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1    # -*- perl -*-
2    ########################################################################
3    # Copyright (c) 2003-2006 University of Chicago and Fellowship
4    # for Interpretations of Genomes. All Rights Reserved.
5    #
6    # This file is part of the SEED Toolkit.
7    #
8    # The SEED Toolkit is free software. You can redistribute
9    # it and/or modify it under the terms of the SEED Toolkit
10    # Public License.
11    #
12    # You should have received a copy of the SEED Toolkit Public License
13    # along with this program; if not write to the University of Chicago
14    # at info@ci.uchicago.edu or the Fellowship for Interpretation of
15    # Genomes at veronika@thefig.info or download a copy from
16    # 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);      @EXPORT = qw(Trace T TSetup QTrace Confess Cluck Min Max Assert Open OpenDir TICK StandardSetup EmergencyKey ETracing ScriptSetup ScriptFinish Insure ChDir Emergency);
24          @EXPORT_OK = qw(GetFile GetOptions Merge MergeOptions ParseCommand ParseRecord UnEscape);      @EXPORT_OK = qw(GetFile GetOptions Merge MergeOptions ParseCommand ParseRecord UnEscape Escape);
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;
29        use FIG_Config;
30        use PageBuilder;
31        use Digest::MD5;
32        use File::Basename;
33        use File::Path;
34        use File::stat;
35        use LWP::UserAgent;
36        use Time::HiRes 'gettimeofday';
37        use URI::Escape;
38        use Time::Local;
39    
40  =head1 Tracing and Debugging Helpers  =head1 Tracing and Debugging Helpers
41    
42  =head2 Introduction  =head2 Tracing
43    
44  This package provides simple tracing for debugging and reporting purposes. To use it simply call the  This package provides simple tracing for debugging and reporting purposes. To use it simply call the
45  L</TSetup> method to set the options and call L</Trace> to write out trace messages. Each trace  L</TSetup> or L</ETracing> method to set the options and call L</Trace> to write out trace messages.
46  message has a I<trace level> and I<category> associated with it. In addition, the tracing package itself  L</TSetup> and L</ETracing> both establish a I<trace level> and a list of I<categories>. Similarly,
47  has a list of categories and a single trace level set by the B<TSetup> method. Only messages whose trace  each trace message has a I<trace level> and I<category> associated with it. Only messages whose trace
48  level is less than or equal to this package's trace level and whose category is activated will  level is less than or equal to the setup trace level and whose category is activated will
49  be written. Thus, a higher trace level on a message indicates that the message  be written. Thus, a higher trace level on a message indicates that the message
50  is less likely to be seen. A higher trace level passed to B<Setup> means more trace messages will  is less likely to be seen, while a higher trace level passed to B<TSetup> means more trace messages will
51  appear. To generate a trace message, use the following syntax.  appear.
52    
53    =head3 Putting Trace Messages in Your Code
54    
55  C<< Trace($message) if T(errors => 4); >>  To generate a trace message, use the following syntax.
56    
57        Trace($message) if T(errors => 4);
58    
59  This statement will produce a trace message if the trace level is 4 or more and the C<errors>  This statement will produce a trace message if the trace level is 4 or more and the C<errors>
60  category is active. Note that the special category C<main> is always active, so  category is active. There is a special category C<main> that is always active, so
61    
62  C<< Trace($message) if T(main => 4); >>      Trace($message) if T(main => 4);
63    
64  will trace if the trace level is 4 or more.  will trace if the trace level is 4 or more.
65    
# Line 34  Line 67 
67  following call is made in the B<Sprout> package, it will appear if the C<Sprout> category is  following call is made in the B<Sprout> package, it will appear if the C<Sprout> category is
68  active and the trace level is 2 or more.  active and the trace level is 2 or more.
69    
70  C<< Trace($message) if T(2); >>      Trace($message) if T(2);
71    
72    In scripts, where no package name is available, the category defaults to C<main>.
73    
74  To set up tracing, you call the C</Setup> method. The method takes as input a trace level, a list  =head3 Custom Tracing
75  of category names, and a set of options. The trace level and list of category names are  
76    Many programs have customized tracing configured using the L</TSetup> method. This is no longer
77    the preferred method, but a knowledge of how custom tracing works can make the more modern
78    L</Emergency Tracing> easier to understand.
79    
80    To set up custom tracing, you call the L</TSetup> method. The method takes as input a trace level,
81    a list of category names, and a destination. The trace level and list of category names are
82  specified as a space-delimited string. Thus  specified as a space-delimited string. Thus
83    
84  C<< TSetup('3 errors Sprout ERDB', 'HTML'); >>      TSetup('3 errors Sprout ERDB', 'TEXT');
85    
86    sets the trace level to 3, activates the C<errors>, C<Sprout>, and C<ERDB> categories, and
87    specifies that messages should be sent to the standard output.
88    
89    To turn on tracing for ALL categories, use an asterisk. The call below sets every category to
90    level 3 and writes the output to the standard error output. This sort of thing might be
91    useful in a CGI environment.
92    
93  sets the trace level to 3, activated the C<errors>, C<Sprout>, and C<ERDB> categories, and      TSetup('3 *', 'WARN');
 specifies that messages should be output as HTML paragraphs. The idea is to make it easier to  
 input tracing configuration on a web form.  
94    
95  In addition to HTML and file output for trace messages, you can specify that the trace messages  In addition standard error and file output for trace messages, you can specify that the trace messages
96  be queued. The messages can then be retrieved by calling the L</QTrace> method. This approach  be queued. The messages can then be retrieved by calling the L</QTrace> method. This approach
97  is useful if you are building a web page. Instead of having the trace messages interspersed with  is useful if you are building a web page. Instead of having the trace messages interspersed with
98  the page output, they can be gathered together and displayed at the end of the page. This makes  the page output, they can be gathered together and displayed at the end of the page. This makes
99  it easier to debug page formatting problems.  it easier to debug page formatting problems.
100    
101  Finally, you can specify that all trace messages be emitted as warnings.  Finally, you can specify that all trace messages be emitted to a file, or the standard output and
102    a file at the same time. To trace to a file, specify the filename with an output character in front
103    of it.
104    
105        TSetup('4 SQL', ">$fileName");
106    
107    To trace to the standard output and a file at the same time, put a C<+> in front of the angle
108    bracket.
109    
110        TSetup('3 *', "+>$fileName");
111    
112  The flexibility of tracing makes it superior to simple use of directives like C<die> and C<warn>.  The flexibility of tracing makes it superior to simple use of directives like C<die> and C<warn>.
113  Tracer calls can be left in the code with minimal overhead and then turned on only when needed.  Tracer calls can be left in the code with minimal overhead and then turned on only when needed.
114  Thus, debugging information is available and easily retrieved even when the application is  Thus, debugging information is available and easily retrieved even when the application is
115  being used out in the field.  being used out in the field.
116    
117    =head3 Trace Levels
118    
119    There is no hard and fast rule on how to use trace levels. The following is therefore only
120    a suggestion.
121    
122    =over 4
123    
124    =item Error 0
125    
126    Message indicates an error that may lead to incorrect results or that has stopped the
127    application entirely.
128    
129    =item Warning 1
130    
131    Message indicates something that is unexpected but that probably did not interfere
132    with program execution.
133    
134    =item Notice 2
135    
136    Message indicates the beginning or end of a major task.
137    
138    =item Information 3
139    
140    Message indicates a subtask. In the FIG system, a subtask generally relates to a single
141    genome. This would be a big loop that is not expected to execute more than 500 times or so.
142    
143    =item Detail 4
144    
145    Message indicates a low-level loop iteration.
146    
147    =back
148    
149    The format of trace messages is important because some utilities analyze trace files.
150    There are three fields-- the time stamp, the category name, and the text.
151    The time stamp is between square brackets and the category name between angle brackets.
152    After the category name there is a colon (C<:>) followed by the message text.
153    If the square brackets or angle brackets are missing, then the trace management
154    utilities assume that they are encountering a set of pre-formatted lines.
155    
156    Note, however, that this formatting is done automatically by the tracing functions. You
157    only need to know about it if you want to parse a trace file.
158    
159    =head3 Emergency Tracing
160    
161    Sometimes, you need a way for tracing to happen automatically without putting parameters
162    in a form or on the command line. Emergency tracing does this. You invoke emergency tracing
163    from the debug form, which is accessed from I<MySeedInstance>C</FIG/Html/SetPassword.html>.
164    Emergency tracing requires you specify a tracing key. For command-line tools, the key is
165    taken from the C<TRACING> environment variable. For web services, the key is taken from
166    a cookie. Either way, the key tells the tracing facility who you are, so that you control
167    the tracing in your environment without stepping on other users.
168    
169    The key can be anything you want. If you don't have a key, the C<SetPassword> page will
170    generate one for you.
171    
172    You can activate and de-activate emergency tracing from the debugging control panel, as
173    well as display the trace file itself.
174    
175    To enable emergency tracing in your code, call
176    
177        ETracing($cgi)
178    
179    from a web script and
180    
181        ETracing()
182    
183    from a command-line script.
184    
185    The web script will look for the tracing key in the cookies, and the command-line
186    script will look for it in the C<TRACING> environment variable. If you are
187    using the L</StandardScript> or L</StandardSetup> methods, emergency tracing
188    will be configured automatically.
189    
190    NOTE: to configure emergency tracing from the command line instead of the Debugging
191    Control Panel (see below), use the C<trace.pl> script.
192    
193    =head3 Debugging Control Panel
194    
195    The debugging control panel provides several tools to assist in development of
196    SEED and Sprout software. You access the debugging control panel from the URL
197    C</FIG/Html/SetPassword.html> in whichever seed instance you're using. (So,
198    for example, the panel access point for the development NMPDR system is
199    C<http://web-1.nmpdr.org/next/FIG/Html/SetPassword.html>. Contact Bruce to
200    find out what the password is. From this page, you can also specify a tracing
201    key. If you don't specify a key, one will be generated for you.
202    
203    =head4 Emergency Tracing Form
204    
205    At the bottom of the debugging control panel is a form that allows you to
206    specify a trace level and tracing categories. Special and common categories
207    are listed with check boxes. You can hold your mouse over a check box to see
208    what its category does. In general, however, a category name is the same as
209    the name of the package in which the trace message occurs.
210    
211    Additional categories can be entered in an input box, delimited by spaces or commas.
212    
213    The B<Activate> button turns on Emergency tracing at the level you specify with the
214    specified categories active. The B<Terminate> button turns tracing off. The
215    B<Show File> button displays the current contents of the trace file. The tracing
216    form at the bottom of the control panel is designed for emergency tracing, so it
217    will only affect programs that call L</ETracing>, L</StandardScript>,
218    or L</StandardSetup>.
219    
220    =head4 Script Form
221    
222    The top form of the debugging control panel allows you to enter a tiny script and
223    have the output generated in a formatted table. Certain object variables are
224    predefined in the script, including a FIG object (C<$fig>), a CGI object (C<$cgi>),
225    and-- if Sprout is active-- Sprout (C<$sprout>) and SFXlate (C<$sfx>) objects.
226    
227    The last line of the script must be a scalar, but it can be a reference to a hash,
228    a list, a list of lists, and various other combinations. If you select the appropriate
229    data type in the dropdown box, the output will be formatted accordingly. The form
230    also has controls for specifying tracing. These controls override any emergency
231    tracing in effect.
232    
233    =head4 Database Query Forms
234    
235    The forms between the script form and the emergency tracing form allow you to
236    make queries against the database. The FIG query form allows simple queries against
237    a single FIG table. The Sprout query form uses the B<GetAll> method to do a
238    multi-table query against the Sprout database. B<GetAll> is located in the B<ERDB>
239    package, and it takes five parameters.
240    
241        GetAll(\@objectNames, $filterClause, \@parameters, \@fields, $count);
242    
243    Each of the five parameters corresponds to a text box on the query form:
244    
245    =over 4
246    
247    =item Objects
248    
249    Comma-separated list containing the names of the entity and relationship objects to be retrieved.
250    
251    =item Filter
252    
253    WHERE/ORDER BY clause (without the WHERE) to be used to filter and sort the query. The WHERE clause can
254    be parameterized with parameter markers (C<?>). Each field used must be specified in the standard form
255    B<I<objectName>(I<fieldName>)> or B<$I<number>(I<fieldName>)> where I<fieldName> is the name of a
256    field, I<objectName> is the name of the entity or relationship object containing the field, and
257    I<number> is the 1-based position of the object in the object list. Any parameters
258    specified in the filter clause should be specified in the B<Params> field.
259    The fields in a filter clause can come from primary entity relations,
260    relationship relations, or secondary entity relations; however, all of the
261    entities and relationships involved must be included in the list of object names.
262    
263    =item Params
264    
265    List of the parameters to be substituted in for the parameters marks in the filter clause. This
266    is a comma-separated list without any quoting or escaping.
267    
268    =item fields
269    
270    Comma-separated list of the fields to be returned in each element of the list returned. Fields
271    are specified in the same manner as in the filter clause.
272    
273    =item count
274    
275    Maximum number of records to return. If omitted or 0, all available records will be returned.
276    
277    =back
278    
279    B<GetAll> automatically joins together the entities and relationships listed in the object
280    names. This simplifies the coding of the filter clause, but it means that some queries are
281    not possible, since they cannot be expressed in a linear sequence of joins. This is a limitation
282    that has yet to be addressed.
283    
284  =cut  =cut
285    
286  # Declare the configuration variables.  # Declare the configuration variables.
287    
288  my $Destination = "NONE";       # Description of where to send the trace output.  my $Destination = "WARN";   # Description of where to send the trace output.
289    my $TeeFlag = 0;            # TRUE if output is going to a file and to the
290                                # standard output
291  my %Categories = ( main => 1 );  my %Categories = ( main => 1 );
292                                                          # hash of active category names                                                          # hash of active category names
293  my $TraceLevel = 0;                     # trace level; a higher trace level produces more  my $TraceLevel = 0;                     # trace level; a higher trace level produces more
294                                                          # messages                                                          # messages
295  my @Queue = ();                         # queued list of trace messages.  my @Queue = ();                         # queued list of trace messages.
296    my $LastCategory = "main";  # name of the last category interrogated
297    my $SetupCount = 0;         # number of times TSetup called
298    my $AllTrace = 0;           # TRUE if we are tracing all categories.
299    
300    =head2 Tracing Methods
301    
302    =head3 Setups
303    
304        my $count = Tracer::Setups();
305    
306    Return the number of times L</TSetup> has been called.
307    
308  =head2 Public Methods  This method allows for the creation of conditional tracing setups where, for example, we
309    may want to set up tracing if nobody else has done it before us.
310    
311    =cut
312    
313    sub Setups {
314        return $SetupCount;
315    }
316    
317  =head3 TSetup  =head3 TSetup
318    
319  C<< TSetup($categoryList, $target); >>      TSetup($categoryList, $target);
320    
321  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
322  and interrogated by the L</Trace> and L</T> methods.  and interrogated by the L</Trace> and L</T> methods.
# Line 90  Line 332 
332    
333  The destination for the trace output. To send the trace output to a file, specify the file  The destination for the trace output. To send the trace output to a file, specify the file
334  name preceded by a ">" symbol. If a double symbol is used (">>"), then the data is appended  name preceded by a ">" symbol. If a double symbol is used (">>"), then the data is appended
335  to the file. Otherwise the file is cleared before tracing begins. In addition to sending  to the file. Otherwise the file is cleared before tracing begins. Precede the first ">"
336  the trace messages to a file, you can specify a special destination. C<HTML> will cause  symbol with a C<+> to echo output to a file AND to the standard output. In addition to
337  tracing to the standard output with each line formatted as an HTML paragraph. C<TEXT>  sending the trace messages to a file, you can specify a special destination. C<HTML> will
338    cause tracing to the standard output with each line formatted as an HTML paragraph. C<TEXT>
339  will cause tracing to the standard output as ordinary text. C<ERROR> will cause trace  will cause tracing to the standard output as ordinary text. C<ERROR> will cause trace
340  messages to be sent to the standard error output as ordinary text. C<QUEUE> will cause trace  messages to be sent to the standard error output as ordinary text. C<QUEUE> will cause trace
341  messages to be stored in a queue for later retrieval by the L</QTrace> method. C<WARN> will  messages to be stored in a queue for later retrieval by the L</QTrace> method. C<WARN> will
# Line 110  Line 353 
353          my @categoryData = split /\s+/, $categoryList;          my @categoryData = split /\s+/, $categoryList;
354          # Extract the trace level.          # Extract the trace level.
355          $TraceLevel = shift @categoryData;          $TraceLevel = shift @categoryData;
356          # Build the category hash.      # Presume category-based tracing until we learn otherwise.
357        $AllTrace = 0;
358        # Build the category hash. Note that if we find a "*", we turn on non-category
359        # tracing. We must also clear away any pre-existing data.
360        %Categories = ( main => 1 );
361          for my $category (@categoryData) {          for my $category (@categoryData) {
362                  $Categories{$category} = 1;          if ($category eq '*') {
363                $AllTrace = 1;
364            } else {
365                $Categories{lc $category} = 1;
366            }
367          }          }
368          # Now we need to process the destination information. The most important special          # Now we need to process the destination information. The most important special
369          # case is the single ">", which requires we clear the file first. After doing      # cases are the single ">", which requires we clear the file first, and the
370          # so, we tack on another ">" sign so that future trace messages are appended.      # "+" prefix which indicates a double echo.
371        if ($target =~ m/^\+?>>?/) {
372            if ($target =~ m/^\+/) {
373                $TeeFlag = 1;
374                $target = substr($target, 1);
375            }
376          if ($target =~ m/^>[^>]/) {          if ($target =~ m/^>[^>]/) {
377                  open TRACEFILE, $target;                  open TRACEFILE, $target;
378                  print TRACEFILE Now() . " Tracing initialized.\n";              print TRACEFILE "[" . Now() . "] <Tracer>: Tracing initialized.\n";
379                  close TRACEFILE;                  close TRACEFILE;
380                  $Destination = ">$target";                  $Destination = ">$target";
381          } else {          } else {
382                $Destination = $target;
383            }
384        } else {
385                  $Destination = uc($target);                  $Destination = uc($target);
386          }          }
387        # Increment the setup counter.
388        $SetupCount++;
389  }  }
390    
391  =head3 SetLevel  =head3 SetLevel
392    
393  C<< Tracer::SetLevel($newLevel); >>      Tracer::SetLevel($newLevel);
394    
395  Modify the trace level. A higher trace level will cause more messages to appear.  Modify the trace level. A higher trace level will cause more messages to appear.
396    
# Line 147  Line 408 
408      $TraceLevel = $_[0];      $TraceLevel = $_[0];
409  }  }
410    
411  =head3 Now  =head3 ParseTraceDate
412    
413  C<< my $string = Tracer::Now(); >>      my $time = Tracer::ParseTraceDate($dateString);
414    
415  Return a displayable time stamp containing the local time.  Convert a date from the trace file into a PERL timestamp.
416    
417    =over 4
418    
419    =item dateString
420    
421    The date string from the trace file. The format of the string is determined by the
422    L</Now> method.
423    
424    =item RETURN
425    
426    Returns a PERL time, that is, a number of seconds since the epoch, or C<undef> if
427    the time string is invalid.
428    
429    =back
430    
431  =cut  =cut
432    
433  sub Now {  sub ParseTraceDate {
434          my ($sec,$min,$hour,$mday,$mon,$year,$wday,$yday,$isdst) = localtime(time);      # Get the parameters.
435          my $retVal = _p2($mon+1) . "/" . _p2($mday) . "/" . ($year + 1900) . " " .      my ($dateString) = @_;
436                                   _p2($hour) . ":" . _p2($min) . ":" . _p2($sec);      # Declare the return variable.
437          return $retVal;      my $retVal;
438        # Parse the date.
439        if ($dateString =~ m#(\d+)/(\d+)/(\d+)\s+(\d+):(\d+):(\d+)#) {
440            # Create a time object. Note we need to convert the day, month,
441            # and year to a different base. Years count from 1900, and
442            # the internal month value is relocated to January = 0.
443            $retVal = timelocal($6, $5, $4, $2, $1 - 1, $3 - 1900);
444  }  }
445        # Return the result.
446  # Pad a number to 2 digits.      return $retVal;
 sub _p2 {  
         my ($value) = @_;  
         $value = "0$value" if ($value < 10);  
         return $value;  
447  }  }
448    
449  =head3 LogErrors  =head3 LogErrors
450    
451  C<< Tracer::LogErrors($fileName); >>      Tracer::LogErrors($fileName);
452    
453  Route the standard error output to a log file.  Route the standard error output to a log file.
454    
# Line 192  Line 469 
469          open STDERR, '>', $fileName;          open STDERR, '>', $fileName;
470  }  }
471    
472  =head3 ReadOptions  =head3 Trace
   
 C<< my %options = Tracer::ReadOptions($fileName); >>  
   
 Read a set of options from a file. Each option is encoded in a line of text that has the  
 format  
473    
474  I<optionName>C<=>I<optionValue>C<; >I<comment>      Trace($message);
475    
476  The option name must consist entirely of letters, digits, and the punctuation characters  Write a trace message to the target location specified in L</TSetup>. If there has not been
477  C<.> and C<_>, and is case sensitive. Blank lines and lines in which the first nonblank  any prior call to B<TSetup>.
 character is a semi-colon will be ignored. The return hash will map each option name to  
 the corresponding option value.  
478    
479  =over 4  =over 4
480    
481  =item fileName  =item message
   
 Name of the file containing the option data.  
   
 =item RETURN  
482    
483  Returns a hash mapping the option names specified in the file to their corresponding option  Message to write.
 value.  
484    
485  =back  =back
486    
487  =cut  =cut
488    
489  sub ReadOptions {  sub Trace {
490          # Get the parameters.          # Get the parameters.
491          my ($fileName) = @_;      my ($message) = @_;
492          # Open the file.      # Get the timestamp.
493          (open CONFIGFILE, "<$fileName") || Confess("Could not open option file $fileName.");      my $timeStamp = Now();
494          # Count the number of records read.      # Format the message. Note we strip off any line terminators at the end.
495          my ($records, $comments) = 0;      my $prefix = "[$timeStamp] <$LastCategory>: ";
496          # Create the return hash.      my $formatted = $prefix . Strip($message);
497          my %retVal = ();      # Process according to the destination.
498          # Loop through the file, accumulating key-value pairs.      if ($Destination eq "TEXT") {
499          while (my $line = <CONFIGFILE>) {          # Write the message to the standard output.
500                  # Denote we've read a line.          print "$formatted\n";
501                  $records++;      } elsif ($Destination eq "ERROR") {
502                  # Determine the line type.          # Write the message to the error output.
503                  if ($line =~ /^\s*[\n\r]/) {          print STDERR "$formatted\n";
504                          # A blank line is a comment.      } elsif ($Destination eq "QUEUE") {
505                          $comments++;          # Push the message into the queue.
506                  } elsif ($line =~ /^\s*([A-Za-z0-9_\.]+)=([^;]*);/) {          push @Queue, "$formatted";
507                          # Here we have an option assignment.      } elsif ($Destination eq "HTML") {
508                          retVal{$1} = $2;          # Convert the message to HTML and write it to the standard output.
509                  } elsif ($line =~ /^\s*;/) {          my $escapedMessage = CGI::escapeHTML($message);
510                          # Here we have a text comment.          print "<p>$timeStamp $LastCategory: $escapedMessage</p>\n";
511                          $comments++;      } elsif ($Destination eq "WARN") {
512                  } else {         # Emit the message as a warning.
513                          # Here we have an invalid line.         carp $message;
514                          Trace("Invalid option statement in record $records.") if T(0);      } elsif ($Destination =~ m/^>>/) {
515            # Write the trace message to an output file.
516            (open TRACING, $Destination) || die "Tracing open for \"$Destination\" failed: $!";
517            print TRACING "$formatted\n";
518            close TRACING;
519            # If the Tee flag is on, echo it to the standard output.
520            if ($TeeFlag) {
521                print "$formatted\n";
522                  }                  }
523          }          }
         # Return the hash created.  
         return %retVal;  
524  }  }
525    
526  =head3 GetOptions  =head3 T
   
 C<< Tracer::GetOptions(\%defaults, \%options); >>  
   
 Merge a specified set of options into a table of defaults. This method takes two hash references  
 as input and uses the data from the second to update the first. If the second does not exist,  
 there will be no effect. An error will be thrown if one of the entries in the second hash does not  
 exist in the first.  
   
 Consider the following example.  
527    
528  C<< my $optionTable = GetOptions({ dbType => 'mySQL', trace => 0 }, $options); >>      my $switch = T($category, $traceLevel);
529    
530  In this example, the variable B<$options> is expected to contain at most two options-- B<dbType> and      or
 B<trace>. The default database type is C<mySQL> and the default trace level is C<0>. If the value of  
 B<$options> is C<< {dbType => 'Oracle'} >>, then the database type will be changed to C<Oracle> and  
 the trace level will remain at 0. If B<$options> is undefined, then the database type and trace level  
 will remain C<mySQL> and C<0>. If, on the other hand, B<$options> is defined as  
531    
532  C<< {databaseType => 'Oracle'} >>      my $switch = T($traceLevel);
533    
534  an error will occur because the B<databaseType> option does not exist.  Return TRUE if the trace level is at or above a specified value and the specified category
535    is active, else FALSE. If no category is specified, the caller's package name is used.
536    
537  =over 4  =over 4
538    
539  =item defaults  =item category
540    
541  Table of default option values.  Category to which the message belongs. If not specified, the caller's package name is
542    used.
543    
544  =item options  =item traceLevel
545    
546  Table of overrides, if any.  Relevant tracing level.
547    
548  =item RETURN  =item RETURN
549    
550  Returns a reference to the default table passed in as the first parameter.  TRUE if a message at the specified trace level would appear in the trace, else FALSE.
551    
552  =back  =back
553    
554  =cut  =cut
555    
556  sub GetOptions {  sub T {
557        # Declare the return variable.
558        my $retVal = 0;
559        # Only proceed if tracing is turned on.
560        if ($Destination ne "NONE") {
561          # Get the parameters.          # Get the parameters.
562          my ($defaults, $options) = @_;          my ($category, $traceLevel) = @_;
563          # Check for overrides.          if (!defined $traceLevel) {
564          if ($options) {              # Here we have no category, so we need to get the calling package.
565                  # Loop through the overrides.              # The calling package is normally the first parameter. If it is
566                  while (my ($option, $setting) = each %{$options}) {              # omitted, the first parameter will be the tracelevel. So, the
567                          # Insure this override exists.              # first thing we do is shift the so-called category into the
568                          if (!exists $defaults->{$option}) {              # $traceLevel variable where it belongs.
569                                  croak "Unrecognized option $option encountered.";              $traceLevel = $category;
570                my ($package, $fileName, $line) = caller;
571                # If there is no calling package, we default to "main".
572                if (!$package) {
573                    $category = "main";
574                          } else {                          } else {
575                                  # Apply the override.                  my @cats = split /::/, $package;
576                                  $defaults->{$option} = $setting;                  $category = $cats[$#cats];
577                          }                          }
578                  }                  }
579            # Save the category name.
580            $LastCategory = $category;
581            # Convert it to lower case before we hash it.
582            $category = lc $category;
583            # Use the category and tracelevel to compute the result.
584            if (ref $traceLevel) {
585                Confess("Bad trace level.");
586            } elsif (ref $TraceLevel) {
587                Confess("Bad trace config.");
588          }          }
589          # Return the merged table.          $retVal = ($traceLevel <= $TraceLevel && ($AllTrace || exists $Categories{$category}));
590          return $defaults;      }
591        # Return the computed result.
592        return $retVal;
593  }  }
594    
595  =head3 MergeOptions  =head3 QTrace
596    
597  C<< Tracer::MergeOptions(\%table, \%defaults); >>      my $data = QTrace($format);
598    
599  Merge default values into a hash table. This method looks at the key-value pairs in the  Return the queued trace data in the specified format.
 second (default) hash, and if a matching key is not found in the first hash, the default  
 pair is copied in. The process is similar to L</GetOptions>, but there is no error-  
 checking and no return value.  
600    
601  =over 4  =over 4
602    
603  =item table  =item format
   
 Hash table to be updated with the default values.  
   
 =item defaults  
604    
605  Default values to be merged into the first hash table if they are not already present.  C<html> to format the data as an HTML list, C<text> to format it as straight text.
606    
607  =back  =back
608    
609  =cut  =cut
610    
611  sub MergeOptions {  sub QTrace {
612          # Get the parameters.      # Get the parameter.
613          my ($table, $defaults) = @_;      my ($format) = @_;
614          # Loop through the defaults.      # Create the return variable.
615          while (my ($key, $value) = each %{$defaults}) {      my $retVal = "";
616                  if (!exists $table->{$key}) {      # Only proceed if there is an actual queue.
617                          $table->{$key} = $value;      if (@Queue) {
618            # Process according to the format.
619            if ($format =~ m/^HTML$/i) {
620                # Convert the queue into an HTML list.
621                $retVal = "<ul>\n";
622                for my $line (@Queue) {
623                    my $escapedLine = CGI::escapeHTML($line);
624                    $retVal .= "<li>$escapedLine</li>\n";
625                }
626                $retVal .= "</ul>\n";
627            } elsif ($format =~ m/^TEXT$/i) {
628                # Convert the queue into a list of text lines.
629                $retVal = join("\n", @Queue) . "\n";
630                  }                  }
631            # Clear the queue.
632            @Queue = ();
633          }          }
634        # Return the formatted list.
635        return $retVal;
636  }  }
637    
638  =head3 Trace  =head3 Confess
639    
640  C<< Trace($message); >>      Confess($message);
641    
642  Write a trace message to the target location specified in L</TSetup>. If there has not been  Trace the call stack and abort the program with the specified message. When used with
643  any prior call to B<TSetup>.  the OR operator and the L</Assert> method, B<Confess> can function as a debugging assert.
644    So, for example
645    
646        Assert($recNum >= 0) || Confess("Invalid record number $recNum.");
647    
648    Will abort the program with a stack trace if the value of C<$recNum> is negative.
649    
650  =over 4  =over 4
651    
652  =item message  =item message
653    
654  Message to write.  Message to include in the trace.
655    
656  =back  =back
657    
658  =cut  =cut
659    
660  sub Trace {  sub Confess {
661          # Get the parameters.          # Get the parameters.
662          my ($message) = @_;          my ($message) = @_;
663          # Get the timestamp.      if (! defined($FIG_Config::no_tool_hdr)) {
664          my $timeStamp = Now();          # Here we have a tool header. Display its length so that the user can adjust the line numbers.
665          # Format the message.          my $toolHeaderFile = "$FIG_Config::fig_disk/dist/releases/current/$FIG_Config::arch/tool_hdr";
666          my $formatted = "$timeStamp $message";          # Only proceed if the tool header file is actually present.
667          # Process according to the destination.          if (-f $toolHeaderFile) {
668          if ($Destination eq "TEXT") {              my @lines = GetFile($toolHeaderFile);
669                  # Write the message to the standard output.              Trace("Tool header has " . scalar(@lines) . " lines.");
670                  print "$formatted\n";          }
671          } elsif ($Destination eq "ERROR") {      }
672                  # Write the message to the error output.      # Trace the call stack.
673                  print STDERR "$formatted\n";      Cluck($message);
674          } elsif ($Destination eq "QUEUE") {      # Abort the program.
675                  # Push the message into the queue.      croak(">>> $message");
676                  push @Queue, "$formatted";  }
677          } elsif ($Destination eq "HTML") {  
678                  # Convert the message to HTML and write it to the standard output.  =head3 Assert
679                  my $escapedMessage = CGI::escapeHTML($message);  
680                  print "<p>$formatted</p>\n";      Assert($condition1, $condition2, ... $conditionN);
681      } elsif ($Destination eq "WARN") {  
682         # Emit the message as a warning.  Return TRUE if all the conditions are true. This method can be used in conjunction with
683         warn $message;  the OR operator and the L</Confess> method as a debugging assert.
684          } elsif ($Destination =~ m/^>>/) {  So, for example
685                  # Write the trace message to an output file.  
686                  open TRACING, $Destination;      Assert($recNum >= 0) || Confess("Invalid record number $recNum.");
687                  print TRACING "$formatted\n";  
688                  close TRACING;  Will abort the program with a stack trace if the value of C<$recNum> is negative.
689    
690    =cut
691    sub Assert {
692        my $retVal = 1;
693        LOOP: for my $condition (@_) {
694            if (! $condition) {
695                $retVal = 0;
696                last LOOP;
697            }
698          }          }
699        return $retVal;
700  }  }
701    
702  =head3 T  =head3 Cluck
703    
704  C<< my $switch = T($category, $traceLevel); >>      Cluck($message);
705    
706          or  Trace the call stack. Note that for best results, you should qualify the call with a
707    trace condition. For example,
708    
709  C<< my $switch = T($traceLevel); >>      Cluck("Starting record parse.") if T(3);
710    
711  Return TRUE if the trace level is at or above a specified value and the specified category  will only trace the stack if the trace level for the package is 3 or more.
 is active, else FALSE. If no category is specified, the caller's package name is used.  
712    
713  =over 4  =over 4
714    
715  =item category  =item message
716    
717  Category to which the message belongs. If not specified, the caller's package name is  Message to include in the trace.
 used.  
718    
719  =item traceLevel  =back
720    
721  Relevant tracing level.  =cut
722    
723    sub Cluck {
724        # Get the parameters.
725        my ($message) = @_;
726        # Trace what's happening.
727        Trace("Stack trace for event: $message");
728        my $confession = longmess($message);
729        # Convert the confession to a series of trace messages. Note we skip any
730        # messages relating to calls into Tracer.
731        for my $line (split /\s*\n/, $confession) {
732            Trace($line) if ($line !~ /Tracer\.pm/);
733        }
734    }
735    
736    =head3 ScriptSetup
737    
738        my ($cgi, $varHash) = ScriptSetup($noTrace);
739    
740    Perform standard tracing and debugging setup for scripts. The value returned is
741    the CGI object followed by a pre-built variable hash. At the end of the script,
742    the client should call L</ScriptFinish> to output the web page.
743    
744    This method calls L</ETracing> to configure tracing, which allows the tracing
745    to be configured via the emergency tracing form on the debugging control panel.
746    Tracing will then be turned on automatically for all programs that use the L</ETracing>
747    method, which includes every program that uses this method or L</StandardSetup>.
748    
749    =over 4
750    
751    =item noTrace (optional)
752    
753    If specified, tracing will be suppressed. This is useful if the script wants to set up
754    tracing manually.
755    
756  =item RETURN  =item RETURN
757    
758  TRUE if a message at the specified trace level would appear in the trace, else FALSE.  Returns a two-element list consisting of a CGI query object and a variable hash for
759    the output page.
760    
761  =back  =back
762    
763  =cut  =cut
764    
765  sub T {  sub ScriptSetup {
         # Declare the return variable.  
         my $retVal = 0;  
         # Only proceed if tracing is turned on.  
         if ($Destination ne "NONE") {  
766                  # Get the parameters.                  # Get the parameters.
767                  my ($category, $traceLevel) = @_;      my ($noTrace) = @_;
768                  if (!defined $traceLevel) {      # Get the CGI query object.
769                          # Here we have no category, so we need to get the calling package.      my $cgi = CGI->new();
770                          $traceLevel = $category;      # Set up tracing if it's not suppressed.
771                          my ($package, $fileName, $line) = caller;      ETracing($cgi) unless $noTrace;
772              # If there is no calling package, we default to "main".      # Create the variable hash.
773                          if (!$package) {      my $varHash = { results => '' };
774                  $category = "main";      # Return the query object and variable hash.
775        return ($cgi, $varHash);
776    }
777    
778    =head3 ETracing
779    
780        ETracing($parameter);
781    
782    Set up emergency tracing. Emergency tracing is tracing that is turned
783    on automatically for any program that calls this method. The emergency
784    tracing parameters are stored in a a file identified by a tracing key.
785    If this method is called with a CGI object, then the tracing key is
786    taken from a cookie. If it is called with no parameters, then the tracing
787    key is taken from an environment variable. If it is called with a string,
788    the tracing key is that string.
789    
790    =over 4
791    
792    =item parameter
793    
794    A parameter from which the tracing key is computed. If it is a scalar,
795    that scalar is used as the tracing key. If it is a CGI object, the
796    tracing key is taken from the C<IP> cookie. If it is omitted, the
797    tracing key is taken from the C<TRACING> environment variable. If it
798    is a CGI object and emergency tracing is not on, the C<Trace> and
799    C<TF> parameters will be used to determine the type of tracing.
800    
801    =back
802    
803    =cut
804    
805    sub ETracing {
806        # Get the parameter.
807        my ($parameter) = @_;
808        # Check for CGI mode.
809        my $cgi = (ref $parameter eq 'CGI' ? $parameter : undef);
810        # Default to no tracing except errors.
811        my ($tracing, $dest) = ("0", "WARN");
812        # Check for emergency tracing.
813        my $tkey = EmergencyKey($parameter);
814        my $emergencyFile = EmergencyFileName($tkey);
815        if (-e $emergencyFile) {
816            # We have the file. Read in the data.
817            my @tracing = GetFile($emergencyFile);
818            # Pull off the time limit.
819            my $expire = shift @tracing;
820            # Convert it to seconds.
821            $expire *= 3600;
822            # Check the file data.
823            my $stat = stat($emergencyFile);
824            my ($now) = gettimeofday;
825            if ($now - $stat->mtime > $expire) {
826                # Delete the expired file.
827                unlink $emergencyFile;
828                          } else {                          } else {
829                                  $category = $package;              # Emergency tracing is on. Pull off the destination and
830                # the trace level;
831                $dest = shift @tracing;
832                my $level = shift @tracing;
833                # Convert the destination to a real tracing destination.
834                # temp directory.
835                $dest = EmergencyTracingDest($tkey, $dest);
836                # Insure Tracer is specified.
837                my %moduleHash = map { $_ => 1 } @tracing;
838                $moduleHash{Tracer} = 1;
839                # Set the trace parameter.
840                $tracing = join(" ", $level, sort keys %moduleHash);
841            }
842        } elsif (defined $cgi) {
843            # There's no emergency tracing, but we have a CGI object, so check
844            # for tracing from the form parameters.
845            if ($cgi->param('Trace')) {
846                # Here the user has requested tracing via a form.
847                $dest = ($cgi->param('TF') ? ">$FIG_Config::temp/Trace$$.log" : "QUEUE");
848                $tracing = $cgi->param('Trace') . " Tracer";
849            }
850        }
851        # Setup the tracing we've determined from all the stuff above.
852        TSetup($tracing, $dest);
853        # Check to see if we're a web script.
854        if (defined $cgi) {
855            # Yes we are. Trace the form and environment data.
856            TraceParms($cgi);
857            # Check for RAW mode. In raw mode, we print a fake header so that we see everything
858            # emitted by the script in its raw form.
859            if (T(Raw => 3)) {
860                print CGI::header(-type => 'text/plain', -tracing => 'Raw');
861                          }                          }
862                  }                  }
                 # Use the package and tracelevel to compute the result.  
                 $retVal = ($traceLevel <= $TraceLevel && exists $Categories{$category});  
863      }      }
864          # Return the computed result.  
865      return $retVal;  =head3 EmergencyFileName
866    
867        my $fileName = Tracer::EmergencyFileName($tkey);
868    
869    Return the emergency tracing file name. This is the file that specifies
870    the tracing information.
871    
872    =over 4
873    
874    =item tkey
875    
876    Tracing key for the current program.
877    
878    =item RETURN
879    
880    Returns the name of the file to contain the emergency tracing information.
881    
882    =back
883    
884    =cut
885    
886    sub EmergencyFileName {
887        # Get the parameters.
888        my ($tkey) = @_;
889        # Compute the emergency tracing file name.
890        return "$FIG_Config::temp/Emergency$tkey.txt";
891  }  }
892    
893  =head3 ParseCommand  =head3 EmergencyFileTarget
894    
895  C<< my ($options, @arguments) = Tracer::ParseCommand(\%optionTable, @inputList); >>      my $fileName = Tracer::EmergencyFileTarget($tkey);
896    
897  Parse a command line consisting of a list of parameters. The initial parameters may be option  Return the emergency tracing target file name. This is the file that receives
898  specifiers of the form C<->I<option> or C<->I<option>C<=>I<value>. The options are stripped  the tracing output for file-based tracing.
 off and merged into a table of default options. The remainder of the command line is  
 returned as a list of positional arguments. For example, consider the following invocation.  
899    
900  C<< my ($options, @arguments) = ParseCommand({ errors => 0, logFile => 'trace.log'}, @words); >>  =over 4
901    
902  In this case, the list @words will be treated as a command line. There are two options available,  =item tkey
 B<errors> and B<logFile>. If @words has the following format  
903    
904  C<< -logFile=error.log apple orange rutabaga >>  Tracing key for the current program.
905    
906  then at the end of the invocation, C<$options> will be  =item RETURN
907    
908  C<< { errors => 0, logFile => 'error.log' } >>  Returns the name of the file to contain the trace output.
909    
910  and C<@arguments> will contain  =back
911    
912    =cut
913    
914  C<< apple orange rutabaga >>  sub EmergencyFileTarget {
915        # Get the parameters.
916        my ($tkey) = @_;
917        # Compute the emergency tracing file name.
918        return "$FIG_Config::temp/trace$tkey.log";
919    }
920    
921  The parser allows for some escape sequences. See L</UnEscape> for a description. There is no  =head3 EmergencyTracingDest
922  support for quote characters.  
923        my $dest = Tracer::EmergencyTracingDest($tkey, $myDest);
924    
925    This method converts an emergency tracing destination to a real
926    tracing destination. The main difference is that if the
927    destination is C<FILE> or C<APPEND>, we convert it to file
928    output. If the destination is C<DUAL>, we convert it to file
929    and standard output.
930    
931  =over 4  =over 4
932    
933  =item optionTable  =item tkey
934    
935  Table of default options.  Tracing key for this environment.
936    
937  =item inputList  =item myDest
938    
939  List of words on the command line.  Destination from the emergency tracing file.
940    
941  =item RETURN  =item RETURN
942    
943  Returns a reference to the option table and a list of the positional arguments.  Returns a destination that can be passed into L</TSetup>.
944    
945  =back  =back
946    
947  =cut  =cut
948    
949  sub ParseCommand {  sub EmergencyTracingDest {
950          # Get the parameters.          # Get the parameters.
951          my ($optionTable, @inputList) = @_;      my ($tkey, $myDest) = @_;
952          # Process any options in the input list.      # Declare the return variable.
953          my %overrides = ();      my $retVal = $myDest;
954          while ((@inputList > 0) && ($inputList[0] =~ /^-/)) {      # Process according to the destination value.
955                  # Get the current option.      if ($myDest eq 'FILE') {
956                  my $arg = shift @inputList;          $retVal = ">" . EmergencyFileTarget($tkey);
957                  # Pull out the option name.      } elsif ($myDest eq 'APPEND') {
958                  $arg =~ /^-([^=]*)/g;          $retVal = ">>" . EmergencyFileTarget($tkey);
959                  my $name = $1;      } elsif ($myDest eq 'DUAL') {
960                  # Check for an option value.          $retVal = "+>" . EmergencyFileTarget($tkey);
                 if ($arg =~ /\G=(.*)$/g) {  
                         # Here we have a value for the option.  
                         $overrides{$name} = UnEscape($1);  
                 } else {  
                         # Here there is no value, so we use 1.  
                         $overrides{$name} = 1;  
                 }  
961          }          }
962          # Merge the options into the defaults.      # Return the result.
963          GetOptions($optionTable, \%overrides);      return $retVal;
         # Translate the remaining parameters.  
         my @retVal = ();  
         for my $inputParm (@inputList) {  
                 push @retVal, UnEscape($inputParm);  
964          }          }
965          # Return the results.  
966          return ($optionTable, @retVal);  =head3 Emergency
967    
968        Emergency($key, $hours, $dest, $level, @modules);
969    
970    Turn on emergency tracing. This method is normally invoked over the web from
971    a debugging console, but it can also be called by the C<trace.pl> script.
972    The caller specifies the duration of the emergency in hours, the desired tracing
973    destination, the trace level, and a list of the trace modules to activate.
974    For the length of the duration, when a program in an environment with the
975    specified tracing key active invokes a Sprout CGI script, tracing will be
976    turned on automatically. See L</TSetup> for more about tracing setup and
977    L</ETracing> for more about emergency tracing.
978    
979    =over 4
980    
981    =item tkey
982    
983    The tracing key. This is used to identify the control file and the trace file.
984    
985    =item hours
986    
987    Number of hours to keep emergency tracing alive.
988    
989    =item dest
990    
991    Tracing destination. If no path information is specified for a file
992    destination, it is put in the FIG temporary directory.
993    
994    =item level
995    
996    Tracing level. A higher level means more trace messages.
997    
998    =item modules
999    
1000    A list of the tracing modules to activate.
1001    
1002    =back
1003    
1004    =cut
1005    
1006    sub Emergency {
1007        # Get the parameters.
1008        my ($tkey, $hours, $dest, $level, @modules) = @_;
1009        # Create the emergency file.
1010        my $specFile = EmergencyFileName($tkey);
1011        my $outHandle = Open(undef, ">$specFile");
1012        print $outHandle join("\n", $hours, $dest, $level, @modules, "");
1013  }  }
1014    
1015  =head3 UnEscape  =head3 EmergencyKey
1016    
1017  C<< my $realString = Tracer::UnEscape($codedString); >>      my $tkey = EmergencyKey($parameter);
1018    
1019  Replace escape sequences with their actual equivalents. C<\b> will be replaced by a space,  Return the Key to be used for emergency tracing. This could be an IP address,
1020  C<\t> by a tab, C<\n> by a new-line character, and C<\\> by a back-slash.   a session ID, or a user name, depending on the environment.
1021    
1022  =over 4  =over 4
1023    
1024  =item codedString  =item parameter
1025    
1026  String to un-escape.  Parameter defining the method for finding the tracing key. If it is a scalar,
1027    then it is presumed to be the tracing key itself. If it is a CGI object, then
1028    the tracing key is taken from the C<IP> cookie. Otherwise, the tracing key is
1029    taken from the C<TRACING> environment variable.
1030    
1031  =item RETURN  =item RETURN
1032    
1033  Returns a copy of the original string with the escape sequences converted to their actual  Returns the key to be used for labels in emergency tracing.
1034  values.  
1035    =back
1036    
1037    =cut
1038    
1039    sub EmergencyKey {
1040        # Get the parameters.
1041        my ($parameter) = @_;
1042        # Declare the return variable.
1043        my $retVal;
1044        # Determine the parameter type.
1045        if (! defined $parameter) {
1046            # Here we're supposed to check the environment.
1047            $retVal = $ENV{TRACING};
1048        } else {
1049            my $ptype = ref $parameter;
1050            if ($ptype eq 'CGI') {
1051                # Here we were invoked from a web page. Look for a cookie.
1052                $retVal = $parameter->cookie('IP');
1053            } elsif (! $ptype) {
1054                # Here the key was passed in.
1055                $retVal = $parameter;
1056            }
1057        }
1058        # If no luck finding a key, use the PID.
1059        if (! defined $retVal) {
1060            $retVal = $$;
1061        }
1062        # Return the result.
1063        return $retVal;
1064    }
1065    
1066    
1067    =head3 TraceParms
1068    
1069        Tracer::TraceParms($cgi);
1070    
1071    Trace the CGI parameters at trace level CGI => 3 and the environment variables
1072    at level CGI => 4. A self-referencing URL is traced at level CGI => 2.
1073    
1074    =over 4
1075    
1076    =item cgi
1077    
1078    CGI query object containing the parameters to trace.
1079    
1080    =back
1081    
1082    =cut
1083    
1084    sub TraceParms {
1085        # Get the parameters.
1086        my ($cgi) = @_;
1087        if (T(CGI => 2)) {
1088            # Here we trace the GET-style URL for the script.
1089            Trace("URL: " . $cgi->url(-relative => 1, -query => 1));
1090        }
1091        if (T(CGI => 3)) {
1092            # Here we want to trace the parameter data.
1093            my @names = $cgi->param;
1094            for my $parmName (sort @names) {
1095                # Note we skip the Trace parameters, which are for our use only.
1096                if ($parmName ne 'Trace' && $parmName ne 'TF') {
1097                    my @values = $cgi->param($parmName);
1098                    Trace("CGI: $parmName = " . join(", ", @values));
1099                }
1100            }
1101            # Display the request method.
1102            my $method = $cgi->request_method();
1103            Trace("Method: $method");
1104        }
1105        if (T(CGI => 4)) {
1106            # Here we want the environment data too.
1107            for my $envName (sort keys %ENV) {
1108                Trace("ENV: $envName = $ENV{$envName}");
1109            }
1110        }
1111    }
1112    
1113    =head3 TraceImages
1114    
1115        Tracer::TraceImages($htmlString);
1116    
1117    Trace information about all of an html document's images. The tracing
1118    will be for type "IMG" at level 3. The image's source string
1119    will be displayed. This is generally either the URL of the image or
1120    raw data for the image itself. If the source is too long, only the first 300
1121    characters will be shown at trace level 3. The entire source will be shown,
1122    however, at trace level 4. This method is not very smart, and might catch
1123    Javascript code, but it is still useful when debugging the arcane
1124    behavior of images in multiple browser environments.
1125    
1126    =over 4
1127    
1128    =item htmlString
1129    
1130    HTML text for an outgoing web page.
1131    
1132    =back
1133    
1134    =cut
1135    
1136    sub TraceImages {
1137        # Only proceed if we're at the proper trace level.
1138        if (T(IMG => 3)) {
1139            # For performance reasons we're manipulating $_[0] instead of retrieving the string
1140            # into a variable called "$htmlString". This is because we expect html strings to be
1141            # long, and don't want to copy them any more than we have to.
1142            Trace(length($_[0]) . " characters in web page.");
1143            # Loop through the HTML, culling image tags.
1144            while ($_[0] =~ /<img\s+[^>]+?src="([^"]+)"/sgi) {
1145                # Extract the source string and determine whether or not it's too long.
1146                my $srcString = $1;
1147                my $pos = pos($_[0]) - length($srcString);
1148                my $excess = length($srcString) - 300;
1149                # We'll put the display string in here.
1150                my $srcDisplay = $srcString;
1151                # If it's a data string, split it at the comma.
1152                $srcDisplay =~ s/^(data[^,]+,)/$1\n/;
1153                # If there's no excess or we're at trace level 4, we're done. At level 3 with
1154                # a long string, however, we only show the first 300 characters.
1155                if ($excess > 0 && ! T(IMG => 4)) {
1156                    $srcDisplay = substr($srcDisplay,0,300) . "\nplus $excess characters.";
1157                }
1158                # Output the trace message.
1159                Trace("Image tag at position $pos:\n$srcDisplay");
1160            }
1161        }
1162    }
1163    
1164    
1165    =head3 ScriptFinish
1166    
1167        ScriptFinish($webData, $varHash);
1168    
1169    Output a web page at the end of a script. Either the string to be output or the
1170    name of a template file can be specified. If the second parameter is omitted,
1171    it is assumed we have a string to be output; otherwise, it is assumed we have the
1172    name of a template file. The template should have the variable C<DebugData>
1173    specified in any form that invokes a standard script. If debugging mode is turned
1174    on, a form field will be put in that allows the user to enter tracing data.
1175    Trace messages will be placed immediately before the terminal C<BODY> tag in
1176    the output, formatted as a list.
1177    
1178    A typical standard script would loook like the following.
1179    
1180        BEGIN {
1181            # Print the HTML header.
1182            print "CONTENT-TYPE: text/html\n\n";
1183        }
1184        use Tracer;
1185        use CGI;
1186        use FIG;
1187        # ... more uses ...
1188    
1189        my ($cgi, $varHash) = ScriptSetup();
1190        eval {
1191            # ... get data from $cgi, put it in $varHash ...
1192        };
1193        if ($@) {
1194            Trace("Script Error: $@") if T(0);
1195        }
1196        ScriptFinish("Html/MyTemplate.html", $varHash);
1197    
1198    The idea here is that even if the script fails, you'll see trace messages and
1199    useful output.
1200    
1201    =over 4
1202    
1203    =item webData
1204    
1205    A string containing either the full web page to be written to the output or the
1206    name of a template file from which the page is to be constructed. If the name
1207    of a template file is specified, then the second parameter must be present;
1208    otherwise, it must be absent.
1209    
1210    =item varHash (optional)
1211    
1212    If specified, then a reference to a hash mapping variable names for a template
1213    to their values. The template file will be read into memory, and variable markers
1214    will be replaced by data in this hash reference.
1215    
1216    =back
1217    
1218    =cut
1219    
1220    sub ScriptFinish {
1221        # Get the parameters.
1222        my ($webData, $varHash) = @_;
1223        # Check for a template file situation.
1224        my $outputString;
1225        if (defined $varHash) {
1226            # Here we have a template file. We need to determine the template type.
1227            my $template;
1228            if ($FIG_Config::template_url && $webData =~ /\.php$/) {
1229                $template = "$FIG_Config::template_url/$webData";
1230            } else {
1231                $template = "<<$webData";
1232            }
1233            $outputString = PageBuilder::Build($template, $varHash, "Html");
1234        } else {
1235            # Here the user gave us a raw string.
1236            $outputString = $webData;
1237        }
1238        # Check for trace messages.
1239        if ($Destination ne "NONE" && $TraceLevel > 0) {
1240            # We have trace messages, so we want to put them at the end of the body. This
1241            # is either at the end of the whole string or at the beginning of the BODY
1242            # end-tag.
1243            my $pos = length $outputString;
1244            if ($outputString =~ m#</body>#gi) {
1245                $pos = (pos $outputString) - 7;
1246            }
1247            # If the trace messages were queued, we unroll them. Otherwise, we display the
1248            # destination.
1249            my $traceHtml;
1250            if ($Destination eq "QUEUE") {
1251                $traceHtml = QTrace('Html');
1252            } elsif ($Destination =~ /^>>(.+)$/) {
1253                # Here the tracing output it to a file. We code it as a hyperlink so the user
1254                # can copy the file name into the clipboard easily.
1255                my $actualDest = $1;
1256                $traceHtml = "<p>Tracing output to $actualDest.</p>\n";
1257            } else {
1258                # Here we have one of the special destinations.
1259                $traceHtml = "<P>Tracing output type is $Destination.</p>\n";
1260            }
1261            substr $outputString, $pos, 0, $traceHtml;
1262        }
1263        # Write the output string.
1264        print $outputString;
1265    }
1266    
1267    =head2 Command-Line Utility Methods
1268    
1269    =head3 SendSMS
1270    
1271        my $msgID = Tracer::SendSMS($phoneNumber, $msg);
1272    
1273    Send a text message to a phone number using Clickatell. The FIG_Config file must contain the
1274    user name, password, and API ID for the relevant account in the hash reference variable
1275    I<$FIG_Config::phone>, using the keys C<user>, C<password>, and C<api_id>. For
1276    example, if the user name is C<BruceTheHumanPet>, the password is C<silly>, and the API ID
1277    is C<2561022>, then the FIG_Config file must contain
1278    
1279        $phone =  { user => 'BruceTheHumanPet',
1280                    password => 'silly',
1281                    api_id => '2561022' };
1282    
1283    The original purpose of this method was to insure Bruce would be notified immediately when the
1284    Sprout Load terminates. Care should be taken if you do not wish Bruce to be notified immediately
1285    when you call this method.
1286    
1287    The message ID will be returned if successful, and C<undef> if an error occurs.
1288    
1289    =over 4
1290    
1291    =item phoneNumber
1292    
1293    Phone number to receive the message, in international format. A United States phone number
1294    would be prefixed by "1". A British phone number would be prefixed by "44".
1295    
1296    =item msg
1297    
1298    Message to send to the specified phone.
1299    
1300    =item RETURN
1301    
1302    Returns the message ID if successful, and C<undef> if the message could not be sent.
1303    
1304    =back
1305    
1306    =cut
1307    
1308    sub SendSMS {
1309        # Get the parameters.
1310        my ($phoneNumber, $msg) = @_;
1311        # Declare the return variable. If we do not change it, C<undef> will be returned.
1312        my $retVal;
1313        # Only proceed if we have phone support.
1314        if (! defined $FIG_Config::phone) {
1315            Trace("Phone support not present in FIG_Config.") if T(1);
1316        } else {
1317            # Get the phone data.
1318            my $parms = $FIG_Config::phone;
1319            # Get the Clickatell URL.
1320            my $url = "http://api.clickatell.com/http/";
1321            # Create the user agent.
1322            my $ua = LWP::UserAgent->new;
1323            # Request a Clickatell session.
1324            my $resp = $ua->post("$url/sendmsg", { user => $parms->{user},
1325                                         password => $parms->{password},
1326                                         api_id => $parms->{api_id},
1327                                         to => $phoneNumber,
1328                                         text => $msg});
1329            # Check for an error.
1330            if (! $resp->is_success) {
1331                Trace("Alert failed.") if T(1);
1332            } else {
1333                # Get the message ID.
1334                my $rstring = $resp->content;
1335                if ($rstring =~ /^ID:\s+(.*)$/) {
1336                    $retVal = $1;
1337                } else {
1338                    Trace("Phone attempt failed with $rstring") if T(1);
1339                }
1340            }
1341        }
1342        # Return the result.
1343        return $retVal;
1344    }
1345    
1346    =head3 StandardSetup
1347    
1348        my ($options, @parameters) = StandardSetup(\@categories, \%options, $parmHelp, @ARGV);
1349    
1350    This method performs standard command-line parsing and tracing setup. The return
1351    values are a hash of the command-line options and a list of the positional
1352    parameters. Tracing is automatically set up and the command-line options are
1353    validated.
1354    
1355    This is a complex method that does a lot of grunt work. The parameters can
1356    be more easily understood, however, once they are examined individually.
1357    
1358    The I<categories> parameter is the most obtuse. It is a reference to a list of
1359    special-purpose tracing categories. Most tracing categories are PERL package
1360    names. So, for example, if you wanted to turn on tracing inside the B<Sprout>,
1361    B<ERDB>, and B<SproutLoad> packages, you would specify the categories
1362    
1363        ["Sprout", "SproutLoad", "ERDB"]
1364    
1365    This would cause trace messages in the specified three packages to appear in
1366    the output. There are two special tracing categories that are automatically
1367    handled by this method. In other words, if you used L</TSetup> you would need
1368    to include these categories manually, but if you use this method they are turned
1369    on automatically.
1370    
1371    =over 4
1372    
1373    =item SQL
1374    
1375    Traces SQL commands and activity.
1376    
1377    =item Tracer
1378    
1379    Traces error messages and call stacks.
1380    
1381    =back
1382    
1383    C<SQL> is only turned on if the C<-sql> option is specified in the command line.
1384    The trace level is specified using the C<-trace> command-line option. For example,
1385    the following command line for C<TransactFeatures> turns on SQL tracing and runs
1386    all tracing at level 3.
1387    
1388        TransactFeatures -trace=3 -sql register ../xacts IDs.tbl
1389    
1390    Standard tracing is output to the standard output and echoed to the file
1391    C<trace>I<$$>C<.log> in the FIG temporary directory, where I<$$> is the
1392    process ID. You can also specify the C<user> parameter to put a user ID
1393    instead of a process ID in the trace file name. So, for example
1394    
1395    The default trace level is 2. To get all messages, specify a trace level of 4.
1396    For a genome-by-genome update, use 3.
1397    
1398        TransactFeatures -trace=3 -sql -user=Bruce register ../xacts IDs.tbl
1399    
1400    would send the trace output to C<traceBruce.log> in the temporary directory.
1401    
1402    The I<options> parameter is a reference to a hash containing the command-line
1403    options, their default values, and an explanation of what they mean. Command-line
1404    options may be in the form of switches or keywords. In the case of a switch, the
1405    option value is 1 if it is specified and 0 if it is not specified. In the case
1406    of a keyword, the value is separated from the option name by an equal sign. You
1407    can see this last in the command-line example above.
1408    
1409    You can specify a different default trace level by setting C<$options->{trace}>
1410    prior to calling this method.
1411    
1412    An example at this point would help. Consider, for example, the command-line utility
1413    C<TransactFeatures>. It accepts a list of positional parameters plus the options
1414    C<safe>, C<noAlias>, C<start>, and C<tblFiles>. To start up this command, we execute
1415    the following code.
1416    
1417        my ($options, @parameters) = Tracer::StandardSetup(["DocUtils"],
1418                            { safe => [0, "use database transactions"],
1419                              noAlias => [0, "do not expect aliases in CHANGE transactions"],
1420                              start => [' ', "start with this genome"],
1421                              tblFiles => [0, "output TBL files containing the corrected IDs"] },
1422                            "<command> <transactionDirectory> <IDfile>",
1423                          @ARGV);
1424    
1425    
1426    The call to C<ParseCommand> specifies the default values for the options and
1427    stores the actual options in a hash that is returned as C<$options>. The
1428    positional parameters are returned in C<@parameters>.
1429    
1430    The following is a sample command line for C<TransactFeatures>.
1431    
1432        TransactFeatures -trace=2 -noAlias register ../xacts IDs.tbl
1433    
1434    Single and double hyphens are equivalent. So, you could also code the
1435    above command as
1436    
1437        TransactFeatures --trace=2 --noAlias register ../xacts IDs.tbl
1438    
1439    In this case, C<register>, C<../xacts>, and C<IDs.tbl> are the positional
1440    parameters, and would find themselves in I<@parameters> after executing the
1441    above code fragment. The tracing would be set to level 2, and the categories
1442    would be C<Tracer>, and <DocUtils>. C<Tracer> is standard,
1443    and C<DocUtils> was included because it came in within the first parameter
1444    to this method. The I<$options> hash would be
1445    
1446        { trace => 2, sql => 0, safe => 0,
1447          noAlias => 1, start => ' ', tblFiles => 0 }
1448    
1449    Use of C<StandardSetup> in this way provides a simple way of performing
1450    standard tracing setup and command-line parsing. Note that the caller is
1451    not even aware of the command-line switches C<-trace> and C<-sql>, which
1452    are used by this method to control the tracing. If additional tracing features
1453    need to be added in the future, they can be processed by this method without
1454    upsetting the command-line utilities.
1455    
1456    If the C<background> option is specified on the command line, then the
1457    standard and error outputs will be directed to files in the temporary
1458    directory, using the same suffix as the trace file. So, if the command
1459    line specified
1460    
1461        -user=Bruce -background
1462    
1463    then the trace output would go to C<traceBruce.log>, the standard output to
1464    C<outBruce.log>, and the error output to C<errBruce.log>. This is designed to
1465    simplify starting a command in the background.
1466    
1467    The user name is also used as the tracing key for L</Emergency Tracing>.
1468    Specifying a value of C<E> for the trace level causes emergency tracing to
1469    be used instead of custom tracing. If the user name is not specified,
1470    the tracing key is taken from the C<Tracing> environment variable. If there
1471    is no value for that variable, the tracing key will be computed from the PID.
1472    
1473    Finally, if the special option C<-help> is specified, the option
1474    names will be traced at level 0 and the program will exit without processing.
1475    This provides a limited help capability. For example, if the user enters
1476    
1477        TransactFeatures -help
1478    
1479    he would see the following output.
1480    
1481        TransactFeatures [options] <command> <transactionDirectory> <IDfile>
1482            -trace    tracing level (default E)
1483            -sql      trace SQL commands
1484            -safe     use database transactions
1485            -noAlias  do not expect aliases in CHANGE transactions
1486            -start    start with this genome
1487            -tblFiles output TBL files containing the corrected IDs
1488    
1489    The caller has the option of modifying the tracing scheme by placing a value
1490    for C<trace> in the incoming options hash. The default value can be overridden,
1491    or the tracing to the standard output can be turned off by suffixing a minus
1492    sign to the trace level. So, for example,
1493    
1494        { trace => [0, "tracing level (default 0)"],
1495           ...
1496    
1497    would set the default trace level to 0 instead of E, while
1498    
1499        { trace => ["2-", "tracing level (default 2)"],
1500           ...
1501    
1502    would set the default to 2, but trace only to the log file, not to the
1503    standard output.
1504    
1505    The parameters to this method are as follows.
1506    
1507    =over 4
1508    
1509    =item categories
1510    
1511    Reference to a list of tracing category names. These should be names of
1512    packages whose internal workings will need to be debugged to get the
1513    command working.
1514    
1515    =item options
1516    
1517    Reference to a hash containing the legal options for the current command mapped
1518    to their default values and descriptions. The user can override the defaults
1519    by specifying the options as command-line switches prefixed by a hyphen.
1520    Tracing-related options may be added to this hash. If the C<-h> option is
1521    specified on the command line, the option descriptions will be used to
1522    explain the options. To turn off tracing to the standard output, add a
1523    minus sign to the value for C<trace> (see above).
1524    
1525    =item parmHelp
1526    
1527    A string that vaguely describes the positional parameters. This is used
1528    if the user specifies the C<-h> option.
1529    
1530    =item argv
1531    
1532    List of command line parameters, including the option switches, which must
1533    precede the positional parameters and be prefixed by a hyphen.
1534    
1535    =item RETURN
1536    
1537    Returns a list. The first element of the list is the reference to a hash that
1538    maps the command-line option switches to their values. These will either be the
1539    default values or overrides specified on the command line. The remaining
1540    elements of the list are the position parameters, in order.
1541    
1542    =back
1543    
1544    =cut
1545    
1546    sub StandardSetup {
1547        # Get the parameters.
1548        my ($categories, $options, $parmHelp, @argv) = @_;
1549        # Get the default tracing key.
1550        my $tkey = EmergencyKey();
1551        # Add the tracing options.
1552        if (! exists $options->{trace}) {
1553            $options->{trace} = ['2', "tracing level (E for emergency tracing)"];
1554        }
1555        $options->{sql} = [0, "turn on SQL tracing"];
1556        $options->{help} = [0, "display command-line options"];
1557        $options->{user} = [$tkey, "tracing key"];
1558        $options->{background} = [0, "spool standard and error output"];
1559        # Create a parsing hash from the options hash. The parsing hash
1560        # contains the default values rather than the default value
1561        # and the description. While we're at it, we'll memorize the
1562        # length of the longest option name.
1563        my $longestName = 0;
1564        my %parseOptions = ();
1565        for my $key (keys %{$options}) {
1566            if (length $key > $longestName) {
1567                $longestName = length $key;
1568            }
1569            $parseOptions{$key} = $options->{$key}->[0];
1570        }
1571        # Parse the command line.
1572        my ($retOptions, @retParameters) = ParseCommand(\%parseOptions, @argv);
1573        # Get the logfile suffix.
1574        my $suffix = $retOptions->{user};
1575        # Check for background mode.
1576        if ($retOptions->{background}) {
1577            my $outFileName = "$FIG_Config::temp/out$suffix.log";
1578            my $errFileName = "$FIG_Config::temp/err$suffix.log";
1579            open STDOUT, ">$outFileName";
1580            open STDERR, ">$errFileName";
1581            # Check for phone support. If we have phone support and a phone number,
1582            # we want to turn it on.
1583            if ($ENV{PHONE} && defined($FIG_Config::phone)) {
1584                $retOptions->{phone} = $ENV{PHONE};
1585            }
1586        }
1587        # Now we want to set up tracing. First, we need to know if the user
1588        # wants emergency tracing.
1589        if ($retOptions->{trace} eq 'E') {
1590            ETracing($retOptions->{user});
1591        } else {
1592            # Here the tracing is controlled from the command line.
1593            my @cats = @{$categories};
1594            if ($retOptions->{sql}) {
1595                push @cats, "SQL";
1596            }
1597            # Add the default categories.
1598            push @cats, "Tracer";
1599            # Next, we create the category string by joining the categories.
1600            my $cats = join(" ", @cats);
1601            # Check to determine whether or not the caller wants to turn off tracing
1602            # to the standard output.
1603            my $traceLevel = $retOptions->{trace};
1604            my $textOKFlag = 1;
1605            if ($traceLevel =~ /^(.)-/) {
1606                $traceLevel = $1;
1607                $textOKFlag = 0;
1608            }
1609            # Now we set up the trace mode.
1610            my $traceMode;
1611            # Verify that we can open a file in the FIG temporary directory.
1612            my $traceFileName = "$FIG_Config::temp/trace$suffix.log";
1613            if (open TESTTRACE, ">$traceFileName") {
1614                # Here we can trace to a file.
1615                $traceMode = ">$traceFileName";
1616                if ($textOKFlag) {
1617                    # Echo to standard output if the text-OK flag is set.
1618                    $traceMode = "+$traceMode";
1619                }
1620                # Close the test file.
1621                close TESTTRACE;
1622            } else {
1623                # Here we can't trace to a file. We trace to the standard output if it's
1624                # okay, and the error log otherwise.
1625                if ($textOKFlag) {
1626                    $traceMode = "TEXT";
1627                } else {
1628                    $traceMode = "WARN";
1629                }
1630            }
1631            # Now set up the tracing.
1632            TSetup("$traceLevel $cats", $traceMode);
1633        }
1634        # Check for the "help" option. If it is specified, dump the command-line
1635        # options and exit the program.
1636        if ($retOptions->{help}) {
1637            $0 =~ m#[/\\](\w+)(\.pl)?$#i;
1638            print "$1 [options] $parmHelp\n";
1639            for my $key (sort keys %{$options}) {
1640                my $name = Pad($key, $longestName, 0, ' ');
1641                my $desc = $options->{$key}->[1];
1642                if ($options->{$key}->[0]) {
1643                    $desc .= " (default " . $options->{$key}->[0] . ")";
1644                }
1645                print "  $name $desc\n";
1646            }
1647            exit(0);
1648        }
1649        # Trace the options, if applicable.
1650        if (T(3)) {
1651            my @parms = grep { $retOptions->{$_} } keys %{$retOptions};
1652            Trace("Selected options: " . join(", ", sort @parms) . ".");
1653        }
1654        # Return the parsed parameters.
1655        return ($retOptions, @retParameters);
1656    }
1657    
1658    =head3 ReadOptions
1659    
1660        my %options = Tracer::ReadOptions($fileName);
1661    
1662    Read a set of options from a file. Each option is encoded in a line of text that has the
1663    format
1664    
1665    I<optionName>C<=>I<optionValue>C<; >I<comment>
1666    
1667    The option name must consist entirely of letters, digits, and the punctuation characters
1668    C<.> and C<_>, and is case sensitive. Blank lines and lines in which the first nonblank
1669    character is a semi-colon will be ignored. The return hash will map each option name to
1670    the corresponding option value.
1671    
1672    =over 4
1673    
1674    =item fileName
1675    
1676    Name of the file containing the option data.
1677    
1678    =item RETURN
1679    
1680    Returns a hash mapping the option names specified in the file to their corresponding option
1681    value.
1682    
1683    =back
1684    
1685    =cut
1686    
1687    sub ReadOptions {
1688        # Get the parameters.
1689        my ($fileName) = @_;
1690        # Open the file.
1691        (open CONFIGFILE, "<$fileName") || Confess("Could not open option file $fileName.");
1692        # Count the number of records read.
1693        my ($records, $comments) = 0;
1694        # Create the return hash.
1695        my %retVal = ();
1696        # Loop through the file, accumulating key-value pairs.
1697        while (my $line = <CONFIGFILE>) {
1698            # Denote we've read a line.
1699            $records++;
1700            # Determine the line type.
1701            if ($line =~ /^\s*[\n\r]/) {
1702                # A blank line is a comment.
1703                $comments++;
1704            } elsif ($line =~ /^\s*([A-Za-z0-9_\.]+)=([^;]*);/) {
1705                # Here we have an option assignment.
1706                retVal{$1} = $2;
1707            } elsif ($line =~ /^\s*;/) {
1708                # Here we have a text comment.
1709                $comments++;
1710            } else {
1711                # Here we have an invalid line.
1712                Trace("Invalid option statement in record $records.") if T(0);
1713            }
1714        }
1715        # Return the hash created.
1716        return %retVal;
1717    }
1718    
1719    =head3 GetOptions
1720    
1721        Tracer::GetOptions(\%defaults, \%options);
1722    
1723    Merge a specified set of options into a table of defaults. This method takes two hash references
1724    as input and uses the data from the second to update the first. If the second does not exist,
1725    there will be no effect. An error will be thrown if one of the entries in the second hash does not
1726    exist in the first.
1727    
1728    Consider the following example.
1729    
1730        my $optionTable = GetOptions({ dbType => 'mySQL', trace => 0 }, $options);
1731    
1732    In this example, the variable B<$options> is expected to contain at most two options-- B<dbType> and
1733    B<trace>. The default database type is C<mySQL> and the default trace level is C<0>. If the value of
1734    B<$options> is C<< {dbType => 'Oracle'} >>, then the database type will be changed to C<Oracle> and
1735    the trace level will remain at 0. If B<$options> is undefined, then the database type and trace level
1736    will remain C<mySQL> and C<0>. If, on the other hand, B<$options> is defined as
1737    
1738        {databaseType => 'Oracle'}
1739    
1740    an error will occur because the B<databaseType> option does not exist.
1741    
1742    =over 4
1743    
1744    =item defaults
1745    
1746    Table of default option values.
1747    
1748    =item options
1749    
1750    Table of overrides, if any.
1751    
1752    =item RETURN
1753    
1754    Returns a reference to the default table passed in as the first parameter.
1755    
1756    =back
1757    
1758    =cut
1759    
1760    sub GetOptions {
1761        # Get the parameters.
1762        my ($defaults, $options) = @_;
1763        # Check for overrides.
1764        if ($options) {
1765            # Loop through the overrides.
1766            while (my ($option, $setting) = each %{$options}) {
1767                # Insure this override exists.
1768                if (!exists $defaults->{$option}) {
1769                    croak "Unrecognized option $option encountered.";
1770                } else {
1771                    # Apply the override.
1772                    $defaults->{$option} = $setting;
1773                }
1774            }
1775        }
1776        # Return the merged table.
1777        return $defaults;
1778    }
1779    
1780    =head3 MergeOptions
1781    
1782        Tracer::MergeOptions(\%table, \%defaults);
1783    
1784    Merge default values into a hash table. This method looks at the key-value pairs in the
1785    second (default) hash, and if a matching key is not found in the first hash, the default
1786    pair is copied in. The process is similar to L</GetOptions>, but there is no error-
1787    checking and no return value.
1788    
1789    =over 4
1790    
1791    =item table
1792    
1793    Hash table to be updated with the default values.
1794    
1795    =item defaults
1796    
1797    Default values to be merged into the first hash table if they are not already present.
1798    
1799    =back
1800    
1801    =cut
1802    
1803    sub MergeOptions {
1804        # Get the parameters.
1805        my ($table, $defaults) = @_;
1806        # Loop through the defaults.
1807        while (my ($key, $value) = each %{$defaults}) {
1808            if (!exists $table->{$key}) {
1809                $table->{$key} = $value;
1810            }
1811        }
1812    }
1813    
1814    =head3 ParseCommand
1815    
1816        my ($options, @arguments) = Tracer::ParseCommand(\%optionTable, @inputList);
1817    
1818    Parse a command line consisting of a list of parameters. The initial parameters may be option
1819    specifiers of the form C<->I<option> or C<->I<option>C<=>I<value>. The options are stripped
1820    off and merged into a table of default options. The remainder of the command line is
1821    returned as a list of positional arguments. For example, consider the following invocation.
1822    
1823        my ($options, @arguments) = ParseCommand({ errors => 0, logFile => 'trace.log'}, @words);
1824    
1825    In this case, the list @words will be treated as a command line and there are two options available,
1826    B<errors> and B<logFile>. If @words has the following format
1827    
1828        -logFile=error.log apple orange rutabaga
1829    
1830    then at the end of the invocation, C<$options> will be
1831    
1832        { errors => 0, logFile => 'error.log' }
1833    
1834    and C<@arguments> will contain
1835    
1836        apple orange rutabaga
1837    
1838    The parser allows for some escape sequences. See L</UnEscape> for a description. There is no
1839    support for quote characters. Options can be specified with single or double hyphens.
1840    
1841    =over 4
1842    
1843    =item optionTable
1844    
1845    Table of default options.
1846    
1847    =item inputList
1848    
1849    List of words on the command line.
1850    
1851    =item RETURN
1852    
1853    Returns a reference to the option table and a list of the positional arguments.
1854    
1855    =back
1856    
1857    =cut
1858    
1859    sub ParseCommand {
1860        # Get the parameters.
1861        my ($optionTable, @inputList) = @_;
1862        # Process any options in the input list.
1863        my %overrides = ();
1864        while ((@inputList > 0) && ($inputList[0] =~ /^--?/)) {
1865            # Get the current option.
1866            my $arg = shift @inputList;
1867            # Pull out the option name.
1868            $arg =~ /^--?([^=]*)/g;
1869            my $name = $1;
1870            # Check for an option value.
1871            if ($arg =~ /\G=(.*)$/g) {
1872                # Here we have a value for the option.
1873                $overrides{$name} = UnEscape($1);
1874            } else {
1875                # Here there is no value, so we use 1.
1876                $overrides{$name} = 1;
1877            }
1878        }
1879        # Merge the options into the defaults.
1880        GetOptions($optionTable, \%overrides);
1881        # Translate the remaining parameters.
1882        my @retVal = ();
1883        for my $inputParm (@inputList) {
1884            push @retVal, UnEscape($inputParm);
1885        }
1886        # Return the results.
1887        return ($optionTable, @retVal);
1888    }
1889    
1890    
1891    =head2 File Utility Methods
1892    
1893    =head3 GetFile
1894    
1895        my @fileContents = Tracer::GetFile($fileName);
1896    
1897        or
1898    
1899        my $fileContents = Tracer::GetFile($fileName);
1900    
1901    Return the entire contents of a file. In list context, line-ends are removed and
1902    each line is a list element. In scalar context, line-ends are replaced by C<\n>.
1903    
1904    =over 4
1905    
1906    =item fileName
1907    
1908    Name of the file to read.
1909    
1910    =item RETURN
1911    
1912    In a list context, returns the entire file as a list with the line terminators removed.
1913    In a scalar context, returns the entire file as a string. If an error occurs opening
1914    the file, an empty list will be returned.
1915    
1916    =back
1917    
1918    =cut
1919    
1920    sub GetFile {
1921        # Get the parameters.
1922        my ($fileName) = @_;
1923        # Declare the return variable.
1924        my @retVal = ();
1925        # Open the file for input.
1926        my $handle = Open(undef, "<$fileName");
1927        # Read the whole file into the return variable, stripping off any terminator
1928        # characters.
1929        my $lineCount = 0;
1930        while (my $line = <$handle>) {
1931            $lineCount++;
1932            $line = Strip($line);
1933            push @retVal, $line;
1934        }
1935        # Close it.
1936        close $handle;
1937        my $actualLines = @retVal;
1938        Trace("$actualLines lines read from file $fileName.") if T(File => 2);
1939        # Return the file's contents in the desired format.
1940        if (wantarray) {
1941            return @retVal;
1942        } else {
1943            return join "\n", @retVal;
1944        }
1945    }
1946    
1947    =head3 PutFile
1948    
1949        Tracer::PutFile($fileName, \@lines);
1950    
1951    Write out a file from a list of lines of text.
1952    
1953    =over 4
1954    
1955    =item fileName
1956    
1957    Name of the output file.
1958    
1959    =item lines
1960    
1961    Reference to a list of text lines. The lines will be written to the file in order, with trailing
1962    new-line characters. Alternatively, may be a string, in which case the string will be written without
1963    modification.
1964    
1965    =back
1966    
1967    =cut
1968    
1969    sub PutFile {
1970        # Get the parameters.
1971        my ($fileName, $lines) = @_;
1972        # Open the output file.
1973        my $handle = Open(undef, ">$fileName");
1974        # Count the lines written.
1975        if (ref $lines ne 'ARRAY') {
1976            # Here we have a scalar, so we write it raw.
1977            print $handle $lines;
1978            Trace("Scalar put to file $fileName.") if T(File => 3);
1979        } else {
1980            # Write the lines one at a time.
1981            my $count = 0;
1982            for my $line (@{$lines}) {
1983                print $handle "$line\n";
1984                $count++;
1985            }
1986            Trace("$count lines put to file $fileName.") if T(File => 3);
1987        }
1988        # Close the output file.
1989        close $handle;
1990    }
1991    
1992    =head3 ParseRecord
1993    
1994        my @fields = Tracer::ParseRecord($line);
1995    
1996    Parse a tab-delimited data line. The data line is split into field values. Embedded tab
1997    and new-line characters in the data line must be represented as C<\t> and C<\n>, respectively.
1998    These will automatically be converted.
1999    
2000    =over 4
2001    
2002    =item line
2003    
2004    Line of data containing the tab-delimited fields.
2005    
2006    =item RETURN
2007    
2008    Returns a list of the fields found in the data line.
2009    
2010    =back
2011    
2012    =cut
2013    
2014    sub ParseRecord {
2015        # Get the parameter.
2016        my ($line) = @_;
2017        # Remove the trailing new-line, if any.
2018        chomp $line;
2019        # Split the line read into pieces using the tab character.
2020        my @retVal = split /\t/, $line;
2021        # Trim and fix the escapes in each piece.
2022        for my $value (@retVal) {
2023            # Trim leading whitespace.
2024            $value =~ s/^\s+//;
2025            # Trim trailing whitespace.
2026            $value =~ s/\s+$//;
2027            # Delete the carriage returns.
2028            $value =~ s/\r//g;
2029            # Convert the escapes into their real values.
2030            $value =~ s/\\t/"\t"/ge;
2031            $value =~ s/\\n/"\n"/ge;
2032        }
2033        # Return the result.
2034        return @retVal;
2035    }
2036    
2037    =head3 Merge
2038    
2039        my @mergedList = Tracer::Merge(@inputList);
2040    
2041    Sort a list of strings and remove duplicates.
2042    
2043    =over 4
2044    
2045    =item inputList
2046    
2047    List of scalars to sort and merge.
2048    
2049    =item RETURN
2050    
2051    Returns a list containing the same elements sorted in ascending order with duplicates
2052    removed.
2053    
2054    =back
2055    
2056    =cut
2057    
2058    sub Merge {
2059        # Get the input list in sort order.
2060        my @inputList = sort @_;
2061        # Only proceed if the list has at least two elements.
2062        if (@inputList > 1) {
2063            # Now we want to move through the list splicing out duplicates.
2064            my $i = 0;
2065            while ($i < @inputList) {
2066                # Get the current entry.
2067                my $thisEntry = $inputList[$i];
2068                # Find out how many elements duplicate the current entry.
2069                my $j = $i + 1;
2070                my $dup1 = $i + 1;
2071                while ($j < @inputList && $inputList[$j] eq $thisEntry) { $j++; };
2072                # If the number is nonzero, splice out the duplicates found.
2073                if ($j > $dup1) {
2074                    splice @inputList, $dup1, $j - $dup1;
2075                }
2076                # Now the element at position $dup1 is different from the element before it
2077                # at position $i. We push $i forward one position and start again.
2078                $i++;
2079            }
2080        }
2081        # Return the merged list.
2082        return @inputList;
2083    }
2084    
2085    =head3 Open
2086    
2087        my $handle = Open($fileHandle, $fileSpec, $message);
2088    
2089    Open a file.
2090    
2091    The I<$fileSpec> is essentially the second argument of the PERL C<open>
2092    function. The mode is specified using Unix-like shell information. So, for
2093    example,
2094    
2095        Open(\*LOGFILE, '>>/usr/spool/news/twitlog', "Could not open twit log.");
2096    
2097    would open for output appended to the specified file, and
2098    
2099        Open(\*DATASTREAM, "| sort -u >$outputFile", "Could not open $outputFile.");
2100    
2101    would open a pipe that sorts the records written and removes duplicates. Note
2102    the use of file handle syntax in the Open call. To use anonymous file handles,
2103    code as follows.
2104    
2105        my $logFile = Open(undef, '>>/usr/spool/news/twitlog', "Could not open twit log.");
2106    
2107    The I<$message> parameter is used if the open fails. If it is set to C<0>, then
2108    the open returns TRUE if successful and FALSE if an error occurred. Otherwise, a
2109    failed open will throw an exception and the third parameter will be used to construct
2110    an error message. If the parameter is omitted, a standard message is constructed
2111    using the file spec.
2112    
2113        Could not open "/usr/spool/news/twitlog"
2114    
2115    Note that the mode characters are automatically cleaned from the file name.
2116    The actual error message from the file system will be captured and appended to the
2117    message in any case.
2118    
2119        Could not open "/usr/spool/news/twitlog": file not found.
2120    
2121    In some versions of PERL the only error message we get is a number, which
2122    corresponds to the C++ C<errno> value.
2123    
2124        Could not open "/usr/spool/news/twitlog": 6.
2125    
2126    =over 4
2127    
2128    =item fileHandle
2129    
2130    File handle. If this parameter is C<undef>, a file handle will be generated
2131    and returned as the value of this method.
2132    
2133    =item fileSpec
2134    
2135    File name and mode, as per the PERL C<open> function.
2136    
2137    =item message (optional)
2138    
2139    Error message to use if the open fails. If omitted, a standard error message
2140    will be generated. In either case, the error information from the file system
2141    is appended to the message. To specify a conditional open that does not throw
2142    an error if it fails, use C<0>.
2143    
2144    =item RETURN
2145    
2146    Returns the name of the file handle assigned to the file, or C<undef> if the
2147    open failed.
2148    
2149    =back
2150    
2151    =cut
2152    
2153    sub Open {
2154        # Get the parameters.
2155        my ($fileHandle, $fileSpec, $message) = @_;
2156        # Attempt to open the file.
2157        my $rv = open $fileHandle, $fileSpec;
2158        # If the open failed, generate an error message.
2159        if (! $rv) {
2160            # Save the system error message.
2161            my $sysMessage = $!;
2162            # See if we need a default message.
2163            if (!$message) {
2164                # Clean any obvious mode characters and leading spaces from the
2165                # filename.
2166                my ($fileName) = FindNamePart($fileSpec);
2167                $message = "Could not open \"$fileName\"";
2168            }
2169            # Terminate with an error using the supplied message and the
2170            # error message from the file system.
2171            Confess("$message: $!");
2172        }
2173        # Return the file handle.
2174        return $fileHandle;
2175    }
2176    
2177    =head3 FindNamePart
2178    
2179        my ($fileName, $start, $len) = Tracer::FindNamePart($fileSpec);
2180    
2181    Extract the portion of a file specification that contains the file name.
2182    
2183    A file specification is the string passed to an C<open> call. It specifies the file
2184    mode and name. In a truly complex situation, it can specify a pipe sequence. This
2185    method assumes that the file name is whatever follows the first angle bracket
2186    sequence.  So, for example, in the following strings the file name is
2187    C</usr/fig/myfile.txt>.
2188    
2189        >>/usr/fig/myfile.txt
2190        </usr/fig/myfile.txt
2191        | sort -u > /usr/fig/myfile.txt
2192    
2193    If the method cannot find a file name using its normal methods, it will return the
2194    whole incoming string.
2195    
2196    =over 4
2197    
2198    =item fileSpec
2199    
2200    File specification string from which the file name is to be extracted.
2201    
2202    =item RETURN
2203    
2204    Returns a three-element list. The first element contains the file name portion of
2205    the specified string, or the whole string if a file name cannot be found via normal
2206    methods. The second element contains the start position of the file name portion and
2207    the third element contains the length.
2208    
2209    =back
2210    
2211    =cut
2212    #: Return Type $;
2213    sub FindNamePart {
2214        # Get the parameters.
2215        my ($fileSpec) = @_;
2216        # Default to the whole input string.
2217        my ($retVal, $pos, $len) = ($fileSpec, 0, length $fileSpec);
2218        # Parse out the file name if we can.
2219        if ($fileSpec =~ m/(<|>>?)(.+?)(\s*)$/) {
2220            $retVal = $2;
2221            $len = length $retVal;
2222            $pos = (length $fileSpec) - (length $3) - $len;
2223        }
2224        # Return the result.
2225        return ($retVal, $pos, $len);
2226    }
2227    
2228    =head3 OpenDir
2229    
2230        my @files = OpenDir($dirName, $filtered, $flag);
2231    
2232    Open a directory and return all the file names. This function essentially performs
2233    the functions of an C<opendir> and C<readdir>. If the I<$filtered> parameter is
2234    set to TRUE, all filenames beginning with a period (C<.>), dollar sign (C<$>),
2235    or pound sign (C<#>) and all filenames ending with a tilde C<~>) will be
2236    filtered out of the return list. If the directory does not open and I<$flag> is not
2237    set, an exception is thrown. So, for example,
2238    
2239        my @files = OpenDir("/Volumes/fig/contigs", 1);
2240    
2241    is effectively the same as
2242    
2243        opendir(TMP, "/Volumes/fig/contigs") || Confess("Could not open /Volumes/fig/contigs.");
2244        my @files = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir(TMP);
2245    
2246    Similarly, the following code
2247    
2248        my @files = grep { $_ =~ /^\d/ } OpenDir("/Volumes/fig/orgs", 0, 1);
2249    
2250    Returns the names of all files in C</Volumes/fig/orgs> that begin with digits and
2251    automatically returns an empty list if the directory fails to open.
2252    
2253    =over 4
2254    
2255    =item dirName
2256    
2257    Name of the directory to open.
2258    
2259    =item filtered
2260    
2261    TRUE if files whose names begin with a period (C<.>) should be automatically removed
2262    from the list, else FALSE.
2263    
2264    =item flag
2265    
2266    TRUE if a failure to open is okay, else FALSE
2267    
2268    =back
2269    
2270    =cut
2271    #: Return Type @;
2272    sub OpenDir {
2273        # Get the parameters.
2274        my ($dirName, $filtered, $flag) = @_;
2275        # Declare the return variable.
2276        my @retVal = ();
2277        # Open the directory.
2278        if (opendir(my $dirHandle, $dirName)) {
2279            # The directory opened successfully. Get the appropriate list according to the
2280            # strictures of the filter parameter.
2281            if ($filtered) {
2282                @retVal = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir $dirHandle;
2283            } else {
2284                @retVal = readdir $dirHandle;
2285            }
2286        } elsif (! $flag) {
2287            # Here the directory would not open and it's considered an error.
2288            Confess("Could not open directory $dirName.");
2289        }
2290        # Return the result.
2291        return @retVal;
2292    }
2293    
2294    
2295    =head3 Insure
2296    
2297        Insure($dirName, $chmod);
2298    
2299    Insure a directory is present.
2300    
2301    =over 4
2302    
2303    =item dirName
2304    
2305    Name of the directory to check. If it does not exist, it will be created.
2306    
2307    =item chmod (optional)
2308    
2309    Security privileges to be given to the directory if it is created.
2310    
2311    =back
2312    
2313    =cut
2314    
2315    sub Insure {
2316        my ($dirName, $chmod) = @_;
2317        if (! -d $dirName) {
2318            Trace("Creating $dirName directory.") if T(2);
2319            eval {
2320                mkpath $dirName;
2321                # If we have permissions specified, set them here.
2322                if (defined($chmod)) {
2323                    chmod $chmod, $dirName;
2324                }
2325            };
2326            if ($@) {
2327                Confess("Error creating $dirName: $@");
2328            }
2329        }
2330    }
2331    
2332    =head3 ChDir
2333    
2334        ChDir($dirName);
2335    
2336    Change to the specified directory.
2337    
2338    =over 4
2339    
2340    =item dirName
2341    
2342    Name of the directory to which we want to change.
2343    
2344    =back
2345    
2346    =cut
2347    
2348    sub ChDir {
2349        my ($dirName) = @_;
2350        if (! -d $dirName) {
2351            Confess("Cannot change to directory $dirName: no such directory.");
2352        } else {
2353            Trace("Changing to directory $dirName.") if T(File => 4);
2354            my $okFlag = chdir $dirName;
2355            if (! $okFlag) {
2356                Confess("Error switching to directory $dirName.");
2357            }
2358        }
2359    }
2360    
2361    =head3 SetPermissions
2362    
2363        Tracer::SetPermissions($dirName, $group, $mask, %otherMasks);
2364    
2365    Set the permissions for a directory and all the files and folders inside it.
2366    In addition, the group ownership will be changed to the specified value.
2367    
2368    This method is more vulnerable than most to permission and compatability
2369    problems, so it does internal error recovery.
2370    
2371    =over 4
2372    
2373    =item dirName
2374    
2375    Name of the directory to process.
2376    
2377    =item group
2378    
2379    Name of the group to be assigned.
2380    
2381    =item mask
2382    
2383    Permission mask. Bits that are C<1> in this mask will be ORed into the
2384    permission bits of any file or directory that does not already have them
2385    set to 1.
2386    
2387    =item otherMasks
2388    
2389    Map of search patterns to permission masks. If a directory name matches
2390    one of the patterns, that directory and all its members and subdirectories
2391    will be assigned the new pattern. For example, the following would
2392    assign 01664 to most files, but would use 01777 for directories named C<tmp>.
2393    
2394        Tracer::SetPermissions($dirName, 'fig', 01664, '^tmp$' => 01777);
2395    
2396    The list is ordered, so the following would use 0777 for C<tmp1> and
2397    0666 for C<tmp>, C<tmp2>, or C<tmp3>.
2398    
2399        Tracer::SetPermissions($dirName, 'fig', 01664, '^tmp1' => 0777,
2400                                                       '^tmp' => 0666);
2401    
2402    Note that the pattern matches are all case-insensitive, and only directory
2403    names are matched, not file names.
2404    
2405    =back
2406    
2407    =cut
2408    
2409    sub SetPermissions {
2410        # Get the parameters.
2411        my ($dirName, $group, $mask, @otherMasks) = @_;
2412        # Set up for error recovery.
2413        eval {
2414            # Switch to the specified directory.
2415            ChDir($dirName);
2416            # Get the group ID.
2417            my $gid = getgrnam($group);
2418            # Get the mask for tracing.
2419            my $traceMask = sprintf("%04o", $mask) . "($mask)";
2420            Trace("Fixing permissions for directory $dirName using group $group($gid) and mask $traceMask.") if T(File => 2);
2421            my $fixCount = 0;
2422            my $lookCount = 0;
2423            # @dirs will be a stack of directories to be processed.
2424            my @dirs = (getcwd());
2425            while (scalar(@dirs) > 0) {
2426                # Get the current directory.
2427                my $dir = pop @dirs;
2428                # Check for a match to one of the specified directory names. To do
2429                # that, we need to pull the individual part of the name off of the
2430                # whole path.
2431                my $simpleName = $dir;
2432                if ($dir =~ m!/([^/]+)$!) {
2433                    $simpleName = $1;
2434                }
2435                Trace("Simple directory name for $dir is $simpleName.") if T(File => 4);
2436                # Search for a match.
2437                my $match = 0;
2438                my $i;
2439                for ($i = 0; $i < $#otherMasks && ! $match; $i += 2) {
2440                    my $pattern = $otherMasks[$i];
2441                    if ($simpleName =~ /$pattern/i) {
2442                        $match = 1;
2443                    }
2444                }
2445                # Check for a match. Note we use $i-1 because the loop added 2
2446                # before terminating due to the match.
2447                if ($match && $otherMasks[$i-1] != $mask) {
2448                    # This directory matches one of the incoming patterns, and it's
2449                    # a different mask, so we process it recursively with that mask.
2450                    SetPermissions($dir, $group, $otherMasks[$i-1], @otherMasks);
2451                } else {
2452                    # Here we can process normally. Get all of the non-hidden members.
2453                    my @submems = OpenDir($dir, 1);
2454                    for my $submem (@submems) {
2455                        # Get the full name.
2456                        my $thisMem = "$dir/$submem";
2457                        Trace("Checking member $thisMem.") if T(4);
2458                        $lookCount++;
2459                        if ($lookCount % 1000 == 0) {
2460                            Trace("$lookCount members examined. Current is $thisMem. Mask is $traceMask") if T(File => 3);
2461                        }
2462                        # Fix the group.
2463                        chown -1, $gid, $thisMem;
2464                        # Insure this member is not a symlink.
2465                        if (! -l $thisMem) {
2466                            # Get its info.
2467                            my $fileInfo = stat $thisMem;
2468                            # Only proceed if we got the info. Otherwise, it's a hard link
2469                            # and we want to skip it anyway.
2470                            if ($fileInfo) {
2471                                my $fileMode = $fileInfo->mode;
2472                                if (($fileMode & $mask) != $mask) {
2473                                    # Fix this member.
2474                                    $fileMode |= $mask;
2475                                    chmod $fileMode, $thisMem;
2476                                    $fixCount++;
2477                                }
2478                                # If it's a subdirectory, stack it.
2479                                if (-d $thisMem) {
2480                                    push @dirs, $thisMem;
2481                                }
2482                            }
2483                        }
2484                    }
2485                }
2486            }
2487            Trace("$lookCount files and directories processed, $fixCount fixed.") if T(File => 2);
2488        };
2489        # Check for an error.
2490        if ($@) {
2491            Confess("SetPermissions error: $@");
2492        }
2493    }
2494    
2495    =head3 GetLine
2496    
2497        my @data = Tracer::GetLine($handle);
2498    
2499    Read a line of data from a tab-delimited file.
2500    
2501    =over 4
2502    
2503    =item handle
2504    
2505    Open file handle from which to read.
2506    
2507    =item RETURN
2508    
2509    Returns a list of the fields in the record read. The fields are presumed to be
2510    tab-delimited. If we are at the end of the file, then an empty list will be
2511    returned. If an empty line is read, a single list item consisting of a null
2512    string will be returned.
2513    
2514    =back
2515    
2516    =cut
2517    
2518    sub GetLine {
2519        # Get the parameters.
2520        my ($handle) = @_;
2521        # Declare the return variable.
2522        my @retVal = ();
2523        Trace("File position is " . tell($handle) . ". EOF flag is " . eof($handle) . ".") if T(File => 4);
2524        # Read from the file.
2525        my $line = <$handle>;
2526        # Only proceed if we found something.
2527        if (defined $line) {
2528            # Remove the new-line. We are a bit over-cautious here because the file may be coming in via an
2529            # upload control and have a nonstandard EOL combination.
2530            $line =~ s/(\r|\n)+$//;
2531            # Here we do some fancy tracing to help in debugging complicated EOL marks.
2532            if (T(File => 4)) {
2533                my $escapedLine = $line;
2534                $escapedLine =~ s/\n/\\n/g;
2535                $escapedLine =~ s/\r/\\r/g;
2536                $escapedLine =~ s/\t/\\t/g;
2537                Trace("Line read: -->$escapedLine<--");
2538            }
2539            # If the line is empty, return a single empty string; otherwise, parse
2540            # it into fields.
2541            if ($line eq "") {
2542                push @retVal, "";
2543            } else {
2544                push @retVal, split /\t/,$line;
2545            }
2546        } else {
2547            # Trace the reason the read failed.
2548            Trace("End of file: $!") if T(File => 3);
2549        }
2550        # Return the result.
2551        return @retVal;
2552    }
2553    
2554    =head3 PutLine
2555    
2556        Tracer::PutLine($handle, \@fields, $eol);
2557    
2558    Write a line of data to a tab-delimited file. The specified field values will be
2559    output in tab-separated form, with a trailing new-line.
2560    
2561    =over 4
2562    
2563    =item handle
2564    
2565    Output file handle.
2566    
2567    =item fields
2568    
2569    List of field values.
2570    
2571    =item eol (optional)
2572    
2573    End-of-line character (default is "\n").
2574    
2575    =back
2576    
2577    =cut
2578    
2579    sub PutLine {
2580        # Get the parameters.
2581        my ($handle, $fields, $eol) = @_;
2582        # Write the data.
2583        print $handle join("\t", @{$fields}) . ($eol || "\n");
2584    }
2585    
2586    
2587    
2588    =head2 Other Useful Methods
2589    
2590    =head3 ParseParm
2591    
2592        my $listValue = Tracer::ParseParm($string);
2593    
2594    Convert a parameter into a list reference. If the parameter is undefined,
2595    an undefined value will be returned. Otherwise, it will be parsed as a
2596    comma-separated list of values.
2597    
2598    =over 4
2599    
2600    =item string
2601    
2602    Incoming string.
2603    
2604    =item RETURN
2605    
2606    Returns a reference to a list of values, or C<undef> if the incoming value
2607    was undefined.
2608    
2609    =back
2610    
2611    =cut
2612    
2613    sub ParseParm {
2614        # Get the parameters.
2615        my ($string) = @_;
2616        # Declare the return variable.
2617        my $retVal;
2618        # Check for data.
2619        if (defined $string) {
2620            # We have some, so split it into a list.
2621            $retVal = [ split /\s*,\s*/, $string];
2622        }
2623        # Return the result.
2624        return $retVal;
2625    }
2626    
2627    
2628    
2629    
2630    =head3 Now
2631    
2632        my $string = Tracer::Now();
2633    
2634    Return a displayable time stamp containing the local time.
2635    
2636    =cut
2637    
2638    sub Now {
2639        my ($sec,$min,$hour,$mday,$mon,$year,$wday,$yday,$isdst) = localtime(time);
2640        my $retVal = _p2($mon+1) . "/" . _p2($mday) . "/" . ($year + 1900) . " " .
2641                     _p2($hour) . ":" . _p2($min) . ":" . _p2($sec);
2642        return $retVal;
2643    }
2644    
2645    # Pad a number to 2 digits.
2646    sub _p2 {
2647        my ($value) = @_;
2648        $value = "0$value" if ($value < 10);
2649        return $value;
2650    }
2651    
2652    =head3 Escape
2653    
2654        my $codedString = Tracer::Escape($realString);
2655    
2656    Escape a string for use in a command. Tabs will be replaced by C<\t>, new-lines
2657    replaced by C<\n>, carriage returns will be deleted, and backslashes will be doubled. The
2658    result is to reverse the effect of L</UnEscape>.
2659    
2660    =over 4
2661    
2662    =item realString
2663    
2664    String to escape.
2665    
2666    =item RETURN
2667    
2668    Escaped equivalent of the real string.
2669    
2670    =back
2671    
2672    =cut
2673    
2674    sub Escape {
2675        # Get the parameter.
2676        my ($realString) = @_;
2677        # Initialize the return variable.
2678        my $retVal = "";
2679        # Loop through the parameter string, looking for sequences to escape.
2680        while (length $realString > 0) {
2681            # Look for the first sequence to escape.
2682            if ($realString =~ /^(.*?)([\n\t\r\\])/) {
2683                # Here we found it. The text preceding the sequence is in $1. The sequence
2684                # itself is in $2. First, move the clear text to the return variable.
2685                $retVal .= $1;
2686                # Strip the processed section off the real string.
2687                $realString = substr $realString, (length $2) + (length $1);
2688                # Get the matched character.
2689                my $char = $2;
2690                # If we have a CR, we are done.
2691                if ($char ne "\r") {
2692                    # It's not a CR, so encode the escape sequence.
2693                    $char =~ tr/\t\n/tn/;
2694                    $retVal .= "\\" . $char;
2695                }
2696            } else {
2697                # Here there are no more escape sequences. The rest of the string is
2698                # transferred unmodified.
2699                $retVal .= $realString;
2700                $realString = "";
2701            }
2702        }
2703        # Return the result.
2704        return $retVal;
2705    }
2706    
2707    =head3 UnEscape
2708    
2709        my $realString = Tracer::UnEscape($codedString);
2710    
2711    Replace escape sequences with their actual equivalents. C<\t> will be replaced by
2712    a tab, C<\n> by a new-line character, and C<\\> by a backslash. C<\r> codes will
2713    be deleted.
2714    
2715    =over 4
2716    
2717    =item codedString
2718    
2719    String to un-escape.
2720    
2721    =item RETURN
2722    
2723    Returns a copy of the original string with the escape sequences converted to their actual
2724    values.
2725    
2726    =back
2727    
2728    =cut
2729    
2730    sub UnEscape {
2731        # Get the parameter.
2732        my ($codedString) = @_;
2733        # Initialize the return variable.
2734        my $retVal = "";
2735        # Only proceed if the incoming string is nonempty.
2736        if (defined $codedString) {
2737            # Loop through the parameter string, looking for escape sequences. We can't do
2738            # translating because it causes problems with the escaped slash. ("\\t" becomes
2739            # "\<tab>" no matter what we do.)
2740            while (length $codedString > 0) {
2741                # Look for the first escape sequence.
2742                if ($codedString =~ /^(.*?)\\(\\|n|t|r)/) {
2743                    # Here we found it. The text preceding the sequence is in $1. The sequence
2744                    # itself is in $2. First, move the clear text to the return variable.
2745                    $retVal .= $1;
2746                    $codedString = substr $codedString, (2 + length $1);
2747                    # Get the escape value.
2748                    my $char = $2;
2749                    # If we have a "\r", we are done.
2750                    if ($char ne 'r') {
2751                        # Here it's not an 'r', so we convert it.
2752                        $char =~ tr/\\tn/\\\t\n/;
2753                        $retVal .= $char;
2754                    }
2755                } else {
2756                    # Here there are no more escape sequences. The rest of the string is
2757                    # transferred unmodified.
2758                    $retVal .= $codedString;
2759                    $codedString = "";
2760                }
2761            }
2762        }
2763        # Return the result.
2764        return $retVal;
2765    }
2766    
2767    =head3 Percent
2768    
2769        my $percent = Tracer::Percent($number, $base);
2770    
2771    Returns the percent of the base represented by the given number. If the base
2772    is zero, returns zero.
2773    
2774    =over 4
2775    
2776    =item number
2777    
2778    Percent numerator.
2779    
2780    =item base
2781    
2782    Percent base.
2783    
2784    =item RETURN
2785    
2786    Returns the percentage of the base represented by the numerator.
2787    
2788    =back
2789    
2790    =cut
2791    
2792    sub Percent {
2793        # Get the parameters.
2794        my ($number, $base) = @_;
2795        # Declare the return variable.
2796        my $retVal = 0;
2797        # Compute the percent.
2798        if ($base != 0) {
2799            $retVal = $number * 100 / $base;
2800        }
2801        # Return the result.
2802        return $retVal;
2803    }
2804    
2805    =head3 Min
2806    
2807        my $min = Min($value1, $value2, ... $valueN);
2808    
2809    Return the minimum argument. The arguments are treated as numbers.
2810    
2811    =over 4
2812    
2813    =item $value1, $value2, ... $valueN
2814    
2815    List of numbers to compare.
2816    
2817    =item RETURN
2818    
2819    Returns the lowest number in the list.
2820    
2821    =back
2822    
2823    =cut
2824    
2825    sub Min {
2826        # Get the parameters. Note that we prime the return value with the first parameter.
2827        my ($retVal, @values) = @_;
2828        # Loop through the remaining parameters, looking for the lowest.
2829        for my $value (@values) {
2830            if ($value < $retVal) {
2831                $retVal = $value;
2832            }
2833        }
2834        # Return the minimum found.
2835        return $retVal;
2836    }
2837    
2838    =head3 Max
2839    
2840        my $max = Max($value1, $value2, ... $valueN);
2841    
2842    Return the maximum argument. The arguments are treated as numbers.
2843    
2844    =over 4
2845    
2846    =item $value1, $value2, ... $valueN
2847    
2848    List of numbers to compare.
2849    
2850    =item RETURN
2851    
2852    Returns the highest number in the list.
2853    
2854    =back
2855    
2856    =cut
2857    
2858    sub Max {
2859        # Get the parameters. Note that we prime the return value with the first parameter.
2860        my ($retVal, @values) = @_;
2861        # Loop through the remaining parameters, looking for the highest.
2862        for my $value (@values) {
2863            if ($value > $retVal) {
2864                $retVal = $value;
2865            }
2866        }
2867        # Return the maximum found.
2868        return $retVal;
2869    }
2870    
2871    =head3 DebugMode
2872    
2873        if (Tracer::DebugMode) { ...code... }
2874    
2875  =back  Return TRUE if debug mode has been turned on, else abort.
2876    
2877    Certain CGI scripts are too dangerous to exist in the production
2878    environment. This method provides a simple way to prevent them
2879    from working unless they are explicitly turned on by creating a password
2880    cookie via the B<SetPassword> script.  If debugging mode
2881    is not turned on, an error will occur.
2882    
2883  =cut  =cut
2884    
2885  sub UnEscape {  sub DebugMode {
2886          # Get the parameter.      # Declare the return variable.
2887          my ($codedString) = @_;      my $retVal = 0;
2888          # Initialize the return variable.      # Check the debug configuration.
2889          my $retVal = "";      my $password = CGI::cookie("DebugMode");
2890          # Loop through the parameter string, looking for escape sequences. We can't do      my $encrypted = Digest::MD5::md5_hex($password);
2891          # translating because it causes problems with the escaped slash. ("\\b" becomes      if ($encrypted eq "252dec43280e0c0d6a75ffcec486e61d") {
2892          # "\ " no matter what we do.)          $retVal = 1;
         while (length $codedString > 0) {  
                 # Look for the first escape sequence.  
                 if ($codedString =~ /^(.*?)\\(\\|b|n|t)/) {  
                         # Here we found it. The text preceding the sequence is in $1. The sequence  
                         # itself is in $2. First, move the clear text to the return variable.  
                         $retVal .= $1;  
                         $codedString = substr $codedString, (2 + length $1);  
                         # Decode the escape sequence.  
                         my $char = $2;  
                         $char =~ tr/\\btn/\\ \t\n/;  
                         $retVal .= $char;  
2893                  } else {                  } else {
2894                          # Here there are no more escape sequences. The rest of the string is          # Here debug mode is off, so we generate an error.
2895                          # transferred unmodified.          Confess("Cannot use this facility without logging in.");
                         $retVal .= $codedString;  
                         $codedString = "";  
2896                  }                  }
2897          }      # Return the determination indicator.
         # Return the result.  
2898          return $retVal;          return $retVal;
2899  }  }
2900    
2901  =head3 ParseRecord  =head3 Strip
2902    
2903  C<< my @fields = Tracer::ParseRecord($line); >>      my $string = Tracer::Strip($line);
2904    
2905  Parse a tab-delimited data line. The data line is split into field values. Embedded tab  Strip all line terminators off a string. This is necessary when dealing with files
2906  and new-line characters in the data line must be represented as C<\t> and C<\n>, respectively.  that may have been transferred back and forth several times among different
2907  These will automatically be converted.  operating environments.
2908    
2909  =over 4  =over 4
2910    
2911  =item line  =item line
2912    
2913  Line of data containing the tab-delimited fields.  Line of text to be stripped.
2914    
2915  =item RETURN  =item RETURN
2916    
2917  Returns a list of the fields found in the data line.  The same line of text with all the line-ending characters chopped from the end.
2918    
2919  =back  =back
2920    
2921  =cut  =cut
2922    
2923  sub ParseRecord {  sub Strip {
2924          # Get the parameter.      # Get a copy of the parameter string.
2925          my ($line) = @_;      my ($string) = @_;
2926          # Remove the trailing new-line, if any.      my $retVal = (defined $string ? $string : "");
2927          chomp $line;      # Strip the line terminator characters.
2928          # Split the line read into pieces using the tab character.      $retVal =~ s/(\r|\n)+$//g;
         my @retVal = split /\t/, $line;  
         # Trim and fix the escapes in each piece.  
         for my $value (@retVal) {  
                 # Trim leading whitespace.  
                 $value =~ s/^\s+//;  
                 # Trim trailing whitespace.  
                 $value =~ s/\s+$//;  
                 # Delete the carriage returns.  
                 $value =~ s/\r//g;  
                 # Convert the escapes into their real values.  
                 $value =~ s/\\t/"\t"/ge;  
                 $value =~ s/\\n/"\n"/ge;  
         }  
2929          # Return the result.          # Return the result.
2930          return @retVal;      return $retVal;
2931  }  }
2932    
2933  =head3 Merge  =head3 Pad
2934    
2935  C<< my @mergedList = Tracer::Merge(@inputList); >>      my $paddedString = Tracer::Pad($string, $len, $left, $padChar);
2936    
2937  Sort a list of strings and remove duplicates.  Pad a string to a specified length. The pad character will be a
2938    space, and the padding will be on the right side unless specified
2939    in the third parameter.
2940    
2941  =over 4  =over 4
2942    
2943  =item inputList  =item string
2944    
2945  List of scalars to sort and merge.  String to be padded.
2946    
2947    =item len
2948    
2949    Desired length of the padded string.
2950    
2951    =item left (optional)
2952    
2953    TRUE if the string is to be left-padded; otherwise it will be padded on the right.
2954    
2955    =item padChar (optional)
2956    
2957    Character to use for padding. The default is a space.
2958    
2959  =item RETURN  =item RETURN
2960    
2961  Returns a list containing the same elements sorted in ascending order with duplicates  Returns a copy of the original string with the pad character added to the
2962  removed.  specified end so that it achieves the desired length.
2963    
2964  =back  =back
2965    
2966  =cut  =cut
2967    
2968  sub Merge {  sub Pad {
2969          # Get the input list in sort order.      # Get the parameters.
2970          my @inputList = sort @_;      my ($string, $len, $left, $padChar) = @_;
2971          # Only proceed if the list has at least two elements.      # Compute the padding character.
2972          if (@inputList > 1) {      if (! defined $padChar) {
2973                  # Now we want to move through the list splicing out duplicates.          $padChar = " ";
2974                  my $i = 0;      }
2975                  while ($i < @inputList) {      # Compute the number of spaces needed.
2976                          # Get the current entry.      my $needed = $len - length $string;
2977                          my $thisEntry = $inputList[$i];      # Copy the string into the return variable.
2978                          # Find out how many elements duplicate the current entry.      my $retVal = $string;
2979                          my $j = $i + 1;      # Only proceed if padding is needed.
2980                          my $dup1 = $i + 1;      if ($needed > 0) {
2981                          while ($j < @inputList && $inputList[$j] eq $thisEntry) { $j++; };          # Create the pad string.
2982                          # If the number is nonzero, splice out the duplicates found.          my $pad = $padChar x $needed;
2983                          if ($j > $dup1) {          # Affix it to the return value.
2984                                  splice @inputList, $dup1, $j - $dup1;          if ($left) {
2985                $retVal = $pad . $retVal;
2986            } else {
2987                $retVal .= $pad;
2988                          }                          }
                         # Now the element at position $dup1 is different from the element before it  
                         # at position $i. We push $i forward one position and start again.  
                         $i++;  
2989                  }                  }
2990        # Return the result.
2991        return $retVal;
2992          }          }
2993          # Return the merged list.  
2994          return @inputList;  =head3 EOF
2995    
2996    This is a constant that is lexically greater than any useful string.
2997    
2998    =cut
2999    
3000    sub EOF {
3001        return "\xFF\xFF\xFF\xFF\xFF";
3002  }  }
3003    
3004  =head3 GetFile  =head3 TICK
3005    
3006        my @results = TICK($commandString);
3007    
3008  C<< my @fileContents = Tracer::GetFile($fileName); >>  Perform a back-tick operation on a command. If this is a Windows environment, any leading
3009    dot-slash (C<./> will be removed. So, for example, if you were doing
3010    
3011  Return the entire contents of a file.      `./protein.cgi`
3012    
3013    from inside a CGI script, it would work fine in Unix, but would issue an error message
3014    in Windows complaining that C<'.'> is not a valid command. If instead you code
3015    
3016        TICK("./protein.cgi")
3017    
3018    it will work correctly in both environments.
3019    
3020  =over 4  =over 4
3021    
3022  =item fileName  =item commandString
3023    
3024  Name of the file to read.  The command string to pass to the system.
3025    
3026  =item RETURN  =item RETURN
3027    
3028  In a list context, returns the entire file as a list with the line terminators removed.  Returns the standard output from the specified command, as a list.
 In a scalar context, returns the entire file as a string.  
3029    
3030  =back  =back
3031    
3032  =cut  =cut
3033    #: Return Type @;
3034  sub GetFile {  sub TICK {
3035          # Get the parameters.          # Get the parameters.
3036          my ($fileName) = @_;      my ($commandString) = @_;
3037          # Declare the return variable.      # Chop off the dot-slash if this is Windows.
3038          my @retVal = ();      if ($FIG_Config::win_mode) {
3039          # Open the file for input.          $commandString =~ s!^\./!!;
         my $ok = open INPUTFILE, "<$fileName";  
         if (!$ok) {  
                 # If we had an error, trace it. We will automatically return a null value.  
                 Trace("Could not open \"$fileName\" for input.") if T(0);  
         } else {  
                 # Read the whole file into the return variable, stripping off an terminator  
         # characters.  
         my $lineCount = 0;  
                 while (my $line = <INPUTFILE>) {  
             $lineCount++;  
             $line =~ s/(\r|\n)+$//g;  
                         push @retVal, $line;  
                 }  
                 # Close it.  
                 close INPUTFILE;  
         my $actualLines = @retVal;  
         Trace("$lineCount lines read from $fileName. $actualLines processed.") if T(0);  
         }  
         # Return the file's contents in the desired format.  
     if (wantarray) {  
             return @retVal;  
     } else {  
         return join "\n", @retVal;  
3040      }      }
3041        # Activate the command and return the result.
3042        return `$commandString`;
3043  }  }
3044    
 =head3 QTrace  
3045    
3046  C<< my $data = QTrace($format); >>  =head3 CommaFormat
3047    
3048  Return the queued trace data in the specified format.      my $formatted = Tracer::CommaFormat($number);
3049    
3050    Insert commas into a number.
3051    
3052  =over 4  =over 4
3053    
3054  =item format  =item number
3055    
3056  C<html> to format the data as an HTML list, C<text> to format it as straight text.  A sequence of digits.
3057    
3058    =item RETURN
3059    
3060    Returns the same digits with commas strategically inserted.
3061    
3062  =back  =back
3063    
3064  =cut  =cut
3065    
3066  sub QTrace {  sub CommaFormat {
3067          # Get the parameter.      # Get the parameters.
3068          my ($format) = @_;      my ($number) = @_;
3069          # Create the return variable.      # Pad the length up to a multiple of three.
3070          my $retVal = "";      my $padded = "$number";
3071          # Process according to the format.      $padded = " " . $padded while length($padded) % 3 != 0;
3072          if ($format =~ m/^HTML$/i) {      # This is a fancy PERL trick. The parentheses in the SPLIT pattern
3073                  # Convert the queue into an HTML list.      # cause the delimiters to be included in the output stream. The
3074                  $retVal = "<ul>\n";      # GREP removes the empty strings in between the delimiters.
3075                  for my $line (@Queue) {      my $retVal = join(",", grep { $_ ne '' } split(/(...)/, $padded));
3076                          my $escapedLine = CGI::escapeHTML($line);      # Clean out the spaces.
3077                          $retVal .= "<li>$escapedLine</li>\n";      $retVal =~ s/ //g;
3078                  }      # Return the result.
                 $retVal .= "</ul>\n";  
         } elsif ($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.  
3079          return $retVal;          return $retVal;
3080  }  }
3081    
 =head3 Confess  
   
 C<< Confess($message); >>  
3082    
3083  Trace the call stack and abort the program with the specified message. The stack  =head3 CompareLists
 trace will only appear if the trace level for this package is 1 or more. When used with  
 the OR operator and the L</Assert> method, B<Confess> can function as a debugging assert.  
 So, for example  
3084    
3085  C<< Assert($recNum >= 0) || Confess("Invalid record number $recNum."); >>      my ($inserted, $deleted) = Tracer::CompareLists(\@newList, \@oldList, $keyIndex);
3086    
3087  Will abort the program with a stack trace if the value of C<$recNum> is negative.  Compare two lists of tuples, and return a hash analyzing the differences. The lists
3088    are presumed to be sorted alphabetically by the value in the $keyIndex column.
3089    The return value contains a list of items that are only in the new list
3090    (inserted) and only in the old list (deleted).
3091    
3092  =over 4  =over 4
3093    
3094  =item message  =item newList
   
 Message to include in the trace.  
3095    
3096  =back  Reference to a list of new tuples.
3097    
3098  =cut  =item oldList
3099    
3100  sub Confess {  Reference to a list of old tuples.
         # Get the parameters.  
         my ($message) = @_;  
         # Trace the call stack.  
         Cluck($message) if T(1);  
         # Abort the program.  
         croak(">>> $message");  
 }  
3101    
3102  =head3 Assert  =item keyIndex (optional)
3103    
3104  C<< Assert($condition1, $condition2, ... $conditionN); >>  Index into each tuple of its key field. The default is 0.
3105    
3106  Return TRUE if all the conditions are true. This method can be used in conjunction with  =item RETURN
 the OR operator and the L</Confess> method, B<Assert> can function as a debugging assert.  
 So, for example  
3107    
3108  C<< Assert($recNum >= 0) || Confess("Invalid record number $recNum."); >>  Returns a 2-tuple consisting of a reference to the list of items that are only in the new
3109    list (inserted) followed by a reference to the list of items that are only in the old
3110    list (deleted).
3111    
3112  Will abort the program with a stack trace if the value of C<$recNum> is negative.  =back
3113    
3114  =cut  =cut
3115  sub Assert {  
3116      my $retVal = 1;  sub CompareLists {
3117      LOOP: for my $condition (@_) {      # Get the parameters.
3118          if (! $condition) {      my ($newList, $oldList, $keyIndex) = @_;
3119              $retVal = 0;      if (! defined $keyIndex) {
3120              last LOOP;          $keyIndex = 0;
3121        }
3122        # Declare the return variables.
3123        my ($inserted, $deleted) = ([], []);
3124        # Loop through the two lists simultaneously.
3125        my ($newI, $oldI) = (0, 0);
3126        my ($newN, $oldN) = (scalar @{$newList}, scalar @{$oldList});
3127        while ($newI < $newN || $oldI < $oldN) {
3128            # Get the current object in each list. Note that if one
3129            # of the lists is past the end, we'll get undef.
3130            my $newItem = $newList->[$newI];
3131            my $oldItem = $oldList->[$oldI];
3132            if (! defined($newItem) || defined($oldItem) && $newItem->[$keyIndex] gt $oldItem->[$keyIndex]) {
3133                # The old item is not in the new list, so mark it deleted.
3134                push @{$deleted}, $oldItem;
3135                $oldI++;
3136            } elsif (! defined($oldItem) || $oldItem->[$keyIndex] gt $newItem->[$keyIndex]) {
3137                # The new item is not in the old list, so mark it inserted.
3138                push @{$inserted}, $newItem;
3139                $newI++;
3140            } else {
3141                # The item is in both lists, so push forward.
3142                $oldI++;
3143                $newI++;
3144          }          }
3145      }      }
3146      return $retVal;      # Return the result.
3147        return ($inserted, $deleted);
3148  }  }
3149    
3150  =head3 Cluck  =head3 GenerateURL
3151    
3152  C<< Cluck($message); >>      my $queryUrl = Tracer::GenerateURL($page, %parameters);
3153    
3154  Trace the call stack. Note that for best results, you should qualify the call with a  Generate a GET-style URL for the specified page with the specified parameter
3155  trace condition. For example,  names and values. The values will be URL-escaped automatically. So, for
3156    example
3157    
3158  C<< Cluck("Starting record parse.") if T(3); >>      Tracer::GenerateURL("form.cgi", type => 1, string => "\"high pass\" or highway")
3159    
3160  will only trace the stack if the trace level for the package is 3 or more.  would return
3161    
3162        form.cgi?type=1;string=%22high%20pass%22%20or%20highway
3163    
3164  =over 4  =over 4
3165    
3166  =item message  =item page
3167    
3168  Message to include in the trace.  Page URL.
3169    
3170    =item parameters
3171    
3172    Hash mapping parameter names to parameter values.
3173    
3174    =item RETURN
3175    
3176    Returns a GET-style URL that goes to the specified page and passes in the
3177    specified parameters and values.
3178    
3179  =back  =back
3180    
3181  =cut  =cut
3182    
3183  sub Cluck {  sub GenerateURL {
3184          # Get the parameters.          # Get the parameters.
3185          my ($message) = @_;      my ($page, %parameters) = @_;
3186      # Trace what's happening.      # Prime the return variable with the page URL.
3187      Trace("Stack trace for event: $message");      my $retVal = $page;
3188          my $confession = longmess($message);      # Loop through the parameters, creating parameter elements in a list.
3189          # Convert the confession to a series of trace messages. Note we skip any      my @parmList = map { "$_=" . uri_escape($parameters{$_}) } keys %parameters;
3190      # messages relating to calls into Tracer.      # If the list is nonempty, tack it on.
3191          for my $line (split /\s*\n/, $confession) {      if (@parmList) {
3192                  Trace($line) if ($line !~ /Tracer\.pm/);          $retVal .= "?" . join(";", @parmList);
3193          }          }
3194        # Return the result.
3195        return $retVal;
3196  }  }
3197    
3198  =head3 Min  =head3 ApplyURL
3199    
3200  C<< my $min = Min($value1, $value2, ... $valueN); >>      Tracer::ApplyURL($table, $target, $url);
3201    
3202  Return the minimum argument. The arguments are treated as numbers.  Run through a two-dimensional table (or more accurately, a list of lists), converting the
3203    I<$target> column to HTML text having a hyperlink to a URL in the I<$url> column. The
3204    URL column will be deleted by this process and the target column will be HTML-escaped.
3205    
3206    This provides a simple way to process the results of a database query into something
3207    displayable by combining a URL with text.
3208    
3209  =over 4  =over 4
3210    
3211  =item $value1, $value2, ... $valueN  =item table
3212    
3213  List of numbers to compare.  Reference to a list of lists. The elements in the containing list will be updated by
3214    this method.
3215    
3216  =item RETURN  =item target
3217    
3218  Returns the lowest number in the list.  The index of the column to be converted into HTML.
3219    
3220    =item url
3221    
3222    The index of the column containing the URL. Note that the URL must have a recognizable
3223    C<http:> at the beginning.
3224    
3225  =back  =back
3226    
3227  =cut  =cut
3228    
3229  sub Min {  sub ApplyURL {
3230          # Get the parameters. Note that we prime the return value with the first parameter.      # Get the parameters.
3231          my ($retVal, @values) = @_;      my ($table, $target, $url) = @_;
3232          # Loop through the remaining parameters, looking for the lowest.      # Loop through the table.
3233          for my $value (@values) {      for my $row (@{$table}) {
3234                  if ($value < $retVal) {          # Apply the URL to the target cell.
3235                          $retVal = $value;          $row->[$target] = CombineURL($row->[$target], $row->[$url]);
3236                  }          # Delete the URL from the row.
3237            delete $row->[$url];
3238          }          }
         # Return the minimum found.  
         return $retVal;  
3239  }  }
3240    
3241  =head3 Max  =head3 CombineURL
3242    
3243  C<< my $max = Max($value1, $value2, ... $valueN); >>      my $combinedHtml = Tracer::CombineURL($text, $url);
3244    
3245  Return the maximum argument. The arguments are treated as numbers.  This method will convert the specified text into HTML hyperlinked to the specified
3246    URL. The hyperlinking will only take place if the URL looks legitimate: that is, it
3247    is defined and begins with an C<http:> header.
3248    
3249  =over 4  =over 4
3250    
3251  =item $value1, $value2, ... $valueN  =item text
3252    
3253  List of numbers to compare.  Text to return. This will be HTML-escaped automatically.
3254    
3255    =item url
3256    
3257    A URL to be hyperlinked to the text. If it does not look like a URL, then the text
3258    will be returned without any hyperlinking.
3259    
3260  =item RETURN  =item RETURN
3261    
3262  Returns the highest number in the list.  Returns the original text, HTML-escaped, with the URL hyperlinked to it. If the URL
3263    doesn't look right, the HTML-escaped text will be returned without any further
3264    modification.
3265    
3266  =back  =back
3267    
3268  =cut  =cut
3269    
3270  sub Max {  sub CombineURL {
3271          # Get the parameters. Note that we prime the return value with the first parameter.      # Get the parameters.
3272          my ($retVal, @values) = @_;      my ($text, $url) = @_;
3273          # Loop through the remaining parameters, looking for the highest.      # Declare the return variable.
3274          for my $value (@values) {      my $retVal = CGI::escapeHTML($text);
3275                  if ($value > $retVal) {      # Verify the URL.
3276                          $retVal = $value;      if (defined($url) && $url =~ m!http://!i) {
3277                  }          # It's good, so we apply it to the text.
3278            $retVal = "<a href=\"$url\">$retVal</a>";
3279          }          }
3280          # Return the maximum found.      # Return the result.
3281          return $retVal;          return $retVal;
3282  }  }
3283    
3284  =head3 AddToListMap  =head3 Cmp
3285    
3286  C<< Tracer::AddToListMap(\%hash, $key, $value); >>      my $cmp = Tracer::Cmp($a, $b);
3287    
3288  Add a key-value pair to a hash of lists. If no value exists for the key, a singleton list  This method performs a universal sort comparison. Each value coming in is
3289  is created for the key. Otherwise, the new value is pushed onto the list.  separated into a leading text part and a trailing number part. The text
3290    part is string compared, and if both parts are equal, then the number
3291    parts are compared numerically. A stream of just numbers or a stream of
3292    just strings will sort correctly, and a mixed stream will sort with the
3293    numbers first. Strings with a label and a number will sort in the
3294    expected manner instead of lexically.
3295    
3296  =over 4  =over 4
3297    
3298  =item hash  =item a
3299    
3300  Reference to the target hash.  First item to compare.
3301    
3302  =item key  =item b
3303    
3304  Key for which the value is to be added.  Second item to compare.
3305    
3306  =item value  =item RETURN
3307    
3308  Value to add to the key's value list.  Returns a negative number if the first item should sort first (is less), a positive
3309    number if the first item should sort second (is greater), and a zero if the items are
3310    equal.
3311    
3312  =back  =back
3313    
3314  =cut  =cut
3315    
3316  sub AddToListMap {  sub Cmp {
3317      # Get the parameters.      # Get the parameters.
3318      my ($hash, $key, $value) = @_;      my ($a, $b) = @_;
3319      # Process according to whether or not the key already has a value.      # Declare the return value.
3320      if (! exists $hash->{$key}) {      my $retVal;
3321          $hash->{$key} = [$value];      # Check for nulls.
3322        if (! defined($a)) {
3323            $retVal = (! defined($b) ? 0 : -1);
3324        } elsif (! defined($b)) {
3325            $retVal = 1;
3326      } else {      } else {
3327          push @{$hash->{$key}}, $value;          # Here we have two real values. Parse the two strings.
3328            $a =~ /^(\D*)(\d*)$/;
3329            my $aParsed = [$1, $2];
3330            $b =~ /^(\D*)(\d*)$/;
3331            my $bParsed = [$1, $2];
3332            # Compare the string parts.
3333            $retVal = $aParsed->[0] cmp $bParsed->[0];
3334            if (! $retVal) {
3335                $retVal = $aParsed->[1] <=> $bParsed->[1];
3336      }      }
3337  }  }
3338        # Return the result.
3339        return $retVal;
3340    }
3341    
3342    
3343  1;  1;

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