ...code... } >>      Tracer::SetPermissions($dirName, 'fig', 01664, '^tmp1' => 0777,
2603                                                       '^tmp' => 0666);
2604    
2605  Return TRUE if debug mode has been turned on, else abort.  Note that the pattern matches are all case-insensitive, and only directory
2606    names are matched, not file names.
2607    
2608  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.  
2609    
2610  =cut  =cut
2611    
2612  sub DebugMode {  sub SetPermissions {
2613      # Declare the return variable.      # Get the parameters.
2614      my $retVal = 0;      my ($dirName, $group, $mask, @otherMasks) = @_;
2615      # Check the debug configuration.      # Set up for error recovery.
2616      my $password = CGI::cookie("DebugMode");      eval {
2617      my $encrypted = Digest::MD5::md5_hex($password);          # Switch to the specified directory.
2618      if ($encrypted eq "252dec43280e0c0d6a75ffcec486e61d") {          ChDir($dirName);
2619          $retVal = 1;          # Get the group ID.
2620            my $gid = getgrnam($group);
2621            # Get the mask for tracing.
2622            my $traceMask = sprintf("%04o", $mask) . "($mask)";
2623            Trace("Fixing permissions for directory $dirName using group $group($gid) and mask $traceMask.") if T(File => 2);
2624            my $fixCount = 0;
2625            my $lookCount = 0;
2626            # @dirs will be a stack of directories to be processed.
2627            my @dirs = (getcwd());
2628            while (scalar(@dirs) > 0) {
2629                # Get the current directory.
2630                my $dir = pop @dirs;
2631                # Check for a match to one of the specified directory names. To do
2632                # that, we need to pull the individual part of the name off of the
2633                # whole path.
2634                my $simpleName = $dir;
2635                if ($dir =~ m!/([^/]+)$!) {
2636                    $simpleName = $1;
2637                }
2638                Trace("Simple directory name for $dir is $simpleName.") if T(File => 4);
2639                # Search for a match.
2640                my $match = 0;
2641                my $i;
2642                for ($i = 0; $i < $#otherMasks && ! $match; $i += 2) {
2643                    my $pattern = $otherMasks[$i];
2644                    if ($simpleName =~ /$pattern/i) {
2645                        $match = 1;
2646                    }
2647                }
2648                # Check for a match. Note we use $i-1 because the loop added 2
2649                # before terminating due to the match.
2650                if ($match && $otherMasks[$i-1] != $mask) {
2651                    # This directory matches one of the incoming patterns, and it's
2652                    # a different mask, so we process it recursively with that mask.
2653                    SetPermissions($dir, $group, $otherMasks[$i-1], @otherMasks);
2654      } else {      } else {
2655          # Here debug mode is off, so we generate an error.                  # Here we can process normally. Get all of the non-hidden members.
2656          Confess("Cannot use this facility without logging in.");                  my @submems = OpenDir($dir, 1);
2657                    for my $submem (@submems) {
2658                        # Get the full name.
2659                        my $thisMem = "$dir/$submem";
2660                        Trace("Checking member $thisMem.") if T(4);
2661                        $lookCount++;
2662                        if ($lookCount % 1000 == 0) {
2663                            Trace("$lookCount members examined. Current is $thisMem. Mask is $traceMask") if T(File => 3);
2664                        }
2665                        # Fix the group.
2666                        chown -1, $gid, $thisMem;
2667                        # Insure this member is not a symlink.
2668                        if (! -l $thisMem) {
2669                            # Get its info.
2670                            my $fileInfo = stat $thisMem;
2671                            # Only proceed if we got the info. Otherwise, it's a hard link
2672                            # and we want to skip it anyway.
2673                            if ($fileInfo) {
2674                                my $fileMode = $fileInfo->mode;
2675                                if (($fileMode & $mask) != $mask) {
2676                                    # Fix this member.
2677                                    $fileMode |= $mask;
2678                                    chmod $fileMode, $thisMem;
2679                                    $fixCount++;
2680                                }
2681                                # If it's a subdirectory, stack it.
2682                                if (-d $thisMem) {
2683                                    push @dirs, $thisMem;
2684                                }
2685                            }
2686                        }
2687                    }
2688                }
2689            }
2690            Trace("$lookCount files and directories processed, $fixCount fixed.") if T(File => 2);
2691        };
2692        # Check for an error.
2693        if ($@) {
2694            Confess("SetPermissions error: $@");
2695      }      }
     # Return the determination indicator.  
     return $retVal;  
2696  }  }
2697    
2698  =head3 Strip  =head3 GetLine
2699    
2700  C<< my $string = Tracer::Strip($line); >>      my @data = Tracer::GetLine($handle);
2701    
2702  Strip all line terminators off a string. This is necessary when dealing with files  Read a line of data from a tab-delimited file.
 that may have been transferred back and forth several times among different  
 operating environments.  
2703    
2704  =over 4  =over 4
2705    
2706  =item line  =item handle
2707    
2708  Line of text to be stripped.  Open file handle from which to read.
2709    
2710  =item RETURN  =item RETURN
2711    
2712  The same line of text with all the line-ending characters chopped from the end.  Returns a list of the fields in the record read. The fields are presumed to be
2713    tab-delimited. If we are at the end of the file, then an empty list will be
2714    returned. If an empty line is read, a single list item consisting of a null
2715    string will be returned.
2716    
2717  =back  =back
2718    
2719  =cut  =cut
2720    
2721  sub Strip {  sub GetLine {
2722      # Get a copy of the parameter string.      # Get the parameters.
2723      my ($string) = @_;      my ($handle) = @_;
2724      my $retVal = (defined $string ? $string : "");      # Declare the return variable.
2725      # Strip the line terminator characters.      my @retVal = ();
2726      $retVal =~ s/(\r|\n)+$//g;      Trace("File position is " . tell($handle) . ". EOF flag is " . eof($handle) . ".") if T(File => 4);
2727        # Read from the file.
2728        my $line = <$handle>;
2729        # Only proceed if we found something.
2730        if (defined $line) {
2731            # Remove the new-line. We are a bit over-cautious here because the file may be coming in via an
2732            # upload control and have a nonstandard EOL combination.
2733            $line =~ s/(\r|\n)+$//;
2734            # Here we do some fancy tracing to help in debugging complicated EOL marks.
2735            if (T(File => 4)) {
2736                my $escapedLine = $line;
2737                $escapedLine =~ s/\n/\\n/g;
2738                $escapedLine =~ s/\r/\\r/g;
2739                $escapedLine =~ s/\t/\\t/g;
2740                Trace("Line read: -->$escapedLine<--");
2741            }
2742            # If the line is empty, return a single empty string; otherwise, parse
2743            # it into fields.
2744            if ($line eq "") {
2745                push @retVal, "";
2746            } else {
2747                push @retVal, split /\t/,$line;
2748            }
2749        } else {
2750            # Trace the reason the read failed.
2751            Trace("End of file: $!") if T(File => 3);
2752        }
2753      # Return the result.      # Return the result.
2754      return $retVal;      return @retVal;
2755  }  }
2756    
2757  =head3 Pad  =head3 PutLine
2758    
2759  C<< my $paddedString = Tracer::Pad($string, $len, $left, $padChar); >>      Tracer::PutLine($handle, \@fields, $eol);
2760    
2761  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
2762  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.  
2763    
2764  =over 4  =over 4
2765    
2766  =item string  =item handle
   
 String to be padded.  
   
 =item len  
   
 Desired length of the padded string.  
   
 =item left (optional)  
2767    
2768  TRUE if the string is to be left-padded; otherwise it will be padded on the right.  Output file handle.
2769    
2770  =item padChar (optional)  =item fields
2771    
2772  Character to use for padding. The default is a space.  List of field values.
2773    
2774  =item RETURN  =item eol (optional)
2775    
2776  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.  
2777    
2778  =back  =back
2779    
2780  =cut  =cut
2781    
2782  sub Pad {  sub PutLine {
2783      # Get the parameters.      # Get the parameters.
2784      my ($string, $len, $left, $padChar) = @_;      my ($handle, $fields, $eol) = @_;
2785      # Compute the padding character.      # Write the data.
2786      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";  
2787  }  }
2788    
 =head3 TICK  
   
 C<< my @results = TICK($commandString); >>  
2789    
2790  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`  
2791    
2792  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")  
2793    
2794  it will work correctly in both environments.  Print a line of text with a trailing new-line.
2795    
2796  =over 4  =over 4
2797    
2798  =item commandString  =item line
   
 The command string to pass to the system.  
   
 =item RETURN  
2799    
2800  Returns the standard output from the specified command, as a list.  Line of text to print.
2801    
2802  =back  =back
2803    
2804  =cut  =cut
2805  #: Return Type @;  
2806  sub TICK {  sub PrintLine {
2807      # Get the parameters.      # Get the parameters.
2808      my ($commandString) = @_;      my ($line) = @_;
2809      # Chop off the dot-slash if this is Windows.      # Print the line.
2810      if ($FIG_Config::win_mode) {      print "$line\n";
         $commandString =~ s!^\./!!;  
     }  
     # Activate the command and return the result.  
     return `$commandString`;  
2811  }  }
2812    
 =head3 ScriptSetup  
2813    
2814  C<< my ($cgi, $varHash) = ScriptSetup($noTrace); >>  =head2 Other Useful Methods
2815    
2816  Perform standard tracing and debugging setup for scripts. The value returned is  =head3 ParseParm
 the CGI object followed by a pre-built variable hash.  
2817    
2818  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.  
2819    
2820  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,
2821  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
2822  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>.  
2823    
2824  =over 4  =over 4
2825    
2826  =item noTrace (optional)  =item string
2827    
2828  If specified, tracing will be suppressed. This is useful if the script wants to set up  Incoming string.
 tracing manually.  
2829    
2830  =item RETURN  =item RETURN
2831    
2832  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
2833  the output page.  was undefined.
2834    
2835  =back  =back
2836    
2837  =cut  =cut
2838    
2839  sub ScriptSetup {  sub ParseParm {
2840      # Get the parameters.      # Get the parameters.
2841      my ($noTrace) = @_;      my ($string) = @_;
2842      # Get the CGI query object.      # Declare the return variable.
2843      my $cgi = CGI->new();      my $retVal;
2844      # Set up tracing if it's not suppressed.      # Check for data.
2845      ETracing($cgi) unless $noTrace;      if (defined $string) {
2846      # Create the variable hash.          # We have some, so split it into a list.
2847      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);  
2848      }      }
2849        # Return the result.
2850        return $retVal;
2851  }  }
2852    
2853  =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  
2854    
2855  Returns the name of the file to contain the emergency tracing information.      my $string = Tracer::Now();
2856    
2857  =back  Return a displayable time stamp containing the local time. Whatever format this
2858    method produces must be parseable by L</ParseDate>.
2859    
2860  =cut  =cut
2861    
2862  sub EmergencyFileName {  sub Now {
2863      # Get the parameters.      return DisplayTime(time);
     my ($tkey) = @_;  
     # Compute the emergency tracing file name.  
     return "$FIG_Config::temp/Emergency$tkey.txt";  
2864  }  }
2865    
2866  =head3 EmergencyFileTarget  =head3 DisplayTime
2867    
2868  C<< my $fileName = Tracer::EmergencyFileTarget($tkey); >>      my $string = Tracer::DisplayTime($time);
2869    
2870  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
2871  the tracing output for file-based tracing.  method produces must be parseable by L</ParseDate>.
2872    
2873  =over 4  =over 4
2874    
2875  =item tkey  =item time
2876    
2877  Tracing key for the current program.  Time to display, in seconds since the epoch, or C<undef> if the time is unknown.
2878    
2879  =item RETURN  =item RETURN
2880    
2881  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.
2882    
2883  =back  =back
2884    
2885  =cut  =cut
2886    
2887  sub EmergencyFileTarget {  sub DisplayTime {
2888      # Get the parameters.      my ($time) = @_;
2889      my ($tkey) = @_;      my $retVal = "(n/a)";
2890      # Compute the emergency tracing file name.      if (defined $time) {
2891      return "$FIG_Config::temp/trace$tkey.log";          my ($sec,$min,$hour,$mday,$mon,$year,$wday,$yday,$isdst) = localtime($time);
2892            $retVal = _p2($mon+1) . "/" . _p2($mday) . "/" . ($year + 1900) . " " .
2893                      _p2($hour) . ":" . _p2($min) . ":" . _p2($sec);
2894        }
2895        return $retVal;
2896  }  }
2897    
2898  =head3 EmergencyTracingDest  # Pad a number to 2 digits.
2899    sub _p2 {
2900  C<< my $dest = Tracer::EmergencyTracingDest($tkey, $myDest); >>      my ($value) = @_;
2901        $value = "0$value" if ($value < 10);
2902        return $value;
2903    }
2904    
2905  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.  
2906    
2907  =over 4      my $codedString = Tracer::Escape($realString);
2908    
2909  =item tkey  Escape a string for use in a command. Tabs will be replaced by C<\t>, new-lines
2910    replaced by C<\n>, carriage returns will be deleted, and backslashes will be doubled. The
2911    result is to reverse the effect of L</UnEscape>.
2912    
2913  Tracing key for this environment.  =over 4
2914    
2915  =item myDest  =item realString
2916    
2917  Destination from the emergency tracing file.  String to escape.
2918    
2919  =item RETURN  =item RETURN
2920    
2921  Returns a destination that can be passed into L</TSetup>.  Escaped equivalent of the real string.
2922    
2923  =back  =back
2924    
2925  =cut  =cut
2926    
2927  sub EmergencyTracingDest {  sub Escape {
2928      # Get the parameters.      # Get the parameter.
2929      my ($tkey, $myDest) = @_;      my ($realString) = @_;
2930      # Declare the return variable.      # Initialize the return variable.
2931      my $retVal;      my $retVal = "";
2932      # Process according to the destination value.      # Loop through the parameter string, looking for sequences to escape.
2933      if ($myDest eq 'FILE') {      while (length $realString > 0) {
2934          $retVal = ">" . EmergencyFileTarget($tkey);          # Look for the first sequence to escape.
2935      } elsif ($myDest eq 'APPEND') {          if ($realString =~ /^(.*?)([\n\t\r\\])/) {
2936          $retVal = ">>" . EmergencyFileTarget($tkey);              # Here we found it. The text preceding the sequence is in $1. The sequence
2937                # itself is in $2. First, move the clear text to the return variable.
2938                $retVal .= $1;
2939                # Strip the processed section off the real string.
2940                $realString = substr $realString, (length $2) + (length $1);
2941                # Get the matched character.
2942                my $char = $2;
2943                # If we have a CR, we are done.
2944                if ($char ne "\r") {
2945                    # It's not a CR, so encode the escape sequence.
2946                    $char =~ tr/\t\n/tn/;
2947                    $retVal .= "\\" . $char;
2948                }
2949      } else {      } else {
2950          $retVal = $myDest;              # Here there are no more escape sequences. The rest of the string is
2951                # transferred unmodified.
2952                $retVal .= $realString;
2953                $realString = "";
2954            }
2955      }      }
2956      # Return the result.      # Return the result.
2957      return $retVal;      return $retVal;
2958  }  }
2959    
2960  =head3 Emergency  =head3 UnEscape
2961    
2962  C<< Emergency($key, $hours, $dest, $level, @modules); >>      my $realString = Tracer::UnEscape($codedString);
2963    
2964  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
2965  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
2966  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.  
2967    
2968  =over 4  =over 4
2969    
2970  =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  
2971    
2972  Tracing level. A higher level means more trace messages.  String to un-escape.
2973    
2974  =item modules  =item RETURN
2975    
2976  A list of the tracing modules to activate.  Returns a copy of the original string with the escape sequences converted to their actual
2977    values.
2978    
2979  =back  =back
2980    
2981  =cut  =cut
2982    
2983  sub Emergency {  sub UnEscape {
2984      # Get the parameters.      # Get the parameter.
2985      my ($tkey, $hours, $dest, $level, @modules) = @_;      my ($codedString) = @_;
2986      # Create the emergency file.      # Initialize the return variable.
2987      my $specFile = EmergencyFileName($tkey);      my $retVal = "";
2988      my $outHandle = Open(undef, ">$specFile");      # Only proceed if the incoming string is nonempty.
2989      print $outHandle join("\n", $hours, $dest, $level, @modules, "");      if (defined $codedString) {
2990            # Loop through the parameter string, looking for escape sequences. We can't do
2991            # translating because it causes problems with the escaped slash. ("\\t" becomes
2992            # "\<tab>" no matter what we do.)
2993            while (length $codedString > 0) {
2994                # Look for the first escape sequence.
2995                if ($codedString =~ /^(.*?)\\(\\|n|t|r)/) {
2996                    # Here we found it. The text preceding the sequence is in $1. The sequence
2997                    # itself is in $2. First, move the clear text to the return variable.
2998                    $retVal .= $1;
2999                    $codedString = substr $codedString, (2 + length $1);
3000                    # Get the escape value.
3001                    my $char = $2;
3002                    # If we have a "\r", we are done.
3003                    if ($char ne 'r') {
3004                        # Here it's not an 'r', so we convert it.
3005                        $char =~ tr/\\tn/\\\t\n/;
3006                        $retVal .= $char;
3007                    }
3008                } else {
3009                    # Here there are no more escape sequences. The rest of the string is
3010                    # transferred unmodified.
3011                    $retVal .= $codedString;
3012                    $codedString = "";
3013                }
3014            }
3015        }
3016        # Return the result.
3017        return $retVal;
3018  }  }
3019    
3020  =head3 EmergencyKey  =head3 Percent
3021    
3022  C<< my $tkey = EmergencyKey($parameter); >>      my $percent = Tracer::Percent($number, $base);
3023    
3024  Return the Key to be used for emergency tracing. This could be an IP address,  Returns the percent of the base represented by the given number. If the base
3025   a session ID, or a user name, depending on the environment.  is zero, returns zero.
3026    
3027  =over 4  =over 4
3028    
3029  =item parameter  =item number
3030    
3031  Parameter defining the method for finding the tracing key. If it is a scalar,  Percent numerator.
3032  then it is presumed to be the tracing key itself. If it is a CGI object, then  
3033  the tracing key is taken from the C<IP> cookie. Otherwise, the tracing key is  =item base
3034  taken from the C<TRACING> environment variable.  
3035    Percent base.
3036    
3037  =item RETURN  =item RETURN
3038    
3039  Returns the key to be used for labels in emergency tracing.  Returns the percentage of the base represented by the numerator.
3040    
3041  =back  =back
3042    
3043  =cut  =cut
3044    
3045  sub EmergencyKey {  sub Percent {
3046      # Get the parameters.      # Get the parameters.
3047      my ($parameter) = @_;      my ($number, $base) = @_;
3048      # Declare the return variable.      # Declare the return variable.
3049      my $retVal;      my $retVal = 0;
3050      # Determine the parameter type.      # Compute the percent.
3051      if (! defined $parameter) {      if ($base != 0) {
3052          # 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 = $$;  
3053      }      }
3054      # Return the result.      # Return the result.
3055      return $retVal;      return $retVal;
3056  }  }
3057    
3058    =head3 Constrain
3059    
3060  =head3 TraceParms      my $constrained = Constrain($value, $min, $max);
   
 C<< Tracer::TraceParms($cgi); >>  
3061    
3062  Trace the CGI parameters at trace level CGI => 3 and the environment variables  Modify a numeric value to bring it to a point in between a maximum and a minimum.
 at level CGI => 4.  
3063    
3064  =over 4  =over 4
3065    
3066  =item cgi  =item value
3067    
3068  CGI query object containing the parameters to trace.  Value to constrain.
3069    
3070  =back  =item min (optional)
3071    
3072  =cut  Minimum permissible value. If this parameter is undefined, no minimum constraint will be applied.
3073    
3074  sub TraceParms {  =item max (optional)
     # Get the parameters.  
     my ($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}");  
         }  
     }  
 }  
3075    
3076  =head3 ScriptFinish  Maximum permissible value. If this parameter is undefined, no maximum constraint will be applied.
3077    
3078  C<< ScriptFinish($webData, $varHash); >>  =item RETURN
3079    
3080  Output a web page at the end of a script. Either the string to be output or the  Returns the incoming value, constrained according to the other parameters.
 name of a template file can be specified. If the second parameter is omitted,  
 it is assumed we have a string to be output; otherwise, it is assumed we have the  
 name of a template file. The template should have the variable C<DebugData>  
 specified in any form that invokes a standard script. If debugging mode is turned  
 on, a form field will be put in that allows the user to enter tracing data.  
 Trace messages will be placed immediately before the terminal C<BODY> tag in  
 the output, formatted as a list.  
3081    
3082  A typical standard script would loook like the following.  =back
3083    
3084      BEGIN {  =cut
         # Print the HTML header.  
         print "CONTENT-TYPE: text/html\n\n";  
     }  
     use Tracer;  
     use CGI;  
     use FIG;  
     # ... more uses ...  
3085    
3086      my ($cgi, $varHash) = ScriptSetup();  sub Constrain {
3087      eval {      # Get the parameters.
3088          # ... get data from $cgi, put it in $varHash ...      my ($value, $min, $max) = @_;
3089      };      # Declare the return variable.
3090      if ($@) {      my $retVal = $value;
3091          Trace("Script Error: $@") if T(0);      # Apply the minimum constraint.
3092        if (defined $min && $retVal < $min) {
3093            $retVal = $min;
3094        }
3095        # Apply the maximum constraint.
3096        if (defined $max && $retVal > $max) {
3097            $retVal = $max;
3098        }
3099        # Return the result.
3100        return $retVal;
3101      }      }
     ScriptFinish("Html/MyTemplate.html", $varHash);  
3102    
3103  The idea here is that even if the script fails, you'll see trace messages and  =head3 Min
3104  useful output.  
3105        my $min = Min($value1, $value2, ... $valueN);
3106    
3107    Return the minimum argument. The arguments are treated as numbers.
3108    
3109  =over 4  =over 4
3110    
3111  =item webData  =item $value1, $value2, ... $valueN
3112    
3113  A string containing either the full web page to be written to the output or the  List of numbers to compare.
 name of a template file from which the page is to be constructed. If the name  
 of a template file is specified, then the second parameter must be present;  
 otherwise, it must be absent.  
3114    
3115  =item varHash (optional)  =item RETURN
3116    
3117  If specified, then a reference to a hash mapping variable names for a template  Returns the lowest number in the list.
 to their values. The template file will be read into memory, and variable markers  
 will be replaced by data in this hash reference.  
3118    
3119  =back  =back
3120    
3121  =cut  =cut
3122    
3123  sub ScriptFinish {  sub Min {
3124      # Get the parameters.      # Get the parameters. Note that we prime the return value with the first parameter.
3125      my ($webData, $varHash) = @_;      my ($retVal, @values) = @_;
3126      # Check for a template file situation.      # Loop through the remaining parameters, looking for the lowest.
3127      my $outputString;      for my $value (@values) {
3128      if (defined $varHash) {          if ($value < $retVal) {
3129          # 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";  
3130          }          }
         substr $outputString, $pos, 0, $traceHtml;  
3131      }      }
3132      # Write the output string.      # Return the minimum found.
3133      print $outputString;      return $retVal;
3134  }  }
3135    
3136  =head3 Insure  =head3 Max
3137    
3138  C<< Insure($dirName); >>      my $max = Max($value1, $value2, ... $valueN);
3139    
3140  Insure a directory is present.  Return the maximum argument. The arguments are treated as numbers.
3141    
3142  =over 4  =over 4
3143    
3144  =item dirName  =item $value1, $value2, ... $valueN
3145    
3146  Name of the directory to check. If it does not exist, it will be created.  List of numbers to compare.
3147    
3148    =item RETURN
3149    
3150    Returns the highest number in the list.
3151    
3152  =back  =back
3153    
3154  =cut  =cut
3155    
3156  sub Insure {  sub Max {
3157      my ($dirName) = @_;      # Get the parameters. Note that we prime the return value with the first parameter.
3158      if (! -d $dirName) {      my ($retVal, @values) = @_;
3159          Trace("Creating $dirName directory.") if T(2);      # Loop through the remaining parameters, looking for the highest.
3160          eval { mkpath $dirName; };      for my $value (@values) {
3161          if ($@) {          if ($value > $retVal) {
3162              Confess("Error creating $dirName: $@");              $retVal = $value;
3163          }          }
3164      }      }
3165        # Return the maximum found.
3166        return $retVal;
3167  }  }
3168    
 =head3 ChDir  
3169    
3170  C<< ChDir($dirName); >>  =head3 Strip
3171    
3172        my $string = Tracer::Strip($line);
3173    
3174  Change to the specified directory.  Strip all line terminators off a string. This is necessary when dealing with files
3175    that may have been transferred back and forth several times among different
3176    operating environments.
3177    
3178  =over 4  =over 4
3179    
3180  =item dirName  =item line
3181    
3182  Name of the directory to which we want to change.  Line of text to be stripped.
3183    
3184    =item RETURN
3185    
3186    The same line of text with all the line-ending characters chopped from the end.
3187    
3188  =back  =back
3189    
3190  =cut  =cut
3191    
3192  sub ChDir {  sub Strip {
3193      my ($dirName) = @_;      # Get a copy of the parameter string.
3194      if (! -d $dirName) {      my ($string) = @_;
3195          Confess("Cannot change to directory $dirName: no such directory.");      my $retVal = (defined $string ? $string : "");
3196      } else {      # Strip the line terminator characters.
3197          Trace("Changing to directory $dirName.") if T(4);      $retVal =~ s/(\r|\n)+$//g;
3198          my $okFlag = chdir $dirName;      # Return the result.
3199          if (! $okFlag) {      return $retVal;
             Confess("Error switching to directory $dirName.");  
         }  
     }  
3200  }  }
3201    
3202  =head3 SendSMS  =head3 Pad
3203    
3204  C<< my $msgID = Tracer::SendSMS($phoneNumber, $msg); >>      my $paddedString = Tracer::Pad($string, $len, $left, $padChar);
3205    
3206  Send a text message to a phone number using Clickatell. The FIG_Config file must contain the  Pad a string to a specified length. The pad character will be a
3207  user name, password, and API ID for the relevant account in the hash reference variable  space, and the padding will be on the right side unless specified
3208  I<$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  
3209    
3210      $phone =  { user => 'BruceTheHumanPet',  =over 4
                 password => 'silly',  
                 api_id => '2561022' };  
3211    
3212  The original purpose of this method was to insure Bruce would be notified immediately when the  =item string
 Sprout Load terminates. Care should be taken if you do not wish Bruce to be notified immediately  
 when you call this method.  
3213    
3214  The message ID will be returned if successful, and C<undef> if an error occurs.  String to be padded.
3215    
3216  =over 4  =item len
3217    
3218  =item phoneNumber  Desired length of the padded string.
3219    
3220  Phone number to receive the message, in international format. A United States phone number  =item left (optional)
 would be prefixed by "1". A British phone number would be prefixed by "44".  
3221    
3222  =item msg  TRUE if the string is to be left-padded; otherwise it will be padded on the right.
3223    
3224  Message to send to the specified phone.  =item padChar (optional)
3225    
3226    Character to use for padding. The default is a space.
3227    
3228  =item RETURN  =item RETURN
3229    
3230  Returns the message ID if successful, and C<undef> if the message could not be sent.  Returns a copy of the original string with the pad character added to the
3231    specified end so that it achieves the desired length.
3232    
3233  =back  =back
3234    
3235  =cut  =cut
3236    
3237  sub SendSMS {  sub Pad {
3238      # Get the parameters.      # Get the parameters.
3239      my ($phoneNumber, $msg) = @_;      my ($string, $len, $left, $padChar) = @_;
3240      # Declare the return variable. If we do not change it, C<undef> will be returned.      # Compute the padding character.
3241      my $retVal;      if (! defined $padChar) {
3242      # Only proceed if we have phone support.          $padChar = " ";
3243      if (! defined $FIG_Config::phone) {      }
3244          Trace("Phone support not present in FIG_Config.") if T(1);      # Compute the number of spaces needed.
3245      } else {      my $needed = $len - length $string;
3246          # Get the phone data.      # Copy the string into the return variable.
3247          my $parms = $FIG_Config::phone;      my $retVal = $string;
3248          # Get the Clickatell URL.      # Only proceed if padding is needed.
3249          my $url = "http://api.clickatell.com/http/";      if ($needed > 0) {
3250          # Create the user agent.          # Create the pad string.
3251          my $ua = LWP::UserAgent->new;          my $pad = $padChar x $needed;
3252          # Request a Clickatell session.          # Affix it to the return value.
3253          my $resp = $ua->post("$url/sendmsg", { user => $parms->{user},          if ($left) {
3254                                       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;  
3255              } else {              } else {
3256                  Trace("Phone attempt failed with $rstring") if T(1);              $retVal .= $pad;
3257              }              }
3258          }          }
3259        # Return the result.
3260        return $retVal;
3261    }
3262    
3263    =head3 EOF
3264    
3265    This is a constant that is lexically greater than any useful string.
3266    
3267    =cut
3268    
3269    sub EOF {
3270        return "\xFF\xFF\xFF\xFF\xFF";
3271    }
3272    
3273    =head3 TICK
3274    
3275        my @results = TICK($commandString);
3276    
3277    Perform a back-tick operation on a command. If this is a Windows environment, any leading
3278    dot-slash (C<./> will be removed. So, for example, if you were doing
3279    
3280        `./protein.cgi`
3281    
3282    from inside a CGI script, it would work fine in Unix, but would issue an error message
3283    in Windows complaining that C<'.'> is not a valid command. If instead you code
3284    
3285        TICK("./protein.cgi")
3286    
3287    it will work correctly in both environments.
3288    
3289    =over 4
3290    
3291    =item commandString
3292    
3293    The command string to pass to the system.
3294    
3295    =item RETURN
3296    
3297    Returns the standard output from the specified command, as a list.
3298    
3299    =back
3300    
3301    =cut
3302    #: Return Type @;
3303    sub TICK {
3304        # Get the parameters.
3305        my ($commandString) = @_;
3306        # Chop off the dot-slash if this is Windows.
3307        if ($FIG_Config::win_mode) {
3308            $commandString =~ s!^\./!!;
3309      }      }
3310      # Return the result.      # Activate the command and return the result.
3311      return $retVal;      return `$commandString`;
3312  }  }
3313    
3314    
3315  =head3 CommaFormat  =head3 CommaFormat
3316    
3317  C<< my $formatted = Tracer::CommaFormat($number); >>      my $formatted = Tracer::CommaFormat($number);
3318    
3319  Insert commas into a number.  Insert commas into a number.
3320    
# Line 2695  Line 3347 
3347      # Return the result.      # Return the result.
3348      return $retVal;      return $retVal;
3349  }  }
 =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  
3350    
 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: $@");  
     }  
 }  
3351    
3352  =head3 CompareLists  =head3 CompareLists
3353    
3354  C<< my ($inserted, $deleted) = Tracer::CompareLists(\@newList, \@oldList, $keyIndex); >>      my ($inserted, $deleted) = Tracer::CompareLists(\@newList, \@oldList, $keyIndex);
3355    
3356  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
3357  are presumed to be sorted alphabetically by the value in the $keyIndex column.  are presumed to be sorted alphabetically by the value in the $keyIndex column.
# Line 2896  Line 3416 
3416      return ($inserted, $deleted);      return ($inserted, $deleted);
3417  }  }
3418    
3419  =head3 GetLine  =head3 GenerateURL
3420    
3421  C<< my @data = Tracer::GetLine($handle); >>      my $queryUrl = Tracer::GenerateURL($page, %parameters);
3422    
3423  Read a line of data from a tab-delimited file.  Generate a GET-style URL for the specified page with the specified parameter
3424    names and values. The values will be URL-escaped automatically. So, for
3425    example
3426    
3427        Tracer::GenerateURL("form.cgi", type => 1, string => "\"high pass\" or highway")
3428    
3429    would return
3430    
3431        form.cgi?type=1;string=%22high%20pass%22%20or%20highway
3432    
3433  =over 4  =over 4