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# Line 1  Line 1 
1    #
2    # Copyright (c) 2003-2006 University of Chicago and Fellowship
3    # for Interpretations of Genomes. All Rights Reserved.
4    #
5    # This file is part of the SEED Toolkit.
6    #
7    # The SEED Toolkit is free software. You can redistribute
8    # it and/or modify it under the terms of the SEED Toolkit
9    # Public License.
10    #
11    # You should have received a copy of the SEED Toolkit Public License
12    # along with this program; if not write to the University of Chicago
13    # at info@ci.uchicago.edu or the Fellowship for Interpretation of
14    # Genomes at veronika@thefig.info or download a copy from
15    # http://www.theseed.org/LICENSE.TXT.
16    #
17    
18  package Tracer;  package Tracer;
19    
20          require Exporter;          require Exporter;
21          @ISA = ('Exporter');          @ISA = ('Exporter');
22          @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);
23          @EXPORT_OK = qw(GetFile GetOptions Merge MergeOptions ParseCommand ParseRecord UnEscape);      @EXPORT_OK = qw(GetFile GetOptions Merge MergeOptions ParseCommand ParseRecord UnEscape Escape);
24          use strict;          use strict;
25          use Carp qw(longmess croak);          use Carp qw(longmess croak);
26          use CGI;          use CGI;
27        use Cwd;
28        use FIG_Config;
29        use PageBuilder;
30        use Digest::MD5;
31        use File::Basename;
32        use File::Path;
33        use File::stat;
34        use LWP::UserAgent;
35        use Time::HiRes 'gettimeofday';
36        use URI::Escape;
37        use Time::Local;
38    
39  =head1 Tracing and Debugging Helpers  =head1 Tracing and Debugging Helpers
40    
41  =head2 Introduction  =head2 Tracing
42    
43  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
44  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.
45  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,
46  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
47  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
48  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
49  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
50  appear. To generate a trace message, use the following syntax.  appear.
51    
52    =head3 Putting Trace Messages in Your Code
53    
54  C<< Trace($message) if T(errors => 4); >>  To generate a trace message, use the following syntax.
55    
56        Trace($message) if T(errors => 4);
57    
58  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>
59  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
60    
61  C<< Trace($message) if T(main => 4); >>      Trace($message) if T(main => 4);
62    
63  will trace if the trace level is 4 or more.  will trace if the trace level is 4 or more.
64    
# Line 34  Line 66 
66  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
67  active and the trace level is 2 or more.  active and the trace level is 2 or more.
68    
69  C<< Trace($message) if T(2); >>      Trace($message) if T(2);
70    
71    In scripts, where no package name is available, the category defaults to C<main>.
72    
73  To set up tracing, you call the C</Setup> method. The method takes as input a trace level, a list  =head3 Custom Tracing
74  of category names, and a set of options. The trace level and list of category names are  
75    Many programs have customized tracing configured using the L</TSetup> method. This is no longer
76    the preferred method, but a knowledge of how custom tracing works can make the more modern
77    L</Emergency Tracing> easier to understand.
78    
79    To set up custom tracing, you call the L</TSetup> method. The method takes as input a trace level,
80    a list of category names, and a destination. The trace level and list of category names are
81  specified as a space-delimited string. Thus  specified as a space-delimited string. Thus
82    
83  C<< TSetup('3 errors Sprout ERDB', 'HTML'); >>      TSetup('3 errors Sprout ERDB', 'TEXT');
84    
85    sets the trace level to 3, activates the C<errors>, C<Sprout>, and C<ERDB> categories, and
86    specifies that messages should be sent to the standard output.
87    
88    To turn on tracing for ALL categories, use an asterisk. The call below sets every category to
89    level 3 and writes the output to the standard error output. This sort of thing might be
90    useful in a CGI environment.
91    
92  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.  
93    
94  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
95  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
96  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
97  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
98  it easier to debug page formatting problems.  it easier to debug page formatting problems.
99    
100  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
101    a file at the same time. To trace to a file, specify the filename with an output character in front
102    of it.
103    
104        TSetup('4 SQL', ">$fileName");
105    
106    To trace to the standard output and a file at the same time, put a C<+> in front of the angle
107    bracket.
108    
109        TSetup('3 *', "+>$fileName");
110    
111  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>.
112  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.
113  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
114  being used out in the field.  being used out in the field.
115    
116    =head3 Trace Levels
117    
118    There is no hard and fast rule on how to use trace levels. The following is therefore only
119    a suggestion.
120    
121    =over 4
122    
123    =item Error 0
124    
125    Message indicates an error that may lead to incorrect results or that has stopped the
126    application entirely.
127    
128    =item Warning 1
129    
130    Message indicates something that is unexpected but that probably did not interfere
131    with program execution.
132    
133    =item Notice 2
134    
135    Message indicates the beginning or end of a major task.
136    
137    =item Information 3
138    
139    Message indicates a subtask. In the FIG system, a subtask generally relates to a single
140    genome. This would be a big loop that is not expected to execute more than 500 times or so.
141    
142    =item Detail 4
143    
144    Message indicates a low-level loop iteration.
145    
146    =back
147    
148    The format of trace messages is important because some utilities analyze trace files.
149    There are three fields-- the time stamp, the category name, and the text.
150    The time stamp is between square brackets and the category name between angle brackets.
151    After the category name there is a colon (C<:>) followed by the message text.
152    If the square brackets or angle brackets are missing, then the trace management
153    utilities assume that they are encountering a set of pre-formatted lines.
154    
155    Note, however, that this formatting is done automatically by the tracing functions. You
156    only need to know about it if you want to parse a trace file.
157    
158    =head3 Emergency Tracing
159    
160    Sometimes, you need a way for tracing to happen automatically without putting parameters
161    in a form or on the command line. Emergency tracing does this. You invoke emergency tracing
162    from the debug form, which is accessed from I<MySeedInstance>C</FIG/Html/SetPassword.html>.
163    Emergency tracing requires you specify a tracing key. For command-line tools, the key is
164    taken from the C<TRACING> environment variable. For web services, the key is taken from
165    a cookie. Either way, the key tells the tracing facility who you are, so that you control
166    the tracing in your environment without stepping on other users.
167    
168    The key can be anything you want. If you don't have a key, the C<SetPassword> page will
169    generate one for you.
170    
171    You can activate and de-activate emergency tracing from the debugging control panel, as
172    well as display the trace file itself.
173    
174    To enable emergency tracing in your code, call
175    
176        ETracing($cgi)
177    
178    from a web script and
179    
180        ETracing()
181    
182    from a command-line script.
183    
184    The web script will look for the tracing key in the cookies, and the command-line
185    script will look for it in the C<TRACING> environment variable. If you are
186    using the L</StandardScript> or L</StandardSetup> methods, emergency tracing
187    will be configured automatically.
188    
189    NOTE: to configure emergency tracing from the command line instead of the Debugging
190    Control Panel (see below), use the C<trace.pl> script.
191    
192    =head3 Debugging Control Panel
193    
194    The debugging control panel provides several tools to assist in development of
195    SEED and Sprout software. You access the debugging control panel from the URL
196    C</FIG/Html/SetPassword.html> in whichever seed instance you're using. (So,
197    for example, the panel access point for the development NMPDR system is
198    C<http://web-1.nmpdr.org/next/FIG/Html/SetPassword.html>. Contact Bruce to
199    find out what the password is. From this page, you can also specify a tracing
200    key. If you don't specify a key, one will be generated for you.
201    
202    =head4 Emergency Tracing Form
203    
204    At the bottom of the debugging control panel is a form that allows you to
205    specify a trace level and tracing categories. Special and common categories
206    are listed with check boxes. You can hold your mouse over a check box to see
207    what its category does. In general, however, a category name is the same as
208    the name of the package in which the trace message occurs.
209    
210    Additional categories can be entered in an input box, delimited by spaces or commas.
211    
212    The B<Activate> button turns on Emergency tracing at the level you specify with the
213    specified categories active. The B<Terminate> button turns tracing off. The
214    B<Show File> button displays the current contents of the trace file. The tracing
215    form at the bottom of the control panel is designed for emergency tracing, so it
216    will only affect programs that call L</ETracing>, L</StandardScript>,
217    or L</StandardSetup>.
218    
219    =head4 Script Form
220    
221    The top form of the debugging control panel allows you to enter a tiny script and
222    have the output generated in a formatted table. Certain object variables are
223    predefined in the script, including a FIG object (C<$fig>), a CGI object (C<$cgi>),
224    and-- if Sprout is active-- Sprout (C<$sprout>) and SFXlate (C<$sfx>) objects.
225    
226    The last line of the script must be a scalar, but it can be a reference to a hash,
227    a list, a list of lists, and various other combinations. If you select the appropriate
228    data type in the dropdown box, the output will be formatted accordingly. The form
229    also has controls for specifying tracing. These controls override any emergency
230    tracing in effect.
231    
232    =head4 Database Query Forms
233    
234    The forms between the script form and the emergency tracing form allow you to
235    make queries against the database. The FIG query form allows simple queries against
236    a single FIG table. The Sprout query form uses the B<GetAll> method to do a
237    multi-table query against the Sprout database. B<GetAll> is located in the B<ERDB>
238    package, and it takes five parameters.
239    
240        GetAll(\@objectNames, $filterClause, \@parameters, \@fields, $count);
241    
242    Each of the five parameters corresponds to a text box on the query form:
243    
244    =over 4
245    
246    =item Objects
247    
248    Comma-separated list containing the names of the entity and relationship objects to be retrieved.
249    
250    =item Filter
251    
252    WHERE/ORDER BY clause (without the WHERE) to be used to filter and sort the query. The WHERE clause can
253    be parameterized with parameter markers (C<?>). Each field used must be specified in the standard form
254    B<I<objectName>(I<fieldName>)> or B<$I<number>(I<fieldName>)> where I<fieldName> is the name of a
255    field, I<objectName> is the name of the entity or relationship object containing the field, and
256    I<number> is the 1-based position of the object in the object list. Any parameters
257    specified in the filter clause should be specified in the B<Params> field.
258    The fields in a filter clause can come from primary entity relations,
259    relationship relations, or secondary entity relations; however, all of the
260    entities and relationships involved must be included in the list of object names.
261    
262    =item Params
263    
264    List of the parameters to be substituted in for the parameters marks in the filter clause. This
265    is a comma-separated list without any quoting or escaping.
266    
267    =item fields
268    
269    Comma-separated list of the fields to be returned in each element of the list returned. Fields
270    are specified in the same manner as in the filter clause.
271    
272    =item count
273    
274    Maximum number of records to return. If omitted or 0, all available records will be returned.
275    
276    =back
277    
278    B<GetAll> automatically joins together the entities and relationships listed in the object
279    names. This simplifies the coding of the filter clause, but it means that some queries are
280    not possible, since they cannot be expressed in a linear sequence of joins. This is a limitation
281    that has yet to be addressed.
282    
283  =cut  =cut
284    
285  # Declare the configuration variables.  # Declare the configuration variables.
286    
287  my $Destination = "NONE";       # Description of where to send the trace output.  my $Destination = "WARN";   # Description of where to send the trace output.
288    my $TeeFlag = 0;            # TRUE if output is going to a file and to the
289                                # standard output
290  my %Categories = ( main => 1 );  my %Categories = ( main => 1 );
291                                                          # hash of active category names                                                          # hash of active category names
292  my $TraceLevel = 0;                     # trace level; a higher trace level produces more  my $TraceLevel = 0;                     # trace level; a higher trace level produces more
293                                                          # messages                                                          # messages
294  my @Queue = ();                         # queued list of trace messages.  my @Queue = ();                         # queued list of trace messages.
295    my $LastCategory = "main";  # name of the last category interrogated
296    my $SetupCount = 0;         # number of times TSetup called
297    my $AllTrace = 0;           # TRUE if we are tracing all categories.
298    
299    =head2 Tracing Methods
300    
301    =head3 Setups
302    
303        my $count = Tracer::Setups();
304    
305    Return the number of times L</TSetup> has been called.
306    
307  =head2 Public Methods  This method allows for the creation of conditional tracing setups where, for example, we
308    may want to set up tracing if nobody else has done it before us.
309    
310    =cut
311    
312    sub Setups {
313        return $SetupCount;
314    }
315    
316  =head3 TSetup  =head3 TSetup
317    
318  C<< TSetup($categoryList, $target); >>      TSetup($categoryList, $target);
319    
320  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
321  and interrogated by the L</Trace> and L</T> methods.  and interrogated by the L</Trace> and L</T> methods.
# Line 90  Line 331 
331    
332  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
333  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
334  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 ">"
335  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
336  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
337    cause tracing to the standard output with each line formatted as an HTML paragraph. C<TEXT>
338  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
339  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
340  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 352 
352          my @categoryData = split /\s+/, $categoryList;          my @categoryData = split /\s+/, $categoryList;
353          # Extract the trace level.          # Extract the trace level.
354          $TraceLevel = shift @categoryData;          $TraceLevel = shift @categoryData;
355          # Build the category hash.      # Presume category-based tracing until we learn otherwise.
356        $AllTrace = 0;
357        # Build the category hash. Note that if we find a "*", we turn on non-category
358        # tracing. We must also clear away any pre-existing data.
359        %Categories = ( main => 1 );
360          for my $category (@categoryData) {          for my $category (@categoryData) {
361                  $Categories{$category} = 1;          if ($category eq '*') {
362                $AllTrace = 1;
363            } else {
364                $Categories{lc $category} = 1;
365            }
366          }          }
367          # Now we need to process the destination information. The most important special          # Now we need to process the destination information. The most important special
368          # case is the single ">", which requires we clear the file first. After doing      # cases are the single ">", which requires we clear the file first, and the
369          # so, we tack on another ">" sign so that future trace messages are appended.      # "+" prefix which indicates a double echo.
370        if ($target =~ m/^\+?>>?/) {
371            if ($target =~ m/^\+/) {
372                $TeeFlag = 1;
373                $target = substr($target, 1);
374            }
375          if ($target =~ m/^>[^>]/) {          if ($target =~ m/^>[^>]/) {
376                  open TRACEFILE, $target;                  open TRACEFILE, $target;
377                  print TRACEFILE Now() . " Tracing initialized.\n";              print TRACEFILE "[" . Now() . "] <Tracer>: Tracing initialized.\n";
378                  close TRACEFILE;                  close TRACEFILE;
379                  $Destination = ">$target";                  $Destination = ">$target";
380          } else {          } else {
381                $Destination = $target;
382            }
383        } else {
384                  $Destination = uc($target);                  $Destination = uc($target);
385          }          }
386        # Increment the setup counter.
387        $SetupCount++;
388  }  }
389    
390  =head3 SetLevel  =head3 SetLevel
391    
392  C<< Tracer::SetLevel($newLevel); >>      Tracer::SetLevel($newLevel);
393    
394  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.
395    
# Line 147  Line 407 
407      $TraceLevel = $_[0];      $TraceLevel = $_[0];
408  }  }
409    
410  =head3 Now  =head3 ParseTraceDate
411    
412  C<< my $string = Tracer::Now(); >>      my $time = Tracer::ParseTraceDate($dateString);
413    
414  Return a displayable time stamp containing the local time.  Convert a date from the trace file into a PERL timestamp.
415    
416    =over 4
417    
418    =item dateString
419    
420    The date string from the trace file. The format of the string is determined by the
421    L</Now> method.
422    
423    =item RETURN
424    
425    Returns a PERL time, that is, a number of seconds since the epoch, or C<undef> if
426    the time string is invalid.
427    
428    =back
429    
430  =cut  =cut
431    
432  sub Now {  sub ParseTraceDate {
433          my ($sec,$min,$hour,$mday,$mon,$year,$wday,$yday,$isdst) = localtime(time);      # Get the parameters.
434          my $retVal = _p2($mon+1) . "/" . _p2($mday) . "/" . ($year + 1900) . " " .      my ($dateString) = @_;
435                                   _p2($hour) . ":" . _p2($min) . ":" . _p2($sec);      # Declare the return variable.
436          return $retVal;      my $retVal;
437        # Parse the date.
438        if ($dateString =~ m#(\d+)/(\d+)/(\d+)\s+(\d+):(\d+):(\d+)#) {
439            # Create a time object. Note we need to convert the day, month,
440            # and year to a different base. Years count from 1900, and
441            # the internal month value is relocated to January = 0.
442            $retVal = timelocal($6, $5, $4, $2, $1 - 1, $3 - 1900);
443  }  }
444        # Return the result.
445  # Pad a number to 2 digits.      return $retVal;
 sub _p2 {  
         my ($value) = @_;  
         $value = "0$value" if ($value < 10);  
         return $value;  
446  }  }
447    
448  =head3 LogErrors  =head3 LogErrors
449    
450  C<< Tracer::LogErrors($fileName); >>      Tracer::LogErrors($fileName);
451    
452  Route the standard error output to a log file.  Route the standard error output to a log file.
453    
# Line 192  Line 468 
468          open STDERR, '>', $fileName;          open STDERR, '>', $fileName;
469  }  }
470    
471  =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  
472    
473  I<optionName>C<=>I<optionValue>C<; >I<comment>      Trace($message);
474    
475  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
476  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.  
477    
478  =over 4  =over 4
479    
480  =item fileName  =item message
   
 Name of the file containing the option data.  
   
 =item RETURN  
481    
482  Returns a hash mapping the option names specified in the file to their corresponding option  Message to write.
 value.  
483    
484  =back  =back
485    
486  =cut  =cut
487    
488  sub ReadOptions {  sub Trace {
489          # Get the parameters.          # Get the parameters.
490          my ($fileName) = @_;      my ($message) = @_;
491          # Open the file.      # Get the timestamp.
492          (open CONFIGFILE, "<$fileName") || Confess("Could not open option file $fileName.");      my $timeStamp = Now();
493          # Count the number of records read.      # Format the message. Note we strip off any line terminators at the end.
494          my ($records, $comments) = 0;      my $prefix = "[$timeStamp] <$LastCategory>: ";
495          # Create the return hash.      my $formatted = $prefix . Strip($message);
496          my %retVal = ();      # Process according to the destination.
497          # Loop through the file, accumulating key-value pairs.      if ($Destination eq "TEXT") {
498          while (my $line = <CONFIGFILE>) {          # Write the message to the standard output.
499                  # Denote we've read a line.          print "$formatted\n";
500                  $records++;      } elsif ($Destination eq "ERROR") {
501                  # Determine the line type.          # Write the message to the error output.
502                  if ($line =~ /^\s*[\n\r]/) {          print STDERR "$formatted\n";
503                          # A blank line is a comment.      } elsif ($Destination eq "QUEUE") {
504                          $comments++;          # Push the message into the queue.
505                  } elsif ($line =~ /^\s*([A-Za-z0-9_\.]+)=([^;]*);/) {          push @Queue, "$formatted";
506                          # Here we have an option assignment.      } elsif ($Destination eq "HTML") {
507                          retVal{$1} = $2;          # Convert the message to HTML and write it to the standard output.
508                  } elsif ($line =~ /^\s*;/) {          my $escapedMessage = CGI::escapeHTML($message);
509                          # Here we have a text comment.          print "<p>$timeStamp $LastCategory: $escapedMessage</p>\n";
510                          $comments++;      } elsif ($Destination eq "WARN") {
511                  } else {         # Emit the message as a warning.
512                          # Here we have an invalid line.         warn $message;
513                          Trace("Invalid option statement in record $records.") if T(0);      } elsif ($Destination =~ m/^>>/) {
514            # Write the trace message to an output file.
515            (open TRACING, $Destination) || die "Tracing open for \"$Destination\" failed: $!";
516            print TRACING "$formatted\n";
517            close TRACING;
518            # If the Tee flag is on, echo it to the standard output.
519            if ($TeeFlag) {
520                print "$formatted\n";
521                  }                  }
522          }          }
         # Return the hash created.  
         return %retVal;  
523  }  }
524    
525  =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.  
526    
527  C<< my $optionTable = GetOptions({ dbType => 'mySQL', trace => 0 }, $options); >>      my $switch = T($category, $traceLevel);
528    
529  In this example, the variable B<$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  
530    
531  C<< {databaseType => 'Oracle'} >>      my $switch = T($traceLevel);
532    
533  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
534    is active, else FALSE. If no category is specified, the caller's package name is used.
535    
536  =over 4  =over 4
537    
538  =item defaults  =item category
539    
540  Table of default option values.  Category to which the message belongs. If not specified, the caller's package name is
541    used.
542    
543  =item options  =item traceLevel
544    
545  Table of overrides, if any.  Relevant tracing level.
546    
547  =item RETURN  =item RETURN
548    
549  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.
550    
551  =back  =back
552    
553  =cut  =cut
554    
555  sub GetOptions {  sub T {
556        # Declare the return variable.
557        my $retVal = 0;
558        # Only proceed if tracing is turned on.
559        if ($Destination ne "NONE") {
560          # Get the parameters.          # Get the parameters.
561          my ($defaults, $options) = @_;          my ($category, $traceLevel) = @_;
562          # Check for overrides.          if (!defined $traceLevel) {
563          if ($options) {              # Here we have no category, so we need to get the calling package.
564                  # Loop through the overrides.              # The calling package is normally the first parameter. If it is
565                  while (my ($option, $setting) = each %{$options}) {              # omitted, the first parameter will be the tracelevel. So, the
566                          # Insure this override exists.              # first thing we do is shift the so-called category into the
567                          if (!exists $defaults->{$option}) {              # $traceLevel variable where it belongs.
568                                  croak "Unrecognized option $option encountered.";              $traceLevel = $category;
569                my ($package, $fileName, $line) = caller;
570                # If there is no calling package, we default to "main".
571                if (!$package) {
572                    $category = "main";
573                          } else {                          } else {
574                                  # Apply the override.                  my @cats = split /::/, $package;
575                                  $defaults->{$option} = $setting;                  $category = $cats[$#cats];
576                          }                          }
577                  }                  }
578            # Save the category name.
579            $LastCategory = $category;
580            # Convert it to lower case before we hash it.
581            $category = lc $category;
582            # Use the category and tracelevel to compute the result.
583            if (ref $traceLevel) {
584                Confess("Bad trace level.");
585            } elsif (ref $TraceLevel) {
586                Confess("Bad trace config.");
587          }          }
588          # Return the merged table.          $retVal = ($traceLevel <= $TraceLevel && ($AllTrace || exists $Categories{$category}));
589          return $defaults;      }
590        # Return the computed result.
591        return $retVal;
592  }  }
593    
594  =head3 MergeOptions  =head3 QTrace
595    
596  C<< Tracer::MergeOptions(\%table, \%defaults); >>      my $data = QTrace($format);
597    
598  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.  
599    
600  =over 4  =over 4
601    
602  =item table  =item format
   
 Hash table to be updated with the default values.  
   
 =item defaults  
603    
604  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.
605    
606  =back  =back
607    
608  =cut  =cut
609    
610  sub MergeOptions {  sub QTrace {
611          # Get the parameters.      # Get the parameter.
612          my ($table, $defaults) = @_;      my ($format) = @_;
613          # Loop through the defaults.      # Create the return variable.
614          while (my ($key, $value) = each %{$defaults}) {      my $retVal = "";
615                  if (!exists $table->{$key}) {      # Only proceed if there is an actual queue.
616                          $table->{$key} = $value;      if (@Queue) {
617            # Process according to the format.
618            if ($format =~ m/^HTML$/i) {
619                # Convert the queue into an HTML list.
620                $retVal = "<ul>\n";
621                for my $line (@Queue) {
622                    my $escapedLine = CGI::escapeHTML($line);
623                    $retVal .= "<li>$escapedLine</li>\n";
624                }
625                $retVal .= "</ul>\n";
626            } elsif ($format =~ m/^TEXT$/i) {
627                # Convert the queue into a list of text lines.
628                $retVal = join("\n", @Queue) . "\n";
629                  }                  }
630            # Clear the queue.
631            @Queue = ();
632          }          }
633        # Return the formatted list.
634        return $retVal;
635  }  }
636    
637  =head3 Trace  =head3 Confess
638    
639  C<< Trace($message); >>      Confess($message);
640    
641  Write a trace message to the target location specified in L</TSetup>. If there has not been  Trace the call stack and abort the program with the specified message. When used with
642  any prior call to B<TSetup>.  the OR operator and the L</Assert> method, B<Confess> can function as a debugging assert.
643    So, for example
644    
645        Assert($recNum >= 0) || Confess("Invalid record number $recNum.");
646    
647    Will abort the program with a stack trace if the value of C<$recNum> is negative.
648    
649  =over 4  =over 4
650    
651  =item message  =item message
652    
653  Message to write.  Message to include in the trace.
654    
655  =back  =back
656    
657  =cut  =cut
658    
659  sub Trace {  sub Confess {
660          # Get the parameters.          # Get the parameters.
661          my ($message) = @_;          my ($message) = @_;
662          # Get the timestamp.      if (! defined($FIG_Config::no_tool_hdr)) {
663          my $timeStamp = Now();          # Here we have a tool header. Display its length so that the user can adjust the line numbers.
664          # Format the message.          my $toolHeaderFile = "$FIG_Config::fig_disk/dist/releases/current/$FIG_Config::arch/tool_hdr";
665          my $formatted = "$timeStamp $message";          # Only proceed if the tool header file is actually present.
666          # Process according to the destination.          if (-f $toolHeaderFile) {
667          if ($Destination eq "TEXT") {              my @lines = GetFile($toolHeaderFile);
668                  # Write the message to the standard output.              Trace("Tool header has " . scalar(@lines) . " lines.");
669                  print "$formatted\n";          }
670          } elsif ($Destination eq "ERROR") {      }
671                  # Write the message to the error output.      # Trace the call stack.
672                  print STDERR "$formatted\n";      Cluck($message);
673          } elsif ($Destination eq "QUEUE") {      # Abort the program.
674                  # Push the message into the queue.      croak(">>> $message");
675                  push @Queue, "$formatted";  }
676          } elsif ($Destination eq "HTML") {  
677                  # Convert the message to HTML and write it to the standard output.  =head3 Assert
678                  my $escapedMessage = CGI::escapeHTML($message);  
679                  print "<p>$formatted</p>\n";      Assert($condition1, $condition2, ... $conditionN);
680      } elsif ($Destination eq "WARN") {  
681         # Emit the message as a warning.  Return TRUE if all the conditions are true. This method can be used in conjunction with
682         warn $message;  the OR operator and the L</Confess> method as a debugging assert.
683          } elsif ($Destination =~ m/^>>/) {  So, for example
684                  # Write the trace message to an output file.  
685                  open TRACING, $Destination;      Assert($recNum >= 0) || Confess("Invalid record number $recNum.");
686                  print TRACING "$formatted\n";  
687                  close TRACING;  Will abort the program with a stack trace if the value of C<$recNum> is negative.
688    
689    =cut
690    sub Assert {
691        my $retVal = 1;
692        LOOP: for my $condition (@_) {
693            if (! $condition) {
694                $retVal = 0;
695                last LOOP;
696            }
697          }          }
698        return $retVal;
699  }  }
700    
701  =head3 T  =head3 Cluck
702    
703  C<< my $switch = T($category, $traceLevel); >>      Cluck($message);
704    
705          or  Trace the call stack. Note that for best results, you should qualify the call with a
706    trace condition. For example,
707    
708  C<< my $switch = T($traceLevel); >>      Cluck("Starting record parse.") if T(3);
709    
710  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.  
711    
712  =over 4  =over 4
713    
714  =item category  =item message
715    
716  Category to which the message belongs. If not specified, the caller's package name is  Message to include in the trace.
 used.  
717    
718  =item traceLevel  =back
719    
720  Relevant tracing level.  =cut
721    
722    sub Cluck {
723        # Get the parameters.
724        my ($message) = @_;
725        # Trace what's happening.
726        Trace("Stack trace for event: $message");
727        my $confession = longmess($message);
728        # Convert the confession to a series of trace messages. Note we skip any
729        # messages relating to calls into Tracer.
730        for my $line (split /\s*\n/, $confession) {
731            Trace($line) if ($line !~ /Tracer\.pm/);
732        }
733    }
734    
735    =head3 ScriptSetup
736    
737        my ($cgi, $varHash) = ScriptSetup($noTrace);
738    
739    Perform standard tracing and debugging setup for scripts. The value returned is
740    the CGI object followed by a pre-built variable hash. At the end of the script,
741    the client should call L</ScriptFinish> to output the web page.
742    
743    This method calls L</ETracing> to configure tracing, which allows the tracing
744    to be configured via the emergency tracing form on the debugging control panel.
745    Tracing will then be turned on automatically for all programs that use the L</ETracing>
746    method, which includes every program that uses this method or L</StandardSetup>.
747    
748    =over 4
749    
750    =item noTrace (optional)
751    
752    If specified, tracing will be suppressed. This is useful if the script wants to set up
753    tracing manually.
754    
755  =item RETURN  =item RETURN
756    
757  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
758    the output page.
759    
760  =back  =back
761    
762  =cut  =cut
763    
764  sub T {  sub ScriptSetup {
         # Declare the return variable.  
         my $retVal = 0;  
         # Only proceed if tracing is turned on.  
         if ($Destination ne "NONE") {  
765                  # Get the parameters.                  # Get the parameters.
766                  my ($category, $traceLevel) = @_;      my ($noTrace) = @_;
767                  if (!defined $traceLevel) {      # Get the CGI query object.
768                          # Here we have no category, so we need to get the calling package.      my $cgi = CGI->new();
769                          $traceLevel = $category;      # Set up tracing if it's not suppressed.
770                          my ($package, $fileName, $line) = caller;      ETracing($cgi) unless $noTrace;
771              # If there is no calling package, we default to "main".      # Create the variable hash.
772                          if (!$package) {      my $varHash = { results => '' };
773                  $category = "main";      # Return the query object and variable hash.
774        return ($cgi, $varHash);
775    }
776    
777    =head3 ETracing
778    
779        ETracing($parameter);
780    
781    Set up emergency tracing. Emergency tracing is tracing that is turned
782    on automatically for any program that calls this method. The emergency
783    tracing parameters are stored in a a file identified by a tracing key.
784    If this method is called with a CGI object, then the tracing key is
785    taken from a cookie. If it is called with no parameters, then the tracing
786    key is taken from an environment variable. If it is called with a string,
787    the tracing key is that string.
788    
789    =over 4
790    
791    =item parameter
792    
793    A parameter from which the tracing key is computed. If it is a scalar,
794    that scalar is used as the tracing key. If it is a CGI object, the
795    tracing key is taken from the C<IP> cookie. If it is omitted, the
796    tracing key is taken from the C<TRACING> environment variable. If it
797    is a CGI object and emergency tracing is not on, the C<Trace> and
798    C<TF> parameters will be used to determine the type of tracing.
799    
800    =back
801    
802    =cut
803    
804    sub ETracing {
805        # Get the parameter.
806        my ($parameter) = @_;
807        # Check for CGI mode.
808        my $cgi = (ref $parameter eq 'CGI' ? $parameter : undef);
809        # Default to no tracing except errors.
810        my ($tracing, $dest) = ("0", "WARN");
811        # Check for emergency tracing.
812        my $tkey = EmergencyKey($parameter);
813        my $emergencyFile = EmergencyFileName($tkey);
814        if (-e $emergencyFile) {
815            # We have the file. Read in the data.
816            my @tracing = GetFile($emergencyFile);
817            # Pull off the time limit.
818            my $expire = shift @tracing;
819            # Convert it to seconds.
820            $expire *= 3600;
821            # Check the file data.
822            my $stat = stat($emergencyFile);
823            my ($now) = gettimeofday;
824            if ($now - $stat->mtime > $expire) {
825                # Delete the expired file.
826                unlink $emergencyFile;
827                          } else {                          } else {
828                                  $category = $package;              # Emergency tracing is on. Pull off the destination and
829                # the trace level;
830                $dest = shift @tracing;
831                my $level = shift @tracing;
832                # Convert the destination to a real tracing destination.
833                # temp directory.
834                $dest = EmergencyTracingDest($tkey, $dest);
835                # Insure Tracer is specified.
836                my %moduleHash = map { $_ => 1 } @tracing;
837                $moduleHash{Tracer} = 1;
838                # Set the trace parameter.
839                $tracing = join(" ", $level, sort keys %moduleHash);
840            }
841        } elsif (defined $cgi) {
842            # There's no emergency tracing, but we have a CGI object, so check
843            # for tracing from the form parameters.
844            if ($cgi->param('Trace')) {
845                # Here the user has requested tracing via a form.
846                $dest = ($cgi->param('TF') ? ">$FIG_Config::temp/Trace$$.log" : "QUEUE");
847                $tracing = $cgi->param('Trace') . " Tracer";
848            }
849        }
850        # Setup the tracing we've determined from all the stuff above.
851        TSetup($tracing, $dest);
852        # Check to see if we're a web script.
853        if (defined $cgi) {
854            # Yes we are. Trace the form and environment data.
855            TraceParms($cgi);
856            # Check for RAW mode. In raw mode, we print a fake header so that we see everything
857            # emitted by the script in its raw form.
858            if (T(Raw => 3)) {
859                print CGI::header(-type => 'text/plain', -tracing => 'Raw');
860                          }                          }
861                  }                  }
                 # Use the package and tracelevel to compute the result.  
                 $retVal = ($traceLevel <= $TraceLevel && exists $Categories{$category});  
862      }      }
863          # Return the computed result.  
864      return $retVal;  =head3 EmergencyFileName
865    
866        my $fileName = Tracer::EmergencyFileName($tkey);
867    
868    Return the emergency tracing file name. This is the file that specifies
869    the tracing information.
870    
871    =over 4
872    
873    =item tkey
874    
875    Tracing key for the current program.
876    
877    =item RETURN
878    
879    Returns the name of the file to contain the emergency tracing information.
880    
881    =back
882    
883    =cut
884    
885    sub EmergencyFileName {
886        # Get the parameters.
887        my ($tkey) = @_;
888        # Compute the emergency tracing file name.
889        return "$FIG_Config::temp/Emergency$tkey.txt";
890  }  }
891    
892  =head3 ParseCommand  =head3 EmergencyFileTarget
893    
894  C<< my ($options, @arguments) = Tracer::ParseCommand(\%optionTable, @inputList); >>      my $fileName = Tracer::EmergencyFileTarget($tkey);
895    
896  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
897  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.  
898    
899  C<< my ($options, @arguments) = ParseCommand({ errors => 0, logFile => 'trace.log'}, @words); >>  =over 4
900    
901  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  
902    
903  C<< -logFile=error.log apple orange rutabaga >>  Tracing key for the current program.
904    
905  then at the end of the invocation, C<$options> will be  =item RETURN
906    
907  C<< { errors => 0, logFile => 'error.log' } >>  Returns the name of the file to contain the trace output.
908    
909  and C<@arguments> will contain  =back
910    
911  C<< apple orange rutabaga >>  =cut
912    
913  The parser allows for some escape sequences. See L</UnEscape> for a description. There is no  sub EmergencyFileTarget {
914  support for quote characters.      # Get the parameters.
915        my ($tkey) = @_;
916        # Compute the emergency tracing file name.
917        return "$FIG_Config::temp/trace$tkey.log";
918    }
919    
920    =head3 EmergencyTracingDest
921    
922        my $dest = Tracer::EmergencyTracingDest($tkey, $myDest);
923    
924    This method converts an emergency tracing destination to a real
925    tracing destination. The main difference is that if the
926    destination is C<FILE> or C<APPEND>, we convert it to file
927    output. If the destination is C<DUAL>, we convert it to file
928    and standard output.
929    
930  =over 4  =over 4
931    
932  =item optionTable  =item tkey
933    
934  Table of default options.  Tracing key for this environment.
935    
936  =item inputList  =item myDest
937    
938  List of words on the command line.  Destination from the emergency tracing file.
939    
940  =item RETURN  =item RETURN
941    
942  Returns a reference to the option table and a list of the positional arguments.  Returns a destination that can be passed into L</TSetup>.
943    
944  =back  =back
945    
946  =cut  =cut
947    
948  sub ParseCommand {  sub EmergencyTracingDest {
949          # Get the parameters.          # Get the parameters.
950          my ($optionTable, @inputList) = @_;      my ($tkey, $myDest) = @_;
951          # Process any options in the input list.      # Declare the return variable.
952          my %overrides = ();      my $retVal = $myDest;
953          while ((@inputList > 0) && ($inputList[0] =~ /^-/)) {      # Process according to the destination value.
954                  # Get the current option.      if ($myDest eq 'FILE') {
955                  my $arg = shift @inputList;          $retVal = ">" . EmergencyFileTarget($tkey);
956                  # Pull out the option name.      } elsif ($myDest eq 'APPEND') {
957                  $arg =~ /^-([^=]*)/g;          $retVal = ">>" . EmergencyFileTarget($tkey);
958                  my $name = $1;      } elsif ($myDest eq 'DUAL') {
959                  # 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;  
                 }  
960          }          }
961          # Merge the options into the defaults.      # Return the result.
962          GetOptions($optionTable, \%overrides);      return $retVal;
         # Translate the remaining parameters.  
         my @retVal = ();  
         for my $inputParm (@inputList) {  
                 push @retVal, UnEscape($inputParm);  
963          }          }
964          # Return the results.  
965          return ($optionTable, @retVal);  =head3 Emergency
966    
967        Emergency($key, $hours, $dest, $level, @modules);
968    
969    Turn on emergency tracing. This method is normally invoked over the web from
970    a debugging console, but it can also be called by the C<trace.pl> script.
971    The caller specifies the duration of the emergency in hours, the desired tracing
972    destination, the trace level, and a list of the trace modules to activate.
973    For the length of the duration, when a program in an environment with the
974    specified tracing key active invokes a Sprout CGI script, tracing will be
975    turned on automatically. See L</TSetup> for more about tracing setup and
976    L</ETracing> for more about emergency tracing.
977    
978    =over 4
979    
980    =item tkey
981    
982    The tracing key. This is used to identify the control file and the trace file.
983    
984    =item hours
985    
986    Number of hours to keep emergency tracing alive.
987    
988    =item dest
989    
990    Tracing destination. If no path information is specified for a file
991    destination, it is put in the FIG temporary directory.
992    
993    =item level
994    
995    Tracing level. A higher level means more trace messages.
996    
997    =item modules
998    
999    A list of the tracing modules to activate.
1000    
1001    =back
1002    
1003    =cut
1004    
1005    sub Emergency {
1006        # Get the parameters.
1007        my ($tkey, $hours, $dest, $level, @modules) = @_;
1008        # Create the emergency file.
1009        my $specFile = EmergencyFileName($tkey);
1010        my $outHandle = Open(undef, ">$specFile");
1011        print $outHandle join("\n", $hours, $dest, $level, @modules, "");
1012  }  }
1013    
1014  =head3 UnEscape  =head3 EmergencyKey
1015    
1016  C<< my $realString = Tracer::UnEscape($codedString); >>      my $tkey = EmergencyKey($parameter);
1017    
1018  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,
1019  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.
1020    
1021  =over 4  =over 4
1022    
1023  =item codedString  =item parameter
1024    
1025  String to un-escape.  Parameter defining the method for finding the tracing key. If it is a scalar,
1026    then it is presumed to be the tracing key itself. If it is a CGI object, then
1027    the tracing key is taken from the C<IP> cookie. Otherwise, the tracing key is
1028    taken from the C<TRACING> environment variable.
1029    
1030  =item RETURN  =item RETURN
1031    
1032  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.
1033  values.  
1034    =back
1035    
1036    =cut
1037    
1038    sub EmergencyKey {
1039        # Get the parameters.
1040        my ($parameter) = @_;
1041        # Declare the return variable.
1042        my $retVal;
1043        # Determine the parameter type.
1044        if (! defined $parameter) {
1045            # Here we're supposed to check the environment.
1046            $retVal = $ENV{TRACING};
1047        } else {
1048            my $ptype = ref $parameter;
1049            if ($ptype eq 'CGI') {
1050                # Here we were invoked from a web page. Look for a cookie.
1051                $retVal = $parameter->cookie('IP');
1052            } elsif (! $ptype) {
1053                # Here the key was passed in.
1054                $retVal = $parameter;
1055            }
1056        }
1057        # If no luck finding a key, use the PID.
1058        if (! defined $retVal) {
1059            $retVal = $$;
1060        }
1061        # Return the result.
1062        return $retVal;
1063    }
1064    
1065    
1066    =head3 TraceParms
1067    
1068        Tracer::TraceParms($cgi);
1069    
1070    Trace the CGI parameters at trace level CGI => 3 and the environment variables
1071    at level CGI => 4. A self-referencing URL is traced at level CGI => 2.
1072    
1073    =over 4
1074    
1075    =item cgi
1076    
1077    CGI query object containing the parameters to trace.
1078    
1079    =back
1080    
1081    =cut
1082    
1083    sub TraceParms {
1084        # Get the parameters.
1085        my ($cgi) = @_;
1086        if (T(CGI => 2)) {
1087            # Here we trace the GET-style URL for the script.
1088            Trace("URL: " . $cgi->url(-relative => 1, -query => 1));
1089        }
1090        if (T(CGI => 3)) {
1091            # Here we want to trace the parameter data.
1092            my @names = $cgi->param;
1093            for my $parmName (sort @names) {
1094                # Note we skip the Trace parameters, which are for our use only.
1095                if ($parmName ne 'Trace' && $parmName ne 'TF') {
1096                    my @values = $cgi->param($parmName);
1097                    Trace("CGI: $parmName = " . join(", ", @values));
1098                }
1099            }
1100            # Display the request method.
1101            my $method = $cgi->request_method();
1102            Trace("Method: $method");
1103        }
1104        if (T(CGI => 4)) {
1105            # Here we want the environment data too.
1106            for my $envName (sort keys %ENV) {
1107                Trace("ENV: $envName = $ENV{$envName}");
1108            }
1109        }
1110    }
1111    
1112    =head3 TraceImages
1113    
1114        Tracer::TraceImages($htmlString);
1115    
1116    Trace information about all of an html document's images. The tracing
1117    will be for type "IMG" at level 3. The image's source string
1118    will be displayed. This is generally either the URL of the image or
1119    raw data for the image itself. If the source is too long, only the first 300
1120    characters will be shown at trace level 3. The entire source will be shown,
1121    however, at trace level 4. This method is not very smart, and might catch
1122    Javascript code, but it is still useful when debugging the arcane
1123    behavior of images in multiple browser environments.
1124    
1125    =over 4
1126    
1127    =item htmlString
1128    
1129    HTML text for an outgoing web page.
1130    
1131    =back
1132    
1133    =cut
1134    
1135    sub TraceImages {
1136        # Only proceed if we're at the proper trace level.
1137        if (T(IMG => 3)) {
1138            # For performance reasons we're manipulating $_[0] instead of retrieving the string
1139            # into a variable called "$htmlString". This is because we expect html strings to be
1140            # long, and don't want to copy them any more than we have to.
1141            Trace(length($_[0]) . " characters in web page.");
1142            # Loop through the HTML, culling image tags.
1143            while ($_[0] =~ /<img\s+[^>]+?src="([^"]+)"/sgi) {
1144                # Extract the source string and determine whether or not it's too long.
1145                my $srcString = $1;
1146                my $pos = pos($_[0]) - length($srcString);
1147                my $excess = length($srcString) - 300;
1148                # We'll put the display string in here.
1149                my $srcDisplay = $srcString;
1150                # If it's a data string, split it at the comma.
1151                $srcDisplay =~ s/^(data[^,]+,)/$1\n/;
1152                # If there's no excess or we're at trace level 4, we're done. At level 3 with
1153                # a long string, however, we only show the first 300 characters.
1154                if ($excess > 0 && ! T(IMG => 4)) {
1155                    $srcDisplay = substr($srcDisplay,0,300) . "\nplus $excess characters.";
1156                }
1157                # Output the trace message.
1158                Trace("Image tag at position $pos:\n$srcDisplay");
1159            }
1160        }
1161    }
1162    
1163    
1164    =head3 ScriptFinish
1165    
1166        ScriptFinish($webData, $varHash);
1167    
1168    Output a web page at the end of a script. Either the string to be output or the
1169    name of a template file can be specified. If the second parameter is omitted,
1170    it is assumed we have a string to be output; otherwise, it is assumed we have the
1171    name of a template file. The template should have the variable C<DebugData>
1172    specified in any form that invokes a standard script. If debugging mode is turned
1173    on, a form field will be put in that allows the user to enter tracing data.
1174    Trace messages will be placed immediately before the terminal C<BODY> tag in
1175    the output, formatted as a list.
1176    
1177    A typical standard script would loook like the following.
1178    
1179        BEGIN {
1180            # Print the HTML header.
1181            print "CONTENT-TYPE: text/html\n\n";
1182        }
1183        use Tracer;
1184        use CGI;
1185        use FIG;
1186        # ... more uses ...
1187    
1188        my ($cgi, $varHash) = ScriptSetup();
1189        eval {
1190            # ... get data from $cgi, put it in $varHash ...
1191        };
1192        if ($@) {
1193            Trace("Script Error: $@") if T(0);
1194        }
1195        ScriptFinish("Html/MyTemplate.html", $varHash);
1196    
1197    The idea here is that even if the script fails, you'll see trace messages and
1198    useful output.
1199    
1200    =over 4
1201    
1202    =item webData
1203    
1204    A string containing either the full web page to be written to the output or the
1205    name of a template file from which the page is to be constructed. If the name
1206    of a template file is specified, then the second parameter must be present;
1207    otherwise, it must be absent.
1208    
1209    =item varHash (optional)
1210    
1211    If specified, then a reference to a hash mapping variable names for a template
1212    to their values. The template file will be read into memory, and variable markers
1213    will be replaced by data in this hash reference.
1214    
1215    =back
1216    
1217    =cut
1218    
1219    sub ScriptFinish {
1220        # Get the parameters.
1221        my ($webData, $varHash) = @_;
1222        # Check for a template file situation.
1223        my $outputString;
1224        if (defined $varHash) {
1225            # Here we have a template file. We need to determine the template type.
1226            my $template;
1227            if ($FIG_Config::template_url && $webData =~ /\.php$/) {
1228                $template = "$FIG_Config::template_url/$webData";
1229            } else {
1230                $template = "<<$webData";
1231            }
1232            $outputString = PageBuilder::Build($template, $varHash, "Html");
1233        } else {
1234            # Here the user gave us a raw string.
1235            $outputString = $webData;
1236        }
1237        # Check for trace messages.
1238        if ($Destination ne "NONE" && $TraceLevel > 0) {
1239            # We have trace messages, so we want to put them at the end of the body. This
1240            # is either at the end of the whole string or at the beginning of the BODY
1241            # end-tag.
1242            my $pos = length $outputString;
1243            if ($outputString =~ m#</body>#gi) {
1244                $pos = (pos $outputString) - 7;
1245            }
1246            # If the trace messages were queued, we unroll them. Otherwise, we display the
1247            # destination.
1248            my $traceHtml;
1249            if ($Destination eq "QUEUE") {
1250                $traceHtml = QTrace('Html');
1251            } elsif ($Destination =~ /^>>(.+)$/) {
1252                # Here the tracing output it to a file. We code it as a hyperlink so the user
1253                # can copy the file name into the clipboard easily.
1254                my $actualDest = $1;
1255                $traceHtml = "<p>Tracing output to $actualDest.</p>\n";
1256            } else {
1257                # Here we have one of the special destinations.
1258                $traceHtml = "<P>Tracing output type is $Destination.</p>\n";
1259            }
1260            substr $outputString, $pos, 0, $traceHtml;
1261        }
1262        # Write the output string.
1263        print $outputString;
1264    }
1265    
1266    =head2 Command-Line Utility Methods
1267    
1268    =head3 SendSMS
1269    
1270        my $msgID = Tracer::SendSMS($phoneNumber, $msg);
1271    
1272    Send a text message to a phone number using Clickatell. The FIG_Config file must contain the
1273    user name, password, and API ID for the relevant account in the hash reference variable
1274    I<$FIG_Config::phone>, using the keys C<user>, C<password>, and C<api_id>. For
1275    example, if the user name is C<BruceTheHumanPet>, the password is C<silly>, and the API ID
1276    is C<2561022>, then the FIG_Config file must contain
1277    
1278        $phone =  { user => 'BruceTheHumanPet',
1279                    password => 'silly',
1280                    api_id => '2561022' };
1281    
1282    The original purpose of this method was to insure Bruce would be notified immediately when the
1283    Sprout Load terminates. Care should be taken if you do not wish Bruce to be notified immediately
1284    when you call this method.
1285    
1286    The message ID will be returned if successful, and C<undef> if an error occurs.
1287    
1288    =over 4
1289    
1290    =item phoneNumber
1291    
1292    Phone number to receive the message, in international format. A United States phone number
1293    would be prefixed by "1". A British phone number would be prefixed by "44".
1294    
1295    =item msg
1296    
1297    Message to send to the specified phone.
1298    
1299    =item RETURN
1300    
1301    Returns the message ID if successful, and C<undef> if the message could not be sent.
1302    
1303    =back
1304    
1305    =cut
1306    
1307    sub SendSMS {
1308        # Get the parameters.
1309        my ($phoneNumber, $msg) = @_;
1310        # Declare the return variable. If we do not change it, C<undef> will be returned.
1311        my $retVal;
1312        # Only proceed if we have phone support.
1313        if (! defined $FIG_Config::phone) {
1314            Trace("Phone support not present in FIG_Config.") if T(1);
1315        } else {
1316            # Get the phone data.
1317            my $parms = $FIG_Config::phone;
1318            # Get the Clickatell URL.
1319            my $url = "http://api.clickatell.com/http/";
1320            # Create the user agent.
1321            my $ua = LWP::UserAgent->new;
1322            # Request a Clickatell session.
1323            my $resp = $ua->post("$url/sendmsg", { user => $parms->{user},
1324                                         password => $parms->{password},
1325                                         api_id => $parms->{api_id},
1326                                         to => $phoneNumber,
1327                                         text => $msg});
1328            # Check for an error.
1329            if (! $resp->is_success) {
1330                Trace("Alert failed.") if T(1);
1331            } else {
1332                # Get the message ID.
1333                my $rstring = $resp->content;
1334                if ($rstring =~ /^ID:\s+(.*)$/) {
1335                    $retVal = $1;
1336                } else {
1337                    Trace("Phone attempt failed with $rstring") if T(1);
1338                }
1339            }
1340        }
1341        # Return the result.
1342        return $retVal;
1343    }
1344    
1345    =head3 StandardSetup
1346    
1347        my ($options, @parameters) = StandardSetup(\@categories, \%options, $parmHelp, @ARGV);
1348    
1349    This method performs standard command-line parsing and tracing setup. The return
1350    values are a hash of the command-line options and a list of the positional
1351    parameters. Tracing is automatically set up and the command-line options are
1352    validated.
1353    
1354    This is a complex method that does a lot of grunt work. The parameters can
1355    be more easily understood, however, once they are examined individually.
1356    
1357    The I<categories> parameter is the most obtuse. It is a reference to a list of
1358    special-purpose tracing categories. Most tracing categories are PERL package
1359    names. So, for example, if you wanted to turn on tracing inside the B<Sprout>,
1360    B<ERDB>, and B<SproutLoad> packages, you would specify the categories
1361    
1362        ["Sprout", "SproutLoad", "ERDB"]
1363    
1364    This would cause trace messages in the specified three packages to appear in
1365    the output. There are two special tracing categories that are automatically
1366    handled by this method. In other words, if you used L</TSetup> you would need
1367    to include these categories manually, but if you use this method they are turned
1368    on automatically.
1369    
1370    =over 4
1371    
1372    =item SQL
1373    
1374    Traces SQL commands and activity.
1375    
1376    =item Tracer
1377    
1378    Traces error messages and call stacks.
1379    
1380    =back
1381    
1382    C<SQL> is only turned on if the C<-sql> option is specified in the command line.
1383    The trace level is specified using the C<-trace> command-line option. For example,
1384    the following command line for C<TransactFeatures> turns on SQL tracing and runs
1385    all tracing at level 3.
1386    
1387        TransactFeatures -trace=3 -sql register ../xacts IDs.tbl
1388    
1389    Standard tracing is output to the standard output and echoed to the file
1390    C<trace>I<$$>C<.log> in the FIG temporary directory, where I<$$> is the
1391    process ID. You can also specify the C<user> parameter to put a user ID
1392    instead of a process ID in the trace file name. So, for example
1393    
1394    The default trace level is 2. To get all messages, specify a trace level of 4.
1395    For a genome-by-genome update, use 3.
1396    
1397        TransactFeatures -trace=3 -sql -user=Bruce register ../xacts IDs.tbl
1398    
1399    would send the trace output to C<traceBruce.log> in the temporary directory.
1400    
1401    The I<options> parameter is a reference to a hash containing the command-line
1402    options, their default values, and an explanation of what they mean. Command-line
1403    options may be in the form of switches or keywords. In the case of a switch, the
1404    option value is 1 if it is specified and 0 if it is not specified. In the case
1405    of a keyword, the value is separated from the option name by an equal sign. You
1406    can see this last in the command-line example above.
1407    
1408    You can specify a different default trace level by setting C<$options->{trace}>
1409    prior to calling this method.
1410    
1411    An example at this point would help. Consider, for example, the command-line utility
1412    C<TransactFeatures>. It accepts a list of positional parameters plus the options
1413    C<safe>, C<noAlias>, C<start>, and C<tblFiles>. To start up this command, we execute
1414    the following code.
1415    
1416        my ($options, @parameters) = Tracer::StandardSetup(["DocUtils"],
1417                            { safe => [0, "use database transactions"],
1418                              noAlias => [0, "do not expect aliases in CHANGE transactions"],
1419                              start => [' ', "start with this genome"],
1420                              tblFiles => [0, "output TBL files containing the corrected IDs"] },
1421                            "<command> <transactionDirectory> <IDfile>",
1422                          @ARGV);
1423    
1424    
1425    The call to C<ParseCommand> specifies the default values for the options and
1426    stores the actual options in a hash that is returned as C<$options>. The
1427    positional parameters are returned in C<@parameters>.
1428    
1429    The following is a sample command line for C<TransactFeatures>.
1430    
1431        TransactFeatures -trace=2 -noAlias register ../xacts IDs.tbl
1432    
1433    Single and double hyphens are equivalent. So, you could also code the
1434    above command as
1435    
1436        TransactFeatures --trace=2 --noAlias register ../xacts IDs.tbl
1437    
1438    In this case, C<register>, C<../xacts>, and C<IDs.tbl> are the positional
1439    parameters, and would find themselves in I<@parameters> after executing the
1440    above code fragment. The tracing would be set to level 2, and the categories
1441    would be C<Tracer>, and <DocUtils>. C<Tracer> is standard,
1442    and C<DocUtils> was included because it came in within the first parameter
1443    to this method. The I<$options> hash would be
1444    
1445        { trace => 2, sql => 0, safe => 0,
1446          noAlias => 1, start => ' ', tblFiles => 0 }
1447    
1448    Use of C<StandardSetup> in this way provides a simple way of performing
1449    standard tracing setup and command-line parsing. Note that the caller is
1450    not even aware of the command-line switches C<-trace> and C<-sql>, which
1451    are used by this method to control the tracing. If additional tracing features
1452    need to be added in the future, they can be processed by this method without
1453    upsetting the command-line utilities.
1454    
1455    If the C<background> option is specified on the command line, then the
1456    standard and error outputs will be directed to files in the temporary
1457    directory, using the same suffix as the trace file. So, if the command
1458    line specified
1459    
1460        -user=Bruce -background
1461    
1462    then the trace output would go to C<traceBruce.log>, the standard output to
1463    C<outBruce.log>, and the error output to C<errBruce.log>. This is designed to
1464    simplify starting a command in the background.
1465    
1466    The user name is also used as the tracing key for L</Emergency Tracing>.
1467    Specifying a value of C<E> for the trace level causes emergency tracing to
1468    be used instead of custom tracing. If the user name is not specified,
1469    the tracing key is taken from the C<Tracing> environment variable. If there
1470    is no value for that variable, the tracing key will be computed from the PID.
1471    
1472    Finally, if the special option C<-help> is specified, the option
1473    names will be traced at level 0 and the program will exit without processing.
1474    This provides a limited help capability. For example, if the user enters
1475    
1476        TransactFeatures -help
1477    
1478    he would see the following output.
1479    
1480        TransactFeatures [options] <command> <transactionDirectory> <IDfile>
1481            -trace    tracing level (default E)
1482            -sql      trace SQL commands
1483            -safe     use database transactions
1484            -noAlias  do not expect aliases in CHANGE transactions
1485            -start    start with this genome
1486            -tblFiles output TBL files containing the corrected IDs
1487    
1488    The caller has the option of modifying the tracing scheme by placing a value
1489    for C<trace> in the incoming options hash. The default value can be overridden,
1490    or the tracing to the standard output can be turned off by suffixing a minus
1491    sign to the trace level. So, for example,
1492    
1493        { trace => [0, "tracing level (default 0)"],
1494           ...
1495    
1496    would set the default trace level to 0 instead of E, while
1497    
1498        { trace => ["2-", "tracing level (default 2)"],
1499           ...
1500    
1501    would set the default to 2, but trace only to the log file, not to the
1502    standard output.
1503    
1504    The parameters to this method are as follows.
1505    
1506    =over 4
1507    
1508    =item categories
1509    
1510    Reference to a list of tracing category names. These should be names of
1511    packages whose internal workings will need to be debugged to get the
1512    command working.
1513    
1514    =item options
1515    
1516    Reference to a hash containing the legal options for the current command mapped
1517    to their default values and descriptions. The user can override the defaults
1518    by specifying the options as command-line switches prefixed by a hyphen.
1519    Tracing-related options may be added to this hash. If the C<-h> option is
1520    specified on the command line, the option descriptions will be used to
1521    explain the options. To turn off tracing to the standard output, add a
1522    minus sign to the value for C<trace> (see above).
1523    
1524    =item parmHelp
1525    
1526    A string that vaguely describes the positional parameters. This is used
1527    if the user specifies the C<-h> option.
1528    
1529    =item argv
1530    
1531    List of command line parameters, including the option switches, which must
1532    precede the positional parameters and be prefixed by a hyphen.
1533    
1534    =item RETURN
1535    
1536    Returns a list. The first element of the list is the reference to a hash that
1537    maps the command-line option switches to their values. These will either be the
1538    default values or overrides specified on the command line. The remaining
1539    elements of the list are the position parameters, in order.
1540    
1541    =back
1542    
1543    =cut
1544    
1545    sub StandardSetup {
1546        # Get the parameters.
1547        my ($categories, $options, $parmHelp, @argv) = @_;
1548        # Get the default tracing key.
1549        my $tkey = EmergencyKey();
1550        # Add the tracing options.
1551        if (! exists $options->{trace}) {
1552            $options->{trace} = ['2', "tracing level (E for emergency tracing)"];
1553        }
1554        $options->{sql} = [0, "turn on SQL tracing"];
1555        $options->{help} = [0, "display command-line options"];
1556        $options->{user} = [$tkey, "tracing key"];
1557        $options->{background} = [0, "spool standard and error output"];
1558        # Create a parsing hash from the options hash. The parsing hash
1559        # contains the default values rather than the default value
1560        # and the description. While we're at it, we'll memorize the
1561        # length of the longest option name.
1562        my $longestName = 0;
1563        my %parseOptions = ();
1564        for my $key (keys %{$options}) {
1565            if (length $key > $longestName) {
1566                $longestName = length $key;
1567            }
1568            $parseOptions{$key} = $options->{$key}->[0];
1569        }
1570        # Parse the command line.
1571        my ($retOptions, @retParameters) = ParseCommand(\%parseOptions, @argv);
1572        # Get the logfile suffix.
1573        my $suffix = $retOptions->{user};
1574        # Check for background mode.
1575        if ($retOptions->{background}) {
1576            my $outFileName = "$FIG_Config::temp/out$suffix.log";
1577            my $errFileName = "$FIG_Config::temp/err$suffix.log";
1578            open STDOUT, ">$outFileName";
1579            open STDERR, ">$errFileName";
1580            # Check for phone support. If we have phone support and a phone number,
1581            # we want to turn it on.
1582            if ($ENV{PHONE} && defined($FIG_Config::phone)) {
1583                $retOptions->{phone} = $ENV{PHONE};
1584            }
1585        }
1586        # Now we want to set up tracing. First, we need to know if the user
1587        # wants emergency tracing.
1588        if ($retOptions->{trace} eq 'E') {
1589            ETracing($retOptions->{user});
1590        } else {
1591            # Here the tracing is controlled from the command line.
1592            my @cats = @{$categories};
1593            if ($retOptions->{sql}) {
1594                push @cats, "SQL";
1595            }
1596            # Add the default categories.
1597            push @cats, "Tracer";
1598            # Next, we create the category string by joining the categories.
1599            my $cats = join(" ", @cats);
1600            # Check to determine whether or not the caller wants to turn off tracing
1601            # to the standard output.
1602            my $traceLevel = $retOptions->{trace};
1603            my $textOKFlag = 1;
1604            if ($traceLevel =~ /^(.)-/) {
1605                $traceLevel = $1;
1606                $textOKFlag = 0;
1607            }
1608            # Now we set up the trace mode.
1609            my $traceMode;
1610            # Verify that we can open a file in the FIG temporary directory.
1611            my $traceFileName = "$FIG_Config::temp/trace$suffix.log";
1612            if (open TESTTRACE, ">$traceFileName") {
1613                # Here we can trace to a file.
1614                $traceMode = ">$traceFileName";
1615                if ($textOKFlag) {
1616                    # Echo to standard output if the text-OK flag is set.
1617                    $traceMode = "+$traceMode";
1618                }
1619                # Close the test file.
1620                close TESTTRACE;
1621            } else {
1622                # Here we can't trace to a file. We trace to the standard output if it's
1623                # okay, and the error log otherwise.
1624                if ($textOKFlag) {
1625                    $traceMode = "TEXT";
1626                } else {
1627                    $traceMode = "WARN";
1628                }
1629            }
1630            # Now set up the tracing.
1631            TSetup("$traceLevel $cats", $traceMode);
1632        }
1633        # Check for the "help" option. If it is specified, dump the command-line
1634        # options and exit the program.
1635        if ($retOptions->{help}) {
1636            $0 =~ m#[/\\](\w+)(\.pl)?$#i;
1637            print "$1 [options] $parmHelp\n";
1638            for my $key (sort keys %{$options}) {
1639                my $name = Pad($key, $longestName, 0, ' ');
1640                my $desc = $options->{$key}->[1];
1641                if ($options->{$key}->[0]) {
1642                    $desc .= " (default " . $options->{$key}->[0] . ")";
1643                }
1644                print "  $name $desc\n";
1645            }
1646            exit(0);
1647        }
1648        # Trace the options, if applicable.
1649        if (T(3)) {
1650            my @parms = grep { $retOptions->{$_} } keys %{$retOptions};
1651            Trace("Selected options: " . join(", ", sort @parms) . ".");
1652        }
1653        # Return the parsed parameters.
1654        return ($retOptions, @retParameters);
1655    }
1656    
1657    =head3 ReadOptions
1658    
1659        my %options = Tracer::ReadOptions($fileName);
1660    
1661    Read a set of options from a file. Each option is encoded in a line of text that has the
1662    format
1663    
1664    I<optionName>C<=>I<optionValue>C<; >I<comment>
1665    
1666    The option name must consist entirely of letters, digits, and the punctuation characters
1667    C<.> and C<_>, and is case sensitive. Blank lines and lines in which the first nonblank
1668    character is a semi-colon will be ignored. The return hash will map each option name to
1669    the corresponding option value.
1670    
1671    =over 4
1672    
1673    =item fileName
1674    
1675    Name of the file containing the option data.
1676    
1677    =item RETURN
1678    
1679    Returns a hash mapping the option names specified in the file to their corresponding option
1680    value.
1681    
1682    =back
1683    
1684    =cut
1685    
1686    sub ReadOptions {
1687        # Get the parameters.
1688        my ($fileName) = @_;
1689        # Open the file.
1690        (open CONFIGFILE, "<$fileName") || Confess("Could not open option file $fileName.");
1691        # Count the number of records read.
1692        my ($records, $comments) = 0;
1693        # Create the return hash.
1694        my %retVal = ();
1695        # Loop through the file, accumulating key-value pairs.
1696        while (my $line = <CONFIGFILE>) {
1697            # Denote we've read a line.
1698            $records++;
1699            # Determine the line type.
1700            if ($line =~ /^\s*[\n\r]/) {
1701                # A blank line is a comment.
1702                $comments++;
1703            } elsif ($line =~ /^\s*([A-Za-z0-9_\.]+)=([^;]*);/) {
1704                # Here we have an option assignment.
1705                retVal{$1} = $2;
1706            } elsif ($line =~ /^\s*;/) {
1707                # Here we have a text comment.
1708                $comments++;
1709            } else {
1710                # Here we have an invalid line.
1711                Trace("Invalid option statement in record $records.") if T(0);
1712            }
1713        }
1714        # Return the hash created.
1715        return %retVal;
1716    }
1717    
1718    =head3 GetOptions
1719    
1720        Tracer::GetOptions(\%defaults, \%options);
1721    
1722    Merge a specified set of options into a table of defaults. This method takes two hash references
1723    as input and uses the data from the second to update the first. If the second does not exist,
1724    there will be no effect. An error will be thrown if one of the entries in the second hash does not
1725    exist in the first.
1726    
1727    Consider the following example.
1728    
1729        my $optionTable = GetOptions({ dbType => 'mySQL', trace => 0 }, $options);
1730    
1731    In this example, the variable B<$options> is expected to contain at most two options-- B<dbType> and
1732    B<trace>. The default database type is C<mySQL> and the default trace level is C<0>. If the value of
1733    B<$options> is C<< {dbType => 'Oracle'} >>, then the database type will be changed to C<Oracle> and
1734    the trace level will remain at 0. If B<$options> is undefined, then the database type and trace level
1735    will remain C<mySQL> and C<0>. If, on the other hand, B<$options> is defined as
1736    
1737        {databaseType => 'Oracle'}
1738    
1739    an error will occur because the B<databaseType> option does not exist.
1740    
1741    =over 4
1742    
1743    =item defaults
1744    
1745    Table of default option values.
1746    
1747    =item options
1748    
1749    Table of overrides, if any.
1750    
1751    =item RETURN
1752    
1753    Returns a reference to the default table passed in as the first parameter.
1754    
1755    =back
1756    
1757    =cut
1758    
1759    sub GetOptions {
1760        # Get the parameters.
1761        my ($defaults, $options) = @_;
1762        # Check for overrides.
1763        if ($options) {
1764            # Loop through the overrides.
1765            while (my ($option, $setting) = each %{$options}) {
1766                # Insure this override exists.
1767                if (!exists $defaults->{$option}) {
1768                    croak "Unrecognized option $option encountered.";
1769                } else {
1770                    # Apply the override.
1771                    $defaults->{$option} = $setting;
1772                }
1773            }
1774        }
1775        # Return the merged table.
1776        return $defaults;
1777    }
1778    
1779    =head3 MergeOptions
1780    
1781        Tracer::MergeOptions(\%table, \%defaults);
1782    
1783    Merge default values into a hash table. This method looks at the key-value pairs in the
1784    second (default) hash, and if a matching key is not found in the first hash, the default
1785    pair is copied in. The process is similar to L</GetOptions>, but there is no error-
1786    checking and no return value.
1787    
1788    =over 4
1789    
1790    =item table
1791    
1792    Hash table to be updated with the default values.
1793    
1794    =item defaults
1795    
1796    Default values to be merged into the first hash table if they are not already present.
1797    
1798    =back
1799    
1800    =cut
1801    
1802    sub MergeOptions {
1803        # Get the parameters.
1804        my ($table, $defaults) = @_;
1805        # Loop through the defaults.
1806        while (my ($key, $value) = each %{$defaults}) {
1807            if (!exists $table->{$key}) {
1808                $table->{$key} = $value;
1809            }
1810        }
1811    }
1812    
1813    =head3 ParseCommand
1814    
1815        my ($options, @arguments) = Tracer::ParseCommand(\%optionTable, @inputList);
1816    
1817    Parse a command line consisting of a list of parameters. The initial parameters may be option
1818    specifiers of the form C<->I<option> or C<->I<option>C<=>I<value>. The options are stripped
1819    off and merged into a table of default options. The remainder of the command line is
1820    returned as a list of positional arguments. For example, consider the following invocation.
1821    
1822        my ($options, @arguments) = ParseCommand({ errors => 0, logFile => 'trace.log'}, @words);
1823    
1824    In this case, the list @words will be treated as a command line and there are two options available,
1825    B<errors> and B<logFile>. If @words has the following format
1826    
1827        -logFile=error.log apple orange rutabaga
1828    
1829    then at the end of the invocation, C<$options> will be
1830    
1831        { errors => 0, logFile => 'error.log' }
1832    
1833    and C<@arguments> will contain
1834    
1835        apple orange rutabaga
1836    
1837    The parser allows for some escape sequences. See L</UnEscape> for a description. There is no
1838    support for quote characters. Options can be specified with single or double hyphens.
1839    
1840    =over 4
1841    
1842    =item optionTable
1843    
1844    Table of default options.
1845    
1846    =item inputList
1847    
1848    List of words on the command line.
1849    
1850    =item RETURN
1851    
1852    Returns a reference to the option table and a list of the positional arguments.
1853    
1854    =back
1855    
1856    =cut
1857    
1858    sub ParseCommand {
1859        # Get the parameters.
1860        my ($optionTable, @inputList) = @_;
1861        # Process any options in the input list.
1862        my %overrides = ();
1863        while ((@inputList > 0) && ($inputList[0] =~ /^--?/)) {
1864            # Get the current option.
1865            my $arg = shift @inputList;
1866            # Pull out the option name.
1867            $arg =~ /^--?([^=]*)/g;
1868            my $name = $1;
1869            # Check for an option value.
1870            if ($arg =~ /\G=(.*)$/g) {
1871                # Here we have a value for the option.
1872                $overrides{$name} = UnEscape($1);
1873            } else {
1874                # Here there is no value, so we use 1.
1875                $overrides{$name} = 1;
1876            }
1877        }
1878        # Merge the options into the defaults.
1879        GetOptions($optionTable, \%overrides);
1880        # Translate the remaining parameters.
1881        my @retVal = ();
1882        for my $inputParm (@inputList) {
1883            push @retVal, UnEscape($inputParm);
1884        }
1885        # Return the results.
1886        return ($optionTable, @retVal);
1887    }
1888    
1889    
1890    =head2 File Utility Methods
1891    
1892    =head3 GetFile
1893    
1894        my @fileContents = Tracer::GetFile($fileName);
1895    
1896        or
1897    
1898        my $fileContents = Tracer::GetFile($fileName);
1899    
1900    Return the entire contents of a file. In list context, line-ends are removed and
1901    each line is a list element. In scalar context, line-ends are replaced by C<\n>.
1902    
1903    =over 4
1904    
1905    =item fileName
1906    
1907    Name of the file to read.
1908    
1909    =item RETURN
1910    
1911    In a list context, returns the entire file as a list with the line terminators removed.
1912    In a scalar context, returns the entire file as a string. If an error occurs opening
1913    the file, an empty list will be returned.
1914    
1915    =back
1916    
1917    =cut
1918    
1919    sub GetFile {
1920        # Get the parameters.
1921        my ($fileName) = @_;
1922        # Declare the return variable.
1923        my @retVal = ();
1924        # Open the file for input.
1925        my $handle = Open(undef, "<$fileName");
1926        # Read the whole file into the return variable, stripping off any terminator
1927        # characters.
1928        my $lineCount = 0;
1929        while (my $line = <$handle>) {
1930            $lineCount++;
1931            $line = Strip($line);
1932            push @retVal, $line;
1933        }
1934        # Close it.
1935        close $handle;
1936        my $actualLines = @retVal;
1937        Trace("$actualLines lines read from file $fileName.") if T(File => 2);
1938        # Return the file's contents in the desired format.
1939        if (wantarray) {
1940            return @retVal;
1941        } else {
1942            return join "\n", @retVal;
1943        }
1944    }
1945    
1946    =head3 PutFile
1947    
1948        Tracer::PutFile($fileName, \@lines);
1949    
1950    Write out a file from a list of lines of text.
1951    
1952    =over 4
1953    
1954    =item fileName
1955    
1956    Name of the output file.
1957    
1958    =item lines
1959    
1960    Reference to a list of text lines. The lines will be written to the file in order, with trailing
1961    new-line characters. Alternatively, may be a string, in which case the string will be written without
1962    modification.
1963    
1964    =back
1965    
1966    =cut
1967    
1968    sub PutFile {
1969        # Get the parameters.
1970        my ($fileName, $lines) = @_;
1971        # Open the output file.
1972        my $handle = Open(undef, ">$fileName");
1973        # Count the lines written.
1974        if (ref $lines ne 'ARRAY') {
1975            # Here we have a scalar, so we write it raw.
1976            print $handle $lines;
1977            Trace("Scalar put to file $fileName.") if T(File => 3);
1978        } else {
1979            # Write the lines one at a time.
1980            my $count = 0;
1981            for my $line (@{$lines}) {
1982                print $handle "$line\n";
1983                $count++;
1984            }
1985            Trace("$count lines put to file $fileName.") if T(File => 3);
1986        }
1987        # Close the output file.
1988        close $handle;
1989    }
1990    
1991    =head3 ParseRecord
1992    
1993        my @fields = Tracer::ParseRecord($line);
1994    
1995    Parse a tab-delimited data line. The data line is split into field values. Embedded tab
1996    and new-line characters in the data line must be represented as C<\t> and C<\n>, respectively.
1997    These will automatically be converted.
1998    
1999    =over 4
2000    
2001    =item line
2002    
2003    Line of data containing the tab-delimited fields.
2004    
2005    =item RETURN
2006    
2007    Returns a list of the fields found in the data line.
2008    
2009    =back
2010    
2011    =cut
2012    
2013    sub ParseRecord {
2014        # Get the parameter.
2015        my ($line) = @_;
2016        # Remove the trailing new-line, if any.
2017        chomp $line;
2018        # Split the line read into pieces using the tab character.
2019        my @retVal = split /\t/, $line;
2020        # Trim and fix the escapes in each piece.
2021        for my $value (@retVal) {
2022            # Trim leading whitespace.
2023            $value =~ s/^\s+//;
2024            # Trim trailing whitespace.
2025            $value =~ s/\s+$//;
2026            # Delete the carriage returns.
2027            $value =~ s/\r//g;
2028            # Convert the escapes into their real values.
2029            $value =~ s/\\t/"\t"/ge;
2030            $value =~ s/\\n/"\n"/ge;
2031        }
2032        # Return the result.
2033        return @retVal;
2034    }
2035    
2036    =head3 Merge
2037    
2038        my @mergedList = Tracer::Merge(@inputList);
2039    
2040    Sort a list of strings and remove duplicates.
2041    
2042    =over 4
2043    
2044    =item inputList
2045    
2046    List of scalars to sort and merge.
2047    
2048    =item RETURN
2049    
2050    Returns a list containing the same elements sorted in ascending order with duplicates
2051    removed.
2052    
2053    =back
2054    
2055    =cut
2056    
2057    sub Merge {
2058        # Get the input list in sort order.
2059        my @inputList = sort @_;
2060        # Only proceed if the list has at least two elements.
2061        if (@inputList > 1) {
2062            # Now we want to move through the list splicing out duplicates.
2063            my $i = 0;
2064            while ($i < @inputList) {
2065                # Get the current entry.
2066                my $thisEntry = $inputList[$i];
2067                # Find out how many elements duplicate the current entry.
2068                my $j = $i + 1;
2069                my $dup1 = $i + 1;
2070                while ($j < @inputList && $inputList[$j] eq $thisEntry) { $j++; };
2071                # If the number is nonzero, splice out the duplicates found.
2072                if ($j > $dup1) {
2073                    splice @inputList, $dup1, $j - $dup1;
2074                }
2075                # Now the element at position $dup1 is different from the element before it
2076                # at position $i. We push $i forward one position and start again.
2077                $i++;
2078            }
2079        }
2080        # Return the merged list.
2081        return @inputList;
2082    }
2083    
2084    =head3 Open
2085    
2086        my $handle = Open($fileHandle, $fileSpec, $message);
2087    
2088    Open a file.
2089    
2090    The I<$fileSpec> is essentially the second argument of the PERL C<open>
2091    function. The mode is specified using Unix-like shell information. So, for
2092    example,
2093    
2094        Open(\*LOGFILE, '>>/usr/spool/news/twitlog', "Could not open twit log.");
2095    
2096    would open for output appended to the specified file, and
2097    
2098        Open(\*DATASTREAM, "| sort -u >$outputFile", "Could not open $outputFile.");
2099    
2100    would open a pipe that sorts the records written and removes duplicates. Note
2101    the use of file handle syntax in the Open call. To use anonymous file handles,
2102    code as follows.
2103    
2104        my $logFile = Open(undef, '>>/usr/spool/news/twitlog', "Could not open twit log.");
2105    
2106    The I<$message> parameter is used if the open fails. If it is set to C<0>, then
2107    the open returns TRUE if successful and FALSE if an error occurred. Otherwise, a
2108    failed open will throw an exception and the third parameter will be used to construct
2109    an error message. If the parameter is omitted, a standard message is constructed
2110    using the file spec.
2111    
2112        Could not open "/usr/spool/news/twitlog"
2113    
2114    Note that the mode characters are automatically cleaned from the file name.
2115    The actual error message from the file system will be captured and appended to the
2116    message in any case.
2117    
2118        Could not open "/usr/spool/news/twitlog": file not found.
2119    
2120    In some versions of PERL the only error message we get is a number, which
2121    corresponds to the C++ C<errno> value.
2122    
2123        Could not open "/usr/spool/news/twitlog": 6.
2124    
2125    =over 4
2126    
2127    =item fileHandle
2128    
2129    File handle. If this parameter is C<undef>, a file handle will be generated
2130    and returned as the value of this method.
2131    
2132    =item fileSpec
2133    
2134    File name and mode, as per the PERL C<open> function.
2135    
2136    =item message (optional)
2137    
2138    Error message to use if the open fails. If omitted, a standard error message
2139    will be generated. In either case, the error information from the file system
2140    is appended to the message. To specify a conditional open that does not throw
2141    an error if it fails, use C<0>.
2142    
2143    =item RETURN
2144    
2145    Returns the name of the file handle assigned to the file, or C<undef> if the
2146    open failed.
2147    
2148    =back
2149    
2150    =cut
2151    
2152    sub Open {
2153        # Get the parameters.
2154        my ($fileHandle, $fileSpec, $message) = @_;
2155        # Attempt to open the file.
2156        my $rv = open $fileHandle, $fileSpec;
2157        # If the open failed, generate an error message.
2158        if (! $rv) {
2159            # Save the system error message.
2160            my $sysMessage = $!;
2161            # See if we need a default message.
2162            if (!$message) {
2163                # Clean any obvious mode characters and leading spaces from the
2164                # filename.
2165                my ($fileName) = FindNamePart($fileSpec);
2166                $message = "Could not open \"$fileName\"";
2167            }
2168            # Terminate with an error using the supplied message and the
2169            # error message from the file system.
2170            Confess("$message: $!");
2171        }
2172        # Return the file handle.
2173        return $fileHandle;
2174    }
2175    
2176    =head3 FindNamePart
2177    
2178        my ($fileName, $start, $len) = Tracer::FindNamePart($fileSpec);
2179    
2180    Extract the portion of a file specification that contains the file name.
2181    
2182    A file specification is the string passed to an C<open> call. It specifies the file
2183    mode and name. In a truly complex situation, it can specify a pipe sequence. This
2184    method assumes that the file name is whatever follows the first angle bracket
2185    sequence.  So, for example, in the following strings the file name is
2186    C</usr/fig/myfile.txt>.
2187    
2188        >>/usr/fig/myfile.txt
2189        </usr/fig/myfile.txt
2190        | sort -u > /usr/fig/myfile.txt
2191    
2192    If the method cannot find a file name using its normal methods, it will return the
2193    whole incoming string.
2194    
2195    =over 4
2196    
2197    =item fileSpec
2198    
2199    File specification string from which the file name is to be extracted.
2200    
2201    =item RETURN
2202    
2203    Returns a three-element list. The first element contains the file name portion of
2204    the specified string, or the whole string if a file name cannot be found via normal
2205    methods. The second element contains the start position of the file name portion and
2206    the third element contains the length.
2207    
2208    =back
2209    
2210    =cut
2211    #: Return Type $;
2212    sub FindNamePart {
2213        # Get the parameters.
2214        my ($fileSpec) = @_;
2215        # Default to the whole input string.
2216        my ($retVal, $pos, $len) = ($fileSpec, 0, length $fileSpec);
2217        # Parse out the file name if we can.
2218        if ($fileSpec =~ m/(<|>>?)(.+?)(\s*)$/) {
2219            $retVal = $2;
2220            $len = length $retVal;
2221            $pos = (length $fileSpec) - (length $3) - $len;
2222        }
2223        # Return the result.
2224        return ($retVal, $pos, $len);
2225    }
2226    
2227    =head3 OpenDir
2228    
2229        my @files = OpenDir($dirName, $filtered, $flag);
2230    
2231    Open a directory and return all the file names. This function essentially performs
2232    the functions of an C<opendir> and C<readdir>. If the I<$filtered> parameter is
2233    set to TRUE, all filenames beginning with a period (C<.>), dollar sign (C<$>),
2234    or pound sign (C<#>) and all filenames ending with a tilde C<~>) will be
2235    filtered out of the return list. If the directory does not open and I<$flag> is not
2236    set, an exception is thrown. So, for example,
2237    
2238        my @files = OpenDir("/Volumes/fig/contigs", 1);
2239    
2240    is effectively the same as
2241    
2242        opendir(TMP, "/Volumes/fig/contigs") || Confess("Could not open /Volumes/fig/contigs.");
2243        my @files = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir(TMP);
2244    
2245    Similarly, the following code
2246    
2247        my @files = grep { $_ =~ /^\d/ } OpenDir("/Volumes/fig/orgs", 0, 1);
2248    
2249    Returns the names of all files in C</Volumes/fig/orgs> that begin with digits and
2250    automatically returns an empty list if the directory fails to open.
2251    
2252    =over 4
2253    
2254    =item dirName
2255    
2256    Name of the directory to open.
2257    
2258    =item filtered
2259    
2260    TRUE if files whose names begin with a period (C<.>) should be automatically removed
2261    from the list, else FALSE.
2262    
2263    =item flag
2264    
2265    TRUE if a failure to open is okay, else FALSE
2266    
2267    =back
2268    
2269    =cut
2270    #: Return Type @;
2271    sub OpenDir {
2272        # Get the parameters.
2273        my ($dirName, $filtered, $flag) = @_;
2274        # Declare the return variable.
2275        my @retVal = ();
2276        # Open the directory.
2277        if (opendir(my $dirHandle, $dirName)) {
2278            # The directory opened successfully. Get the appropriate list according to the
2279            # strictures of the filter parameter.
2280            if ($filtered) {
2281                @retVal = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir $dirHandle;
2282            } else {
2283                @retVal = readdir $dirHandle;
2284            }
2285        } elsif (! $flag) {
2286            # Here the directory would not open and it's considered an error.
2287            Confess("Could not open directory $dirName.");
2288        }
2289        # Return the result.
2290        return @retVal;
2291    }
2292    
2293    
2294    =head3 Insure
2295    
2296        Insure($dirName, $chmod);
2297    
2298    Insure a directory is present.
2299    
2300    =over 4
2301    
2302    =item dirName
2303    
2304    Name of the directory to check. If it does not exist, it will be created.
2305    
2306    =item chmod (optional)
2307    
2308    Security privileges to be given to the directory if it is created.
2309    
2310    =back
2311    
2312    =cut
2313    
2314    sub Insure {
2315        my ($dirName, $chmod) = @_;
2316        if (! -d $dirName) {
2317            Trace("Creating $dirName directory.") if T(2);
2318            eval {
2319                mkpath $dirName;
2320                # If we have permissions specified, set them here.
2321                if (defined($chmod)) {
2322                    chmod $chmod, $dirName;
2323                }
2324            };
2325            if ($@) {
2326                Confess("Error creating $dirName: $@");
2327            }
2328        }
2329    }
2330    
2331    =head3 ChDir
2332    
2333        ChDir($dirName);
2334    
2335    Change to the specified directory.
2336    
2337    =over 4
2338    
2339    =item dirName
2340    
2341    Name of the directory to which we want to change.
2342    
2343    =back
2344    
2345    =cut
2346    
2347    sub ChDir {
2348        my ($dirName) = @_;
2349        if (! -d $dirName) {
2350            Confess("Cannot change to directory $dirName: no such directory.");
2351        } else {
2352            Trace("Changing to directory $dirName.") if T(File => 4);
2353            my $okFlag = chdir $dirName;
2354            if (! $okFlag) {
2355                Confess("Error switching to directory $dirName.");
2356            }
2357        }
2358    }
2359    
2360    =head3 SetPermissions
2361    
2362        Tracer::SetPermissions($dirName, $group, $mask, %otherMasks);
2363    
2364    Set the permissions for a directory and all the files and folders inside it.
2365    In addition, the group ownership will be changed to the specified value.
2366    
2367    This method is more vulnerable than most to permission and compatability
2368    problems, so it does internal error recovery.
2369    
2370    =over 4
2371    
2372    =item dirName
2373    
2374    Name of the directory to process.
2375    
2376    =item group
2377    
2378    Name of the group to be assigned.
2379    
2380    =item mask
2381    
2382    Permission mask. Bits that are C<1> in this mask will be ORed into the
2383    permission bits of any file or directory that does not already have them
2384    set to 1.
2385    
2386    =item otherMasks
2387    
2388    Map of search patterns to permission masks. If a directory name matches
2389    one of the patterns, that directory and all its members and subdirectories
2390    will be assigned the new pattern. For example, the following would
2391    assign 01664 to most files, but would use 01777 for directories named C<tmp>.
2392    
2393        Tracer::SetPermissions($dirName, 'fig', 01664, '^tmp$' => 01777);
2394    
2395    The list is ordered, so the following would use 0777 for C<tmp1> and
2396    0666 for C<tmp>, C<tmp2>, or C<tmp3>.
2397    
2398        Tracer::SetPermissions($dirName, 'fig', 01664, '^tmp1' => 0777,
2399                                                       '^tmp' => 0666);
2400    
2401    Note that the pattern matches are all case-insensitive, and only directory
2402    names are matched, not file names.
2403    
2404    =back
2405    
2406    =cut
2407    
2408    sub SetPermissions {
2409        # Get the parameters.
2410        my ($dirName, $group, $mask, @otherMasks) = @_;
2411        # Set up for error recovery.
2412        eval {
2413            # Switch to the specified directory.
2414            ChDir($dirName);
2415            # Get the group ID.
2416            my $gid = getgrnam($group);
2417            # Get the mask for tracing.
2418            my $traceMask = sprintf("%04o", $mask) . "($mask)";
2419            Trace("Fixing permissions for directory $dirName using group $group($gid) and mask $traceMask.") if T(File => 2);
2420            my $fixCount = 0;
2421            my $lookCount = 0;
2422            # @dirs will be a stack of directories to be processed.
2423            my @dirs = (getcwd());
2424            while (scalar(@dirs) > 0) {
2425                # Get the current directory.
2426                my $dir = pop @dirs;
2427                # Check for a match to one of the specified directory names. To do
2428                # that, we need to pull the individual part of the name off of the
2429                # whole path.
2430                my $simpleName = $dir;
2431                if ($dir =~ m!/([^/]+)$!) {
2432                    $simpleName = $1;
2433                }
2434                Trace("Simple directory name for $dir is $simpleName.") if T(File => 4);
2435                # Search for a match.
2436                my $match = 0;
2437                my $i;
2438                for ($i = 0; $i < $#otherMasks && ! $match; $i += 2) {
2439                    my $pattern = $otherMasks[$i];
2440                    if ($simpleName =~ /$pattern/i) {
2441                        $match = 1;
2442                    }
2443                }
2444                # Check for a match. Note we use $i-1 because the loop added 2
2445                # before terminating due to the match.
2446                if ($match && $otherMasks[$i-1] != $mask) {
2447                    # This directory matches one of the incoming patterns, and it's
2448                    # a different mask, so we process it recursively with that mask.
2449                    SetPermissions($dir, $group, $otherMasks[$i-1], @otherMasks);
2450                } else {
2451                    # Here we can process normally. Get all of the non-hidden members.
2452                    my @submems = OpenDir($dir, 1);
2453                    for my $submem (@submems) {
2454                        # Get the full name.
2455                        my $thisMem = "$dir/$submem";
2456                        Trace("Checking member $thisMem.") if T(4);
2457                        $lookCount++;
2458                        if ($lookCount % 1000 == 0) {
2459                            Trace("$lookCount members examined. Current is $thisMem. Mask is $traceMask") if T(File => 3);
2460                        }
2461                        # Fix the group.
2462                        chown -1, $gid, $thisMem;
2463                        # Insure this member is not a symlink.
2464                        if (! -l $thisMem) {
2465                            # Get its info.
2466                            my $fileInfo = stat $thisMem;
2467                            # Only proceed if we got the info. Otherwise, it's a hard link
2468                            # and we want to skip it anyway.
2469                            if ($fileInfo) {
2470                                my $fileMode = $fileInfo->mode;
2471                                if (($fileMode & $mask) != $mask) {
2472                                    # Fix this member.
2473                                    $fileMode |= $mask;
2474                                    chmod $fileMode, $thisMem;
2475                                    $fixCount++;
2476                                }
2477                                # If it's a subdirectory, stack it.
2478                                if (-d $thisMem) {
2479                                    push @dirs, $thisMem;
2480                                }
2481                            }
2482                        }
2483                    }
2484                }
2485            }
2486            Trace("$lookCount files and directories processed, $fixCount fixed.") if T(File => 2);
2487        };
2488        # Check for an error.
2489        if ($@) {
2490            Confess("SetPermissions error: $@");
2491        }
2492    }
2493    
2494    =head3 GetLine
2495    
2496        my @data = Tracer::GetLine($handle);
2497    
2498    Read a line of data from a tab-delimited file.
2499    
2500    =over 4
2501    
2502    =item handle
2503    
2504    Open file handle from which to read.
2505    
2506    =item RETURN
2507    
2508    Returns a list of the fields in the record read. The fields are presumed to be
2509    tab-delimited. If we are at the end of the file, then an empty list will be
2510    returned. If an empty line is read, a single list item consisting of a null
2511    string will be returned.
2512    
2513    =back
2514    
2515    =cut
2516    
2517    sub GetLine {
2518        # Get the parameters.
2519        my ($handle) = @_;
2520        # Declare the return variable.
2521        my @retVal = ();
2522        Trace("File position is " . tell($handle) . ". EOF flag is " . eof($handle) . ".") if T(File => 4);
2523        # Read from the file.
2524        my $line = <$handle>;
2525        # Only proceed if we found something.
2526        if (defined $line) {
2527            # Remove the new-line. We are a bit over-cautious here because the file may be coming in via an
2528            # upload control and have a nonstandard EOL combination.
2529            $line =~ s/(\r|\n)+$//;
2530            # Here we do some fancy tracing to help in debugging complicated EOL marks.
2531            if (T(File => 4)) {
2532                my $escapedLine = $line;
2533                $escapedLine =~ s/\n/\\n/g;
2534                $escapedLine =~ s/\r/\\r/g;
2535                $escapedLine =~ s/\t/\\t/g;
2536                Trace("Line read: -->$escapedLine<--");
2537            }
2538            # If the line is empty, return a single empty string; otherwise, parse
2539            # it into fields.
2540            if ($line eq "") {
2541                push @retVal, "";
2542            } else {
2543                push @retVal, split /\t/,$line;
2544            }
2545        } else {
2546            # Trace the reason the read failed.
2547            Trace("End of file: $!") if T(File => 3);
2548        }
2549        # Return the result.
2550        return @retVal;
2551    }
2552    
2553    =head3 PutLine
2554    
2555        Tracer::PutLine($handle, \@fields, $eol);
2556    
2557    Write a line of data to a tab-delimited file. The specified field values will be
2558    output in tab-separated form, with a trailing new-line.
2559    
2560    =over 4
2561    
2562    =item handle
2563    
2564    Output file handle.
2565    
2566    =item fields
2567    
2568    List of field values.
2569    
2570    =item eol (optional)
2571    
2572    End-of-line character (default is "\n").
2573    
2574    =back
2575    
2576    =cut
2577    
2578    sub PutLine {
2579        # Get the parameters.
2580        my ($handle, $fields, $eol) = @_;
2581        # Write the data.
2582        print $handle join("\t", @{$fields}) . ($eol || "\n");
2583    }
2584    
2585    
2586    
2587    =head2 Other Useful Methods
2588    
2589    =head3 ParseParm
2590    
2591        my $listValue = Tracer::ParseParm($string);
2592    
2593    Convert a parameter into a list reference. If the parameter is undefined,
2594    an undefined value will be returned. Otherwise, it will be parsed as a
2595    comma-separated list of values.
2596    
2597    =over 4
2598    
2599    =item string
2600    
2601    Incoming string.
2602    
2603    =item RETURN
2604    
2605    Returns a reference to a list of values, or C<undef> if the incoming value
2606    was undefined.
2607    
2608    =back
2609    
2610    =cut
2611    
2612    sub ParseParm {
2613        # Get the parameters.
2614        my ($string) = @_;
2615        # Declare the return variable.
2616        my $retVal;
2617        # Check for data.
2618        if (defined $string) {
2619            # We have some, so split it into a list.
2620            $retVal = [ split /\s*,\s*/, $string];
2621        }
2622        # Return the result.
2623        return $retVal;
2624    }
2625    
2626    
2627    
2628    
2629    =head3 Now
2630    
2631        my $string = Tracer::Now();
2632    
2633    Return a displayable time stamp containing the local time.
2634    
2635    =cut
2636    
2637    sub Now {
2638        my ($sec,$min,$hour,$mday,$mon,$year,$wday,$yday,$isdst) = localtime(time);
2639        my $retVal = _p2($mon+1) . "/" . _p2($mday) . "/" . ($year + 1900) . " " .
2640                     _p2($hour) . ":" . _p2($min) . ":" . _p2($sec);
2641        return $retVal;
2642    }
2643    
2644    # Pad a number to 2 digits.
2645    sub _p2 {
2646        my ($value) = @_;
2647        $value = "0$value" if ($value < 10);
2648        return $value;
2649    }
2650    
2651    =head3 Escape
2652    
2653        my $codedString = Tracer::Escape($realString);
2654    
2655    Escape a string for use in a command. Tabs will be replaced by C<\t>, new-lines
2656    replaced by C<\n>, carriage returns will be deleted, and backslashes will be doubled. The
2657    result is to reverse the effect of L</UnEscape>.
2658    
2659    =over 4
2660    
2661    =item realString
2662    
2663    String to escape.
2664    
2665    =item RETURN
2666    
2667    Escaped equivalent of the real string.
2668    
2669    =back
2670    
2671    =cut
2672    
2673    sub Escape {
2674        # Get the parameter.
2675        my ($realString) = @_;
2676        # Initialize the return variable.
2677        my $retVal = "";
2678        # Loop through the parameter string, looking for sequences to escape.
2679        while (length $realString > 0) {
2680            # Look for the first sequence to escape.
2681            if ($realString =~ /^(.*?)([\n\t\r\\])/) {
2682                # Here we found it. The text preceding the sequence is in $1. The sequence
2683                # itself is in $2. First, move the clear text to the return variable.
2684                $retVal .= $1;
2685                # Strip the processed section off the real string.
2686                $realString = substr $realString, (length $2) + (length $1);
2687                # Get the matched character.
2688                my $char = $2;
2689                # If we have a CR, we are done.
2690                if ($char ne "\r") {
2691                    # It's not a CR, so encode the escape sequence.
2692                    $char =~ tr/\t\n/tn/;
2693                    $retVal .= "\\" . $char;
2694                }
2695            } else {
2696                # Here there are no more escape sequences. The rest of the string is
2697                # transferred unmodified.
2698                $retVal .= $realString;
2699                $realString = "";
2700            }
2701        }
2702        # Return the result.
2703        return $retVal;
2704    }
2705    
2706    =head3 UnEscape
2707    
2708        my $realString = Tracer::UnEscape($codedString);
2709    
2710    Replace escape sequences with their actual equivalents. C<\t> will be replaced by
2711    a tab, C<\n> by a new-line character, and C<\\> by a backslash. C<\r> codes will
2712    be deleted.
2713    
2714    =over 4
2715    
2716    =item codedString
2717    
2718    String to un-escape.
2719    
2720    =item RETURN
2721    
2722    Returns a copy of the original string with the escape sequences converted to their actual
2723    values.
2724    
2725    =back
2726    
2727    =cut
2728    
2729    sub UnEscape {
2730        # Get the parameter.
2731        my ($codedString) = @_;
2732        # Initialize the return variable.
2733        my $retVal = "";
2734        # Only proceed if the incoming string is nonempty.
2735        if (defined $codedString) {
2736            # Loop through the parameter string, looking for escape sequences. We can't do
2737            # translating because it causes problems with the escaped slash. ("\\t" becomes
2738            # "\<tab>" no matter what we do.)
2739            while (length $codedString > 0) {
2740                # Look for the first escape sequence.
2741                if ($codedString =~ /^(.*?)\\(\\|n|t|r)/) {
2742                    # Here we found it. The text preceding the sequence is in $1. The sequence
2743                    # itself is in $2. First, move the clear text to the return variable.
2744                    $retVal .= $1;
2745                    $codedString = substr $codedString, (2 + length $1);
2746                    # Get the escape value.
2747                    my $char = $2;
2748                    # If we have a "\r", we are done.
2749                    if ($char ne 'r') {
2750                        # Here it's not an 'r', so we convert it.
2751                        $char =~ tr/\\tn/\\\t\n/;
2752                        $retVal .= $char;
2753                    }
2754                } else {
2755                    # Here there are no more escape sequences. The rest of the string is
2756                    # transferred unmodified.
2757                    $retVal .= $codedString;
2758                    $codedString = "";
2759                }
2760            }
2761        }
2762        # Return the result.
2763        return $retVal;
2764    }
2765    
2766    =head3 Percent
2767    
2768        my $percent = Tracer::Percent($number, $base);
2769    
2770    Returns the percent of the base represented by the given number. If the base
2771    is zero, returns zero.
2772    
2773    =over 4
2774    
2775    =item number
2776    
2777    Percent numerator.
2778    
2779    =item base
2780    
2781    Percent base.
2782    
2783    =item RETURN
2784    
2785    Returns the percentage of the base represented by the numerator.
2786    
2787    =back
2788    
2789    =cut
2790    
2791    sub Percent {
2792        # Get the parameters.
2793        my ($number, $base) = @_;
2794        # Declare the return variable.
2795        my $retVal = 0;
2796        # Compute the percent.
2797        if ($base != 0) {
2798            $retVal = $number * 100 / $base;
2799        }
2800        # Return the result.
2801        return $retVal;
2802    }
2803    
2804    =head3 Min
2805    
2806        my $min = Min($value1, $value2, ... $valueN);
2807    
2808    Return the minimum argument. The arguments are treated as numbers.
2809    
2810    =over 4
2811    
2812    =item $value1, $value2, ... $valueN
2813    
2814    List of numbers to compare.
2815    
2816    =item RETURN
2817    
2818    Returns the lowest number in the list.
2819    
2820    =back
2821    
2822    =cut
2823    
2824    sub Min {
2825        # Get the parameters. Note that we prime the return value with the first parameter.
2826        my ($retVal, @values) = @_;
2827        # Loop through the remaining parameters, looking for the lowest.
2828        for my $value (@values) {
2829            if ($value < $retVal) {
2830                $retVal = $value;
2831            }
2832        }
2833        # Return the minimum found.
2834        return $retVal;
2835    }
2836    
2837    =head3 Max
2838    
2839        my $max = Max($value1, $value2, ... $valueN);
2840    
2841    Return the maximum argument. The arguments are treated as numbers.
2842    
2843    =over 4
2844    
2845    =item $value1, $value2, ... $valueN
2846    
2847    List of numbers to compare.
2848    
2849    =item RETURN
2850    
2851    Returns the highest number in the list.
2852    
2853    =back
2854    
2855    =cut
2856    
2857    sub Max {
2858        # Get the parameters. Note that we prime the return value with the first parameter.
2859        my ($retVal, @values) = @_;
2860        # Loop through the remaining parameters, looking for the highest.
2861        for my $value (@values) {
2862            if ($value > $retVal) {
2863                $retVal = $value;
2864            }
2865        }
2866        # Return the maximum found.
2867        return $retVal;
2868    }
2869    
2870    =head3 DebugMode
2871    
2872        if (Tracer::DebugMode) { ...code... }
2873    
2874  =back  Return TRUE if debug mode has been turned on, else abort.
2875    
2876    Certain CGI scripts are too dangerous to exist in the production
2877    environment. This method provides a simple way to prevent them
2878    from working unless they are explicitly turned on by creating a password
2879    cookie via the B<SetPassword> script.  If debugging mode
2880    is not turned on, an error will occur.
2881    
2882  =cut  =cut
2883    
2884  sub UnEscape {  sub DebugMode {
2885          # Get the parameter.      # Declare the return variable.
2886          my ($codedString) = @_;      my $retVal = 0;
2887          # Initialize the return variable.      # Check the debug configuration.
2888          my $retVal = "";      my $password = CGI::cookie("DebugMode");
2889          # Loop through the parameter string, looking for escape sequences. We can't do      my $encrypted = Digest::MD5::md5_hex($password);
2890          # translating because it causes problems with the escaped slash. ("\\b" becomes      if ($encrypted eq "252dec43280e0c0d6a75ffcec486e61d") {
2891          # "\ " 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;  
2892                  } else {                  } else {
2893                          # Here there are no more escape sequences. The rest of the string is          # Here debug mode is off, so we generate an error.
2894                          # transferred unmodified.          Confess("Cannot use this facility without logging in.");
                         $retVal .= $codedString;  
                         $codedString = "";  
2895                  }                  }
2896          }      # Return the determination indicator.
         # Return the result.  
2897          return $retVal;          return $retVal;
2898  }  }
2899    
2900  =head3 ParseRecord  =head3 Strip
2901    
2902  C<< my @fields = Tracer::ParseRecord($line); >>      my $string = Tracer::Strip($line);
2903    
2904  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
2905  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
2906  These will automatically be converted.  operating environments.
2907    
2908  =over 4  =over 4
2909    
2910  =item line  =item line
2911    
2912  Line of data containing the tab-delimited fields.  Line of text to be stripped.
2913    
2914  =item RETURN  =item RETURN
2915    
2916  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.
2917    
2918  =back  =back
2919    
2920  =cut  =cut
2921    
2922  sub ParseRecord {  sub Strip {
2923          # Get the parameter.      # Get a copy of the parameter string.
2924          my ($line) = @_;      my ($string) = @_;
2925          # Remove the trailing new-line, if any.      my $retVal = (defined $string ? $string : "");
2926          chomp $line;      # Strip the line terminator characters.
2927          # 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;  
         }  
2928          # Return the result.          # Return the result.
2929          return @retVal;      return $retVal;
2930  }  }
2931    
2932  =head3 Merge  =head3 Pad
2933    
2934  C<< my @mergedList = Tracer::Merge(@inputList); >>      my $paddedString = Tracer::Pad($string, $len, $left, $padChar);
2935    
2936  Sort a list of strings and remove duplicates.  Pad a string to a specified length. The pad character will be a
2937    space, and the padding will be on the right side unless specified
2938    in the third parameter.
2939    
2940  =over 4  =over 4
2941    
2942  =item inputList  =item string
2943    
2944  List of scalars to sort and merge.  String to be padded.
2945    
2946    =item len
2947    
2948    Desired length of the padded string.
2949    
2950    =item left (optional)
2951    
2952    TRUE if the string is to be left-padded; otherwise it will be padded on the right.
2953    
2954    =item padChar (optional)
2955    
2956    Character to use for padding. The default is a space.
2957    
2958  =item RETURN  =item RETURN
2959    
2960  Returns a list containing the same elements sorted in ascending order with duplicates  Returns a copy of the original string with the pad character added to the
2961  removed.  specified end so that it achieves the desired length.
2962    
2963  =back  =back
2964    
2965  =cut  =cut
2966    
2967  sub Merge {  sub Pad {
2968          # Get the input list in sort order.      # Get the parameters.
2969          my @inputList = sort @_;      my ($string, $len, $left, $padChar) = @_;
2970          # Only proceed if the list has at least two elements.      # Compute the padding character.
2971          if (@inputList > 1) {      if (! defined $padChar) {
2972                  # Now we want to move through the list splicing out duplicates.          $padChar = " ";
2973                  my $i = 0;      }
2974                  while ($i < @inputList) {      # Compute the number of spaces needed.
2975                          # Get the current entry.      my $needed = $len - length $string;
2976                          my $thisEntry = $inputList[$i];      # Copy the string into the return variable.
2977                          # Find out how many elements duplicate the current entry.      my $retVal = $string;
2978                          my $j = $i + 1;      # Only proceed if padding is needed.
2979                          my $dup1 = $i + 1;      if ($needed > 0) {
2980                          while ($j < @inputList && $inputList[$j] eq $thisEntry) { $j++; };          # Create the pad string.
2981                          # If the number is nonzero, splice out the duplicates found.          my $pad = $padChar x $needed;
2982                          if ($j > $dup1) {          # Affix it to the return value.
2983                                  splice @inputList, $dup1, $j - $dup1;          if ($left) {
2984                $retVal = $pad . $retVal;
2985            } else {
2986                $retVal .= $pad;
2987                          }                          }
                         # 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++;  
2988                  }                  }
2989        # Return the result.
2990        return $retVal;
2991          }          }
2992          # Return the merged list.  
2993          return @inputList;  =head3 EOF
2994    
2995    This is a constant that is lexically greater than any useful string.
2996    
2997    =cut
2998    
2999    sub EOF {
3000        return "\xFF\xFF\xFF\xFF\xFF";
3001  }  }
3002    
3003  =head3 GetFile  =head3 TICK
3004    
3005        my @results = TICK($commandString);
3006    
3007  C<< my @fileContents = Tracer::GetFile($fileName); >>  Perform a back-tick operation on a command. If this is a Windows environment, any leading
3008    dot-slash (C<./> will be removed. So, for example, if you were doing
3009    
3010  Return the entire contents of a file.      `./protein.cgi`
3011    
3012    from inside a CGI script, it would work fine in Unix, but would issue an error message
3013    in Windows complaining that C<'.'> is not a valid command. If instead you code
3014    
3015        TICK("./protein.cgi")
3016    
3017    it will work correctly in both environments.
3018    
3019  =over 4  =over 4
3020    
3021  =item fileName  =item commandString
3022    
3023  Name of the file to read.  The command string to pass to the system.
3024    
3025  =item RETURN  =item RETURN
3026    
3027  In a list context, returns the entire file as a list with the line terminators removed.  Returns the standard output from the specified command, as a list.
 In a scalar context, returns the entire file as a string.  
3028    
3029  =back  =back
3030    
3031  =cut  =cut
3032    #: Return Type @;
3033  sub GetFile {  sub TICK {
3034          # Get the parameters.          # Get the parameters.
3035          my ($fileName) = @_;      my ($commandString) = @_;
3036          # Declare the return variable.      # Chop off the dot-slash if this is Windows.
3037          my @retVal = ();      if ($FIG_Config::win_mode) {
3038          # 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. $actualLines processed.") if T(0);  
         }  
         # Return the file's contents in the desired format.  
     if (wantarray) {  
             return @retVal;  
     } else {  
         return join "\n", @retVal;  
3039      }      }
3040        # Activate the command and return the result.
3041        return `$commandString`;
3042  }  }
3043    
 =head3 QTrace  
3044    
3045  C<< my $data = QTrace($format); >>  =head3 CommaFormat
3046    
3047  Return the queued trace data in the specified format.      my $formatted = Tracer::CommaFormat($number);
3048    
3049    Insert commas into a number.
3050    
3051  =over 4  =over 4
3052    
3053  =item format  =item number
3054    
3055  C<html> to format the data as an HTML list, C<text> to format it as straight text.  A sequence of digits.
3056    
3057    =item RETURN
3058    
3059    Returns the same digits with commas strategically inserted.
3060    
3061  =back  =back
3062    
3063  =cut  =cut
3064    
3065  sub QTrace {  sub CommaFormat {
3066          # Get the parameter.      # Get the parameters.
3067          my ($format) = @_;      my ($number) = @_;
3068          # Create the return variable.      # Pad the length up to a multiple of three.
3069          my $retVal = "";      my $padded = "$number";
3070          # Process according to the format.      $padded = " " . $padded while length($padded) % 3 != 0;
3071          if ($format =~ m/^HTML$/i) {      # This is a fancy PERL trick. The parentheses in the SPLIT pattern
3072                  # Convert the queue into an HTML list.      # cause the delimiters to be included in the output stream. The
3073                  $retVal = "<ul>\n";      # GREP removes the empty strings in between the delimiters.
3074                  for my $line (@Queue) {      my $retVal = join(",", grep { $_ ne '' } split(/(...)/, $padded));
3075                          my $escapedLine = CGI::escapeHTML($line);      # Clean out the spaces.
3076                          $retVal .= "<li>$escapedLine</li>\n";      $retVal =~ s/ //g;
3077                  }      # 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.  
3078          return $retVal;          return $retVal;
3079  }  }
3080    
 =head3 Confess  
   
 C<< Confess($message); >>  
3081    
3082  Trace the call stack and abort the program with the specified message. The stack  =head3 CompareLists
 trace will only appear if the trace level for this package is 1 or more. When used with  
 the OR operator and the L</Assert> method, B<Confess> can function as a debugging assert.  
 So, for example  
3083    
3084  C<< Assert($recNum >= 0) || Confess("Invalid record number $recNum."); >>      my ($inserted, $deleted) = Tracer::CompareLists(\@newList, \@oldList, $keyIndex);
3085    
3086  Will abort the program with a stack trace if the value of C<$recNum> is negative.  Compare two lists of tuples, and return a hash analyzing the differences. The lists
3087    are presumed to be sorted alphabetically by the value in the $keyIndex column.
3088    The return value contains a list of items that are only in the new list
3089    (inserted) and only in the old list (deleted).
3090    
3091  =over 4  =over 4
3092    
3093  =item message  =item newList
   
 Message to include in the trace.  
3094    
3095  =back  Reference to a list of new tuples.
3096    
3097  =cut  =item oldList
3098    
3099  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(">>> $message");  
 }  
3100    
3101  =head3 Assert  =item keyIndex (optional)
3102    
3103  C<< Assert($condition1, $condition2, ... $conditionN); >>  Index into each tuple of its key field. The default is 0.
3104    
3105  Return TRUE if all the conditions are true. This method can be used in conjunction with  =item RETURN
 the OR operator and the L</Confess> method, B<Assert> can function as a debugging assert.  
 So, for example  
3106    
3107  C<< Assert($recNum >= 0) || Confess("Invalid record number $recNum."); >>  Returns a 2-tuple consisting of a reference to the list of items that are only in the new
3108    list (inserted) followed by a reference to the list of items that are only in the old
3109    list (deleted).
3110    
3111  Will abort the program with a stack trace if the value of C<$recNum> is negative.  =back
3112    
3113  =cut  =cut
3114  sub Assert {  
3115      my $retVal = 1;  sub CompareLists {
3116      LOOP: for my $condition (@_) {      # Get the parameters.
3117          if (! $condition) {      my ($newList, $oldList, $keyIndex) = @_;
3118              $retVal = 0;      if (! defined $keyIndex) {
3119              last LOOP;          $keyIndex = 0;
3120        }
3121        # Declare the return variables.
3122        my ($inserted, $deleted) = ([], []);
3123        # Loop through the two lists simultaneously.
3124        my ($newI, $oldI) = (0, 0);
3125        my ($newN, $oldN) = (scalar @{$newList}, scalar @{$oldList});
3126        while ($newI < $newN || $oldI < $oldN) {
3127            # Get the current object in each list. Note that if one
3128            # of the lists is past the end, we'll get undef.
3129            my $newItem = $newList->[$newI];
3130            my $oldItem = $oldList->[$oldI];
3131            if (! defined($newItem) || defined($oldItem) && $newItem->[$keyIndex] gt $oldItem->[$keyIndex]) {
3132                # The old item is not in the new list, so mark it deleted.
3133                push @{$deleted}, $oldItem;
3134                $oldI++;
3135            } elsif (! defined($oldItem) || $oldItem->[$keyIndex] gt $newItem->[$keyIndex]) {
3136                # The new item is not in the old list, so mark it inserted.
3137                push @{$inserted}, $newItem;
3138                $newI++;
3139            } else {
3140                # The item is in both lists, so push forward.
3141                $oldI++;
3142                $newI++;
3143          }          }
3144      }      }
3145      return $retVal;      # Return the result.
3146        return ($inserted, $deleted);
3147  }  }
3148    
3149  =head3 Cluck  =head3 GenerateURL
3150    
3151  C<< Cluck($message); >>      my $queryUrl = Tracer::GenerateURL($page, %parameters);
3152    
3153  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
3154  trace condition. For example,  names and values. The values will be URL-escaped automatically. So, for
3155    example
3156    
3157  C<< Cluck("Starting record parse.") if T(3); >>      Tracer::GenerateURL("form.cgi", type => 1, string => "\"high pass\" or highway")
3158    
3159  will only trace the stack if the trace level for the package is 3 or more.  would return
3160    
3161        form.cgi?type=1;string=%22high%20pass%22%20or%20highway
3162    
3163  =over 4  =over 4
3164    
3165  =item message  =item page
3166    
3167  Message to include in the trace.  Page URL.
3168    
3169    =item parameters
3170    
3171    Hash mapping parameter names to parameter values.
3172    
3173    =item RETURN
3174    
3175    Returns a GET-style URL that goes to the specified page and passes in the
3176    specified parameters and values.
3177    
3178  =back  =back
3179    
3180  =cut  =cut
3181    
3182  sub Cluck {  sub GenerateURL {
3183          # Get the parameters.          # Get the parameters.
3184          my ($message) = @_;      my ($page, %parameters) = @_;
3185      # Trace what's happening.      # Prime the return variable with the page URL.
3186      Trace("Stack trace for event: $message");      my $retVal = $page;
3187          my $confession = longmess($message);      # Loop through the parameters, creating parameter elements in a list.
3188          # Convert the confession to a series of trace messages. Note we skip any      my @parmList = map { "$_=" . uri_escape($parameters{$_}) } keys %parameters;
3189      # messages relating to calls into Tracer.      # If the list is nonempty, tack it on.
3190          for my $line (split /\s*\n/, $confession) {      if (@parmList) {
3191                  Trace($line) if ($line !~ /Tracer\.pm/);          $retVal .= "?" . join(";", @parmList);
3192          }          }
3193        # Return the result.
3194        return $retVal;
3195  }  }
3196    
3197  =head3 Min  =head3 ApplyURL
3198    
3199  C<< my $min = Min($value1, $value2, ... $valueN); >>      Tracer::ApplyURL($table, $target, $url);
3200    
3201  Return the minimum argument. The arguments are treated as numbers.  Run through a two-dimensional table (or more accurately, a list of lists), converting the
3202    I<$target> column to HTML text having a hyperlink to a URL in the I<$url> column. The
3203    URL column will be deleted by this process and the target column will be HTML-escaped.
3204    
3205    This provides a simple way to process the results of a database query into something
3206    displayable by combining a URL with text.
3207    
3208  =over 4  =over 4
3209    
3210  =item $value1, $value2, ... $valueN  =item table
3211    
3212  List of numbers to compare.  Reference to a list of lists. The elements in the containing list will be updated by
3213    this method.
3214    
3215  =item RETURN  =item target
3216    
3217  Returns the lowest number in the list.  The index of the column to be converted into HTML.
3218    
3219    =item url
3220    
3221    The index of the column containing the URL. Note that the URL must have a recognizable
3222    C<http:> at the beginning.
3223    
3224  =back  =back
3225    
3226  =cut  =cut
3227    
3228  sub Min {  sub ApplyURL {
3229          # Get the parameters. Note that we prime the return value with the first parameter.      # Get the parameters.
3230          my ($retVal, @values) = @_;      my ($table, $target, $url) = @_;
3231          # Loop through the remaining parameters, looking for the lowest.      # Loop through the table.
3232          for my $value (@values) {      for my $row (@{$table}) {
3233                  if ($value < $retVal) {          # Apply the URL to the target cell.
3234                          $retVal = $value;          $row->[$target] = CombineURL($row->[$target], $row->[$url]);
3235                  }          # Delete the URL from the row.
3236            delete $row->[$url];
3237          }          }
         # Return the minimum found.  
         return $retVal;  
3238  }  }
3239    
3240  =head3 Max  =head3 CombineURL
3241    
3242  C<< my $max = Max($value1, $value2, ... $valueN); >>      my $combinedHtml = Tracer::CombineURL($text, $url);
3243    
3244  Return the maximum argument. The arguments are treated as numbers.  This method will convert the specified text into HTML hyperlinked to the specified
3245    URL. The hyperlinking will only take place if the URL looks legitimate: that is, it
3246    is defined and begins with an C<http:> header.
3247    
3248  =over 4  =over 4
3249    
3250  =item $value1, $value2, ... $valueN  =item text
3251    
3252  List of numbers to compare.  Text to return. This will be HTML-escaped automatically.
3253    
3254    =item url
3255    
3256    A URL to be hyperlinked to the text. If it does not look like a URL, then the text
3257    will be returned without any hyperlinking.
3258    
3259  =item RETURN  =item RETURN
3260    
3261  Returns the highest number in the list.  Returns the original text, HTML-escaped, with the URL hyperlinked to it. If the URL
3262    doesn't look right, the HTML-escaped text will be returned without any further
3263    modification.
3264    
3265  =back  =back
3266    
3267  =cut  =cut
3268    
3269  sub Max {  sub CombineURL {
3270          # Get the parameters. Note that we prime the return value with the first parameter.      # Get the parameters.
3271          my ($retVal, @values) = @_;      my ($text, $url) = @_;
3272          # Loop through the remaining parameters, looking for the highest.      # Declare the return variable.
3273          for my $value (@values) {      my $retVal = CGI::escapeHTML($text);
3274                  if ($value > $retVal) {      # Verify the URL.
3275                          $retVal = $value;      if (defined($url) && $url =~ m!http://!i) {
3276                  }          # It's good, so we apply it to the text.
3277            $retVal = "<a href=\"$url\">$retVal</a>";
3278          }          }
3279          # Return the maximum found.      # Return the result.
3280          return $retVal;          return $retVal;
3281  }  }
3282    
3283  =head3 AddToListMap  =head3 Cmp
3284    
3285  C<< Tracer::AddToListMap(\%hash, $key, $value); >>      my $cmp = Tracer::Cmp($a, $b);
3286    
3287  Add a key-value pair to a hash of lists. If no value exists for the key, a singleton list  This method performs a universal sort comparison. Each value coming in is
3288  is created for the key. Otherwise, the new value is pushed onto the list.  separated into a leading text part and a trailing number part. The text
3289    part is string compared, and if both parts are equal, then the number
3290    parts are compared numerically. A stream of just numbers or a stream of
3291    just strings will sort correctly, and a mixed stream will sort with the
3292    numbers first. Strings with a label and a number will sort in the
3293    expected manner instead of lexically.
3294    
3295  =over 4  =over 4
3296    
3297  =item hash  =item a
3298    
3299  Reference to the target hash.  First item to compare.
3300    
3301  =item key  =item b
3302    
3303  Key for which the value is to be added.  Second item to compare.
3304    
3305  =item value  =item RETURN
3306    
3307  Value to add to the key's value list.  Returns a negative number if the first item should sort first (is less), a positive
3308    number if the first item should sort second (is greater), and a zero if the items are
3309    equal.
3310    
3311  =back  =back
3312    
3313  =cut  =cut
3314    
3315  sub AddToListMap {  sub Cmp {
3316      # Get the parameters.      # Get the parameters.
3317      my ($hash, $key, $value) = @_;      my ($a, $b) = @_;
3318      # Process according to whether or not the key already has a value.      # Declare the return value.
3319      if (! exists $hash->{$key}) {      my $retVal;
3320          $hash->{$key} = [$value];      # Check for nulls.
3321        if (! defined($a)) {
3322            $retVal = (! defined($b) ? 0 : -1);
3323        } elsif (! defined($b)) {
3324            $retVal = 1;
3325      } else {      } else {
3326          push @{$hash->{$key}}, $value;          # Here we have two real values. Parse the two strings.
3327            $a =~ /^(\D*)(\d*)$/;
3328            my $aParsed = [$1, $2];
3329            $b =~ /^(\D*)(\d*)$/;
3330            my $bParsed = [$1, $2];
3331            # Compare the string parts.
3332            $retVal = $aParsed->[0] cmp $bParsed->[0];
3333            if (! $retVal) {
3334                $retVal = $aParsed->[1] <=> $bParsed->[1];
3335      }      }
3336  }  }
3337        # Return the result.
3338        return $retVal;
3339    }
3340    
3341    
3342  1;  1;

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