[Bio] / FigKernelPackages / Tracer.pm Repository:
ViewVC logotype

Diff of /FigKernelPackages/Tracer.pm

Parent Directory Parent Directory | Revision Log Revision Log | View Patch Patch

revision 1.9, Wed May 4 03:05:12 2005 UTC revision 1.84, Thu May 3 12:28:00 2007 UTC
# 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 Escape);          @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;          use FIG_Config;
29      use PageBuilder;      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 36  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  sets the trace level to 3, activates the C<errors>, C<Sprout>, and C<ERDB> categories, and
86  specifies that messages should be output as HTML paragraphs. The parameters are formatted  specifies that messages should be sent to the standard output.
87  to make it easier to input tracing configuration on a web form.  
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        TSetup('3 *', 'WARN');
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 = "NONE";       # 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  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 Public Methods  =head2 Public Methods
300    
# Line 93  Line 316 
316    
317  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
318  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
319  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 ">"
320  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
321  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
322    cause tracing to the standard output with each line formatted as an HTML paragraph. C<TEXT>
323  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
324  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
325  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 113  Line 337 
337          my @categoryData = split /\s+/, $categoryList;          my @categoryData = split /\s+/, $categoryList;
338          # Extract the trace level.          # Extract the trace level.
339          $TraceLevel = shift @categoryData;          $TraceLevel = shift @categoryData;
340          # Build the category hash.      # Presume category-based tracing until we learn otherwise.
341        $AllTrace = 0;
342        # Build the category hash. Note that if we find a "*", we turn on non-category
343        # tracing. We must also clear away any pre-existing data.
344        %Categories = ( main => 1 );
345          for my $category (@categoryData) {          for my $category (@categoryData) {
346                  $Categories{$category} = 1;          if ($category eq '*') {
347                $AllTrace = 1;
348            } else {
349                $Categories{lc $category} = 1;
350            }
351          }          }
352          # Now we need to process the destination information. The most important special          # Now we need to process the destination information. The most important special
353          # case is the single ">", which requires we clear the file first. After doing      # cases are the single ">", which requires we clear the file first, and the
354          # so, we tack on another ">" sign so that future trace messages are appended.      # "+" prefix which indicates a double echo.
355        if ($target =~ m/^\+?>>?/) {
356            if ($target =~ m/^\+/) {
357                $TeeFlag = 1;
358                $target = substr($target, 1);
359            }
360          if ($target =~ m/^>[^>]/) {          if ($target =~ m/^>[^>]/) {
361                  open TRACEFILE, $target;                  open TRACEFILE, $target;
362                  print TRACEFILE Now() . " Tracing initialized.\n";              print TRACEFILE "[" . Now() . "] <Tracer>: Tracing initialized.\n";
363                  close TRACEFILE;                  close TRACEFILE;
364                  $Destination = ">$target";                  $Destination = ">$target";
365          } else {          } else {
366                $Destination = $target;
367            }
368        } else {
369                  $Destination = uc($target);                  $Destination = uc($target);
370          }          }
371        # Increment the setup counter.
372        $SetupCount++;
373  }  }
374    
375  =head3 SetLevel  =head3 StandardSetup
376    
377  C<< Tracer::SetLevel($newLevel); >>  C<< my ($options, @parameters) = StandardSetup(\@categories, \%options, $parmHelp, @ARGV); >>
378    
379  Modify the trace level. A higher trace level will cause more messages to appear.  This method performs standard command-line parsing and tracing setup. The return
380    values are a hash of the command-line options and a list of the positional
381    parameters. Tracing is automatically set up and the command-line options are
382    validated.
383    
384  =over 4  This is a complex method that does a lot of grunt work. The parameters can
385    be more easily understood, however, once they are examined individually.
386    
387  =item newLevel  The I<categories> parameter is the most obtuse. It is a reference to a list of
388    special-purpose tracing categories. Most tracing categories are PERL package
389    names. So, for example, if you wanted to turn on tracing inside the B<Sprout>,
390    B<ERDB>, and B<SproutLoad> packages, you would specify the categories
391    
392  Proposed new trace level.      ["Sprout", "SproutLoad", "ERDB"]
393    
394  =back  This would cause trace messages in the specified three packages to appear in
395    the output. There are two special tracing categories that are automatically
396    handled by this method. In other words, if you used L</TSetup> you would need
397    to include these categories manually, but if you use this method they are turned
398    on automatically.
399    
400  =cut  =over 4
401    
402  sub SetLevel {  =item SQL
     $TraceLevel = $_[0];  
 }  
403    
404  =head3 Now  Traces SQL commands and activity.
405    
406  C<< my $string = Tracer::Now(); >>  =item Tracer
407    
408  Return a displayable time stamp containing the local time.  Traces error messages and call stacks.
409    
410  =cut  =back
411    
412  sub Now {  C<SQL> is only turned on if the C<-sql> option is specified in the command line.
413          my ($sec,$min,$hour,$mday,$mon,$year,$wday,$yday,$isdst) = localtime(time);  The trace level is specified using the C<-trace> command-line option. For example,
414          my $retVal = _p2($mon+1) . "/" . _p2($mday) . "/" . ($year + 1900) . " " .  the following command line for C<TransactFeatures> turns on SQL tracing and runs
415                                   _p2($hour) . ":" . _p2($min) . ":" . _p2($sec);  all tracing at level 3.
         return $retVal;  
 }  
416    
417  # Pad a number to 2 digits.      TransactFeatures -trace=3 -sql register ../xacts IDs.tbl
 sub _p2 {  
         my ($value) = @_;  
         $value = "0$value" if ($value < 10);  
         return $value;  
 }  
418    
419  =head3 LogErrors  Standard tracing is output to the standard output and echoed to the file
420    C<trace>I<$$>C<.log> in the FIG temporary directory, where I<$$> is the
421    process ID. You can also specify the C<user> parameter to put a user ID
422    instead of a process ID in the trace file name. So, for example
423    
424  C<< Tracer::LogErrors($fileName); >>  The default trace level is 2. To get all messages, specify a trace level of 4.
425    For a genome-by-genome update, use 3.
426    
427  Route the standard error output to a log file.      TransactFeatures -trace=3 -sql -user=Bruce register ../xacts IDs.tbl
428    
429  =over 4  would send the trace output to C<traceBruce.log> in the temporary directory.
430    
431  =item fileName  The I<options> parameter is a reference to a hash containing the command-line
432    options, their default values, and an explanation of what they mean. Command-line
433    options may be in the form of switches or keywords. In the case of a switch, the
434    option value is 1 if it is specified and 0 if it is not specified. In the case
435    of a keyword, the value is separated from the option name by an equal sign. You
436    can see this last in the command-line example above.
437    
438  Name of the file to receive the error output.  You can specify a different default trace level by setting C<$options->{trace}>
439    prior to calling this method.
440    
441  =back  An example at this point would help. Consider, for example, the command-line utility
442    C<TransactFeatures>. It accepts a list of positional parameters plus the options
443    C<safe>, C<noAlias>, C<start>, and C<tblFiles>. To start up this command, we execute
444    the following code.
445    
446  =cut      my ($options, @parameters) = Tracer::StandardSetup(["DocUtils"],
447                            { safe => [0, "use database transactions"],
448                              noAlias => [0, "do not expect aliases in CHANGE transactions"],
449                              start => [' ', "start with this genome"],
450                              tblFiles => [0, "output TBL files containing the corrected IDs"] },
451                            "<command> <transactionDirectory> <IDfile>",
452                          @ARGV);
453    
 sub LogErrors {  
         # Get the file name.  
         my ($fileName) = @_;  
         # Open the file as the standard error output.  
         open STDERR, '>', $fileName;  
 }  
454    
455  =head3 ReadOptions  The call to C<ParseCommand> specifies the default values for the options and
456    stores the actual options in a hash that is returned as C<$options>. The
457    positional parameters are returned in C<@parameters>.
458    
459  C<< my %options = Tracer::ReadOptions($fileName); >>  The following is a sample command line for C<TransactFeatures>.
460    
461  Read a set of options from a file. Each option is encoded in a line of text that has the      TransactFeatures -trace=2 -noAlias register ../xacts IDs.tbl
 format  
462    
463  I<optionName>C<=>I<optionValue>C<; >I<comment>  Single and double hyphens are equivalent. So, you could also code the
464    above command as
465    
466  The option name must consist entirely of letters, digits, and the punctuation characters      TransactFeatures --trace=2 --noAlias register ../xacts IDs.tbl
 C<.> and C<_>, and is case sensitive. Blank lines and lines in which the first nonblank  
 character is a semi-colon will be ignored. The return hash will map each option name to  
 the corresponding option value.  
467    
468  =over 4  In this case, C<register>, C<../xacts>, and C<IDs.tbl> are the positional
469    parameters, and would find themselves in I<@parameters> after executing the
470    above code fragment. The tracing would be set to level 2, and the categories
471    would be C<Tracer>, and <DocUtils>. C<Tracer> is standard,
472    and C<DocUtils> was included because it came in within the first parameter
473    to this method. The I<$options> hash would be
474    
475  =item fileName      { trace => 2, sql => 0, safe => 0,
476          noAlias => 1, start => ' ', tblFiles => 0 }
477    
478  Name of the file containing the option data.  Use of C<StandardSetup> in this way provides a simple way of performing
479    standard tracing setup and command-line parsing. Note that the caller is
480    not even aware of the command-line switches C<-trace> and C<-sql>, which
481    are used by this method to control the tracing. If additional tracing features
482    need to be added in the future, they can be processed by this method without
483    upsetting the command-line utilities.
484    
485  =item RETURN  If the C<background> option is specified on the command line, then the
486    standard and error outputs will be directed to files in the temporary
487    directory, using the same suffix as the trace file. So, if the command
488    line specified
489    
490  Returns a hash mapping the option names specified in the file to their corresponding option      -user=Bruce -background
 value.  
491    
492  =back  then the trace output would go to C<traceBruce.log>, the standard output to
493    C<outBruce.log>, and the error output to C<errBruce.log>. This is designed to
494    simplify starting a command in the background.
495    
496  =cut  The user name is also used as the tracing key for L</Emergency Tracing>.
497    Specifying a value of C<E> for the trace level causes emergency tracing to
498    be used instead of custom tracing. If the user name is not specified,
499    the tracing key is taken from the C<Tracing> environment variable. If there
500    is no value for that variable, the tracing key will be computed from the PID.
501    
502  sub ReadOptions {  Finally, if the special option C<-help> is specified, the option
503          # Get the parameters.  names will be traced at level 0 and the program will exit without processing.
504          my ($fileName) = @_;  This provides a limited help capability. For example, if the user enters
         # Open the file.  
         (open CONFIGFILE, "<$fileName") || Confess("Could not open option file $fileName.");  
         # Count the number of records read.  
         my ($records, $comments) = 0;  
         # Create the return hash.  
         my %retVal = ();  
         # Loop through the file, accumulating key-value pairs.  
         while (my $line = <CONFIGFILE>) {  
                 # Denote we've read a line.  
                 $records++;  
                 # Determine the line type.  
                 if ($line =~ /^\s*[\n\r]/) {  
                         # A blank line is a comment.  
                         $comments++;  
                 } elsif ($line =~ /^\s*([A-Za-z0-9_\.]+)=([^;]*);/) {  
                         # Here we have an option assignment.  
                         retVal{$1} = $2;  
                 } elsif ($line =~ /^\s*;/) {  
                         # Here we have a text comment.  
                         $comments++;  
                 } else {  
                         # Here we have an invalid line.  
                         Trace("Invalid option statement in record $records.") if T(0);  
                 }  
         }  
         # Return the hash created.  
         return %retVal;  
 }  
505    
506  =head3 GetOptions      TransactFeatures -help
507    
508  C<< Tracer::GetOptions(\%defaults, \%options); >>  he would see the following output.
509    
510  Merge a specified set of options into a table of defaults. This method takes two hash references      TransactFeatures [options] <command> <transactionDirectory> <IDfile>
511  as input and uses the data from the second to update the first. If the second does not exist,          -trace    tracing level (default E)
512  there will be no effect. An error will be thrown if one of the entries in the second hash does not          -sql      trace SQL commands
513  exist in the first.          -safe     use database transactions
514            -noAlias  do not expect aliases in CHANGE transactions
515            -start    start with this genome
516            -tblFiles output TBL files containing the corrected IDs
517    
518  Consider the following example.  The caller has the option of modifying the tracing scheme by placing a value
519    for C<trace> in the incoming options hash. The default value can be overridden,
520    or the tracing to the standard output can be turned off by suffixing a minus
521    sign to the trace level. So, for example,
522    
523  C<< my $optionTable = GetOptions({ dbType => 'mySQL', trace => 0 }, $options); >>      { trace => [0, "tracing level (default 0)"],
524           ...
525    
526  In this example, the variable B<$options> is expected to contain at most two options-- B<dbType> and  would set the default trace level to 0 instead of E, while
 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  
527    
528  C<< {databaseType => 'Oracle'} >>      { trace => ["2-", "tracing level (default 2)"],
529           ...
530    
531  an error will occur because the B<databaseType> option does not exist.  would set the default to 2, but trace only to the log file, not to the
532    standard output.
533    
534    The parameters to this method are as follows.
535    
536  =over 4  =over 4
537    
538  =item defaults  =item categories
539    
540  Table of default option values.  Reference to a list of tracing category names. These should be names of
541    packages whose internal workings will need to be debugged to get the
542    command working.
543    
544  =item options  =item options
545    
546  Table of overrides, if any.  Reference to a hash containing the legal options for the current command mapped
547    to their default values and descriptions. The user can override the defaults
548    by specifying the options as command-line switches prefixed by a hyphen.
549    Tracing-related options may be added to this hash. If the C<-h> option is
550    specified on the command line, the option descriptions will be used to
551    explain the options. To turn off tracing to the standard output, add a
552    minus sign to the value for C<trace> (see above).
553    
554    =item parmHelp
555    
556    A string that vaguely describes the positional parameters. This is used
557    if the user specifies the C<-h> option.
558    
559    =item argv
560    
561    List of command line parameters, including the option switches, which must
562    precede the positional parameters and be prefixed by a hyphen.
563    
564  =item RETURN  =item RETURN
565    
566  Returns a reference to the default table passed in as the first parameter.  Returns a list. The first element of the list is the reference to a hash that
567    maps the command-line option switches to their values. These will either be the
568    default values or overrides specified on the command line. The remaining
569    elements of the list are the position parameters, in order.
570    
571  =back  =back
572    
573  =cut  =cut
574    
575  sub GetOptions {  sub StandardSetup {
576          # Get the parameters.          # Get the parameters.
577          my ($defaults, $options) = @_;      my ($categories, $options, $parmHelp, @argv) = @_;
578          # Check for overrides.      # Get the default tracing key.
579          if ($options) {      my $tkey = EmergencyKey();
580                  # Loop through the overrides.      # Add the tracing options.
581                  while (my ($option, $setting) = each %{$options}) {      if (! exists $options->{trace}) {
582                          # Insure this override exists.          $options->{trace} = ['E', "tracing level (E for emergency tracing)"];
583                          if (!exists $defaults->{$option}) {      }
584                                  croak "Unrecognized option $option encountered.";      $options->{sql} = [0, "turn on SQL tracing"];
585        $options->{help} = [0, "display command-line options"];
586        $options->{user} = [$tkey, "tracing key"];
587        $options->{background} = [0, "spool standard and error output"];
588        # Create a parsing hash from the options hash. The parsing hash
589        # contains the default values rather than the default value
590        # and the description. While we're at it, we'll memorize the
591        # length of the longest option name.
592        my $longestName = 0;
593        my %parseOptions = ();
594        for my $key (keys %{$options}) {
595            if (length $key > $longestName) {
596                $longestName = length $key;
597            }
598            $parseOptions{$key} = $options->{$key}->[0];
599        }
600        # Parse the command line.
601        my ($retOptions, @retParameters) = ParseCommand(\%parseOptions, @argv);
602        # Get the logfile suffix.
603        my $suffix = $retOptions->{user};
604        # Check for background mode.
605        if ($retOptions->{background}) {
606            my $outFileName = "$FIG_Config::temp/out$suffix.log";
607            my $errFileName = "$FIG_Config::temp/err$suffix.log";
608            open STDOUT, ">$outFileName";
609            open STDERR, ">$errFileName";
610        }
611        # Now we want to set up tracing. First, we need to know if the user
612        # wants emergency tracing.
613        if ($retOptions->{trace} eq 'E') {
614            ETracing($retOptions->{user});
615                          } else {                          } else {
616                                  # Apply the override.          # Here the tracing is controlled from the command line.
617                                  $defaults->{$option} = $setting;          my @cats = @{$categories};
618            if ($retOptions->{sql}) {
619                push @cats, "SQL";
620            }
621            # Add the default categories.
622            push @cats, "Tracer";
623            # Next, we create the category string by joining the categories.
624            my $cats = join(" ", @cats);
625            # Check to determine whether or not the caller wants to turn off tracing
626            # to the standard output.
627            my $traceLevel = $retOptions->{trace};
628            my $textOKFlag = 1;
629            if ($traceLevel =~ /^(.)-/) {
630                $traceLevel = $1;
631                $textOKFlag = 0;
632            }
633            # Now we set up the trace mode.
634            my $traceMode;
635            # Verify that we can open a file in the FIG temporary directory.
636            my $traceFileName = "$FIG_Config::temp/trace$suffix.log";
637            if (open TESTTRACE, ">$traceFileName") {
638                # Here we can trace to a file.
639                $traceMode = ">$traceFileName";
640                if ($textOKFlag) {
641                    # Echo to standard output if the text-OK flag is set.
642                    $traceMode = "+$traceMode";
643                }
644                # Close the test file.
645                close TESTTRACE;
646            } else {
647                # Here we can't trace to a file. We trace to the standard output if it's
648                # okay, and the error log otherwise.
649                if ($textOKFlag) {
650                    $traceMode = "TEXT";
651                } else {
652                    $traceMode = "WARN";
653                          }                          }
654                  }                  }
655            # Now set up the tracing.
656            TSetup("$traceLevel $cats", $traceMode);
657          }          }
658          # Return the merged table.      # Check for the "h" option. If it is specified, dump the command-line
659          return $defaults;      # options and exit the program.
660        if ($retOptions->{help}) {
661            $0 =~ m#[/\\](\w+)(\.pl)?$#i;
662            print "$1 [options] $parmHelp\n";
663            for my $key (sort keys %{$options}) {
664                my $name = Pad($key, $longestName, 0, ' ');
665                my $desc = $options->{$key}->[1];
666                if ($options->{$key}->[0]) {
667                    $desc .= " (default " . $options->{$key}->[0] . ")";
668                }
669                print "  $name $desc\n";
670            }
671            exit(0);
672        }
673        # Trace the options, if applicable.
674        if (T(3)) {
675            my @parms = grep { $retOptions->{$_} } keys %{$retOptions};
676            Trace("Selected options: " . join(", ", sort @parms) . ".");
677        }
678        # Return the parsed parameters.
679        return ($retOptions, @retParameters);
680  }  }
681    
682  =head3 MergeOptions  =head3 Setups
683    
684  C<< Tracer::MergeOptions(\%table, \%defaults); >>  C<< my $count = Tracer::Setups(); >>
685    
686  Merge default values into a hash table. This method looks at the key-value pairs in the  Return the number of times L</TSetup> has been called.
687  second (default) hash, and if a matching key is not found in the first hash, the default  
688  pair is copied in. The process is similar to L</GetOptions>, but there is no error-  This method allows for the creation of conditional tracing setups where, for example, we
689  checking and no return value.  may want to set up tracing if nobody else has done it before us.
690    
691    =cut
692    
693    sub Setups {
694        return $SetupCount;
695    }
696    
697    =head3 Open
698    
699    C<< my $handle = Open($fileHandle, $fileSpec, $message); >>
700    
701    Open a file.
702    
703    The I<$fileSpec> is essentially the second argument of the PERL C<open>
704    function. The mode is specified using Unix-like shell information. So, for
705    example,
706    
707        Open(\*LOGFILE, '>>/usr/spool/news/twitlog', "Could not open twit log.");
708    
709    would open for output appended to the specified file, and
710    
711        Open(\*DATASTREAM, "| sort -u >$outputFile", "Could not open $outputFile.");
712    
713    would open a pipe that sorts the records written and removes duplicates. Note
714    the use of file handle syntax in the Open call. To use anonymous file handles,
715    code as follows.
716    
717        my $logFile = Open(undef, '>>/usr/spool/news/twitlog', "Could not open twit log.");
718    
719    The I<$message> parameter is used if the open fails. If it is set to C<0>, then
720    the open returns TRUE if successful and FALSE if an error occurred. Otherwise, a
721    failed open will throw an exception and the third parameter will be used to construct
722    an error message. If the parameter is omitted, a standard message is constructed
723    using the file spec.
724    
725        Could not open "/usr/spool/news/twitlog"
726    
727    Note that the mode characters are automatically cleaned from the file name.
728    The actual error message from the file system will be captured and appended to the
729    message in any case.
730    
731        Could not open "/usr/spool/news/twitlog": file not found.
732    
733    In some versions of PERL the only error message we get is a number, which
734    corresponds to the C++ C<errno> value.
735    
736        Could not open "/usr/spool/news/twitlog": 6.
737    
738  =over 4  =over 4
739    
740  =item table  =item fileHandle
741    
742  Hash table to be updated with the default values.  File handle. If this parameter is C<undef>, a file handle will be generated
743    and returned as the value of this method.
744    
745  =item defaults  =item fileSpec
746    
747  Default values to be merged into the first hash table if they are not already present.  File name and mode, as per the PERL C<open> function.
748    
749    =item message (optional)
750    
751    Error message to use if the open fails. If omitted, a standard error message
752    will be generated. In either case, the error information from the file system
753    is appended to the message. To specify a conditional open that does not throw
754    an error if it fails, use C<0>.
755    
756    =item RETURN
757    
758    Returns the name of the file handle assigned to the file, or C<undef> if the
759    open failed.
760    
761  =back  =back
762    
763  =cut  =cut
764    
765  sub MergeOptions {  sub Open {
766          # Get the parameters.          # Get the parameters.
767          my ($table, $defaults) = @_;      my ($fileHandle, $fileSpec, $message) = @_;
768          # Loop through the defaults.      # Attempt to open the file.
769          while (my ($key, $value) = each %{$defaults}) {      my $rv = open $fileHandle, $fileSpec;
770                  if (!exists $table->{$key}) {      # If the open failed, generate an error message.
771                          $table->{$key} = $value;      if (! $rv) {
772            # Save the system error message.
773            my $sysMessage = $!;
774            # See if we need a default message.
775            if (!$message) {
776                # Clean any obvious mode characters and leading spaces from the
777                # filename.
778                my ($fileName) = FindNamePart($fileSpec);
779                $message = "Could not open \"$fileName\"";
780                  }                  }
781            # Terminate with an error using the supplied message and the
782            # error message from the file system.
783            Confess("$message: $!");
784          }          }
785        # Return the file handle.
786        return $fileHandle;
787  }  }
788    
789  =head3 Trace  =head3 FindNamePart
790    
791  C<< Trace($message); >>  C<< my ($fileName, $start, $len) = Tracer::FindNamePart($fileSpec); >>
792    
793  Write a trace message to the target location specified in L</TSetup>. If there has not been  Extract the portion of a file specification that contains the file name.
 any prior call to B<TSetup>.  
794    
795  =over 4  A file specification is the string passed to an C<open> call. It specifies the file
796    mode and name. In a truly complex situation, it can specify a pipe sequence. This
797    method assumes that the file name is whatever follows the first angle bracket
798    sequence.  So, for example, in the following strings the file name is
799    C</usr/fig/myfile.txt>.
800    
801  =item message      >>/usr/fig/myfile.txt
802        </usr/fig/myfile.txt
803        | sort -u > /usr/fig/myfile.txt
804    
805  Message to write.  If the method cannot find a file name using its normal methods, it will return the
806    whole incoming string.
807    
808  =back  =over 4
809    
810    =item fileSpec
811    
812    File specification string from which the file name is to be extracted.
813    
814    =item RETURN
815    
816    Returns a three-element list. The first element contains the file name portion of
817    the specified string, or the whole string if a file name cannot be found via normal
818    methods. The second element contains the start position of the file name portion and
819    the third element contains the length.
820    
821    =back
822    
823    =cut
824    #: Return Type $;
825    sub FindNamePart {
826        # Get the parameters.
827        my ($fileSpec) = @_;
828        # Default to the whole input string.
829        my ($retVal, $pos, $len) = ($fileSpec, 0, length $fileSpec);
830        # Parse out the file name if we can.
831        if ($fileSpec =~ m/(<|>>?)(.+?)(\s*)$/) {
832            $retVal = $2;
833            $len = length $retVal;
834            $pos = (length $fileSpec) - (length $3) - $len;
835        }
836        # Return the result.
837        return ($retVal, $pos, $len);
838    }
839    
840    =head3 OpenDir
841    
842    C<< my @files = OpenDir($dirName, $filtered, $flag); >>
843    
844    Open a directory and return all the file names. This function essentially performs
845    the functions of an C<opendir> and C<readdir>. If the I<$filtered> parameter is
846    set to TRUE, all filenames beginning with a period (C<.>), dollar sign (C<$>),
847    or pound sign (C<#>) and all filenames ending with a tilde C<~>) will be
848    filtered out of the return list. If the directory does not open and I<$flag> is not
849    set, an exception is thrown. So, for example,
850    
851        my @files = OpenDir("/Volumes/fig/contigs", 1);
852    
853    is effectively the same as
854    
855        opendir(TMP, "/Volumes/fig/contigs") || Confess("Could not open /Volumes/fig/contigs.");
856        my @files = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir(TMP);
857    
858    Similarly, the following code
859    
860        my @files = grep { $_ =~ /^\d/ } OpenDir("/Volumes/fig/orgs", 0, 1);
861    
862    Returns the names of all files in C</Volumes/fig/orgs> that begin with digits and
863    automatically returns an empty list if the directory fails to open.
864    
865    =over 4
866    
867    =item dirName
868    
869    Name of the directory to open.
870    
871    =item filtered
872    
873    TRUE if files whose names begin with a period (C<.>) should be automatically removed
874    from the list, else FALSE.
875    
876    =item flag
877    
878    TRUE if a failure to open is okay, else FALSE
879    
880    =back
881    
882    =cut
883    #: Return Type @;
884    sub OpenDir {
885        # Get the parameters.
886        my ($dirName, $filtered, $flag) = @_;
887        # Declare the return variable.
888        my @retVal = ();
889        # Open the directory.
890        if (opendir(my $dirHandle, $dirName)) {
891            # The directory opened successfully. Get the appropriate list according to the
892            # strictures of the filter parameter.
893            if ($filtered) {
894                @retVal = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir $dirHandle;
895            } else {
896                @retVal = readdir $dirHandle;
897            }
898        } elsif (! $flag) {
899            # Here the directory would not open and it's considered an error.
900            Confess("Could not open directory $dirName.");
901        }
902        # Return the result.
903        return @retVal;
904    }
905    
906    =head3 SetLevel
907    
908    C<< Tracer::SetLevel($newLevel); >>
909    
910    Modify the trace level. A higher trace level will cause more messages to appear.
911    
912    =over 4
913    
914    =item newLevel
915    
916    Proposed new trace level.
917    
918    =back
919    
920    =cut
921    
922    sub SetLevel {
923        $TraceLevel = $_[0];
924    }
925    
926    =head3 Now
927    
928    C<< my $string = Tracer::Now(); >>
929    
930    Return a displayable time stamp containing the local time.
931    
932    =cut
933    
934    sub Now {
935        my ($sec,$min,$hour,$mday,$mon,$year,$wday,$yday,$isdst) = localtime(time);
936        my $retVal = _p2($mon+1) . "/" . _p2($mday) . "/" . ($year + 1900) . " " .
937                     _p2($hour) . ":" . _p2($min) . ":" . _p2($sec);
938        return $retVal;
939    }
940    
941    # Pad a number to 2 digits.
942    sub _p2 {
943        my ($value) = @_;
944        $value = "0$value" if ($value < 10);
945        return $value;
946    }
947    
948    =head3 ParseTraceDate
949    
950    C<< my $time = Tracer::ParseTraceDate($dateString); >>
951    
952    Convert a date from the trace file into a PERL timestamp.
953    
954    =over 4
955    
956    =item dateString
957    
958    The date string from the trace file. The format of the string is determined by the
959    L</Now> method.
960    
961    =item RETURN
962    
963    Returns a PERL time, that is, a number of seconds since the epoch, or C<undef> if
964    the time string is invalid.
965    
966    =back
967    
968    =cut
969    
970    sub ParseTraceDate {
971        # Get the parameters.
972        my ($dateString) = @_;
973        # Declare the return variable.
974        my $retVal;
975        # Parse the date.
976        if ($dateString =~ m#(\d+)/(\d+)/(\d+)\s+(\d+):(\d+):(\d+)#) {
977            # Create a time object. Note we need to convert the day, month,
978            # and year to a different base. Years count from 1900, and
979            # the internal month value is relocated to January = 0.
980            $retVal = timelocal($6, $5, $4, $2, $1 - 1, $3 - 1900);
981        }
982        # Return the result.
983        return $retVal;
984    }
985    
986    =head3 LogErrors
987    
988    C<< Tracer::LogErrors($fileName); >>
989    
990    Route the standard error output to a log file.
991    
992    =over 4
993    
994    =item fileName
995    
996    Name of the file to receive the error output.
997    
998    =back
999    
1000    =cut
1001    
1002    sub LogErrors {
1003        # Get the file name.
1004        my ($fileName) = @_;
1005        # Open the file as the standard error output.
1006        open STDERR, '>', $fileName;
1007    }
1008    
1009    =head3 ReadOptions
1010    
1011    C<< my %options = Tracer::ReadOptions($fileName); >>
1012    
1013    Read a set of options from a file. Each option is encoded in a line of text that has the
1014    format
1015    
1016    I<optionName>C<=>I<optionValue>C<; >I<comment>
1017    
1018    The option name must consist entirely of letters, digits, and the punctuation characters
1019    C<.> and C<_>, and is case sensitive. Blank lines and lines in which the first nonblank
1020    character is a semi-colon will be ignored. The return hash will map each option name to
1021    the corresponding option value.
1022    
1023    =over 4
1024    
1025    =item fileName
1026    
1027    Name of the file containing the option data.
1028    
1029    =item RETURN
1030    
1031    Returns a hash mapping the option names specified in the file to their corresponding option
1032    value.
1033    
1034    =back
1035    
1036    =cut
1037    
1038    sub ReadOptions {
1039        # Get the parameters.
1040        my ($fileName) = @_;
1041        # Open the file.
1042        (open CONFIGFILE, "<$fileName") || Confess("Could not open option file $fileName.");
1043        # Count the number of records read.
1044        my ($records, $comments) = 0;
1045        # Create the return hash.
1046        my %retVal = ();
1047        # Loop through the file, accumulating key-value pairs.
1048        while (my $line = <CONFIGFILE>) {
1049            # Denote we've read a line.
1050            $records++;
1051            # Determine the line type.
1052            if ($line =~ /^\s*[\n\r]/) {
1053                # A blank line is a comment.
1054                $comments++;
1055            } elsif ($line =~ /^\s*([A-Za-z0-9_\.]+)=([^;]*);/) {
1056                # Here we have an option assignment.
1057                retVal{$1} = $2;
1058            } elsif ($line =~ /^\s*;/) {
1059                # Here we have a text comment.
1060                $comments++;
1061            } else {
1062                # Here we have an invalid line.
1063                Trace("Invalid option statement in record $records.") if T(0);
1064            }
1065        }
1066        # Return the hash created.
1067        return %retVal;
1068    }
1069    
1070    =head3 GetOptions
1071    
1072    C<< Tracer::GetOptions(\%defaults, \%options); >>
1073    
1074    Merge a specified set of options into a table of defaults. This method takes two hash references
1075    as input and uses the data from the second to update the first. If the second does not exist,
1076    there will be no effect. An error will be thrown if one of the entries in the second hash does not
1077    exist in the first.
1078    
1079    Consider the following example.
1080    
1081    C<< my $optionTable = GetOptions({ dbType => 'mySQL', trace => 0 }, $options); >>
1082    
1083    In this example, the variable B<$options> is expected to contain at most two options-- B<dbType> and
1084    B<trace>. The default database type is C<mySQL> and the default trace level is C<0>. If the value of
1085    B<$options> is C<< {dbType => 'Oracle'} >>, then the database type will be changed to C<Oracle> and
1086    the trace level will remain at 0. If B<$options> is undefined, then the database type and trace level
1087    will remain C<mySQL> and C<0>. If, on the other hand, B<$options> is defined as
1088    
1089    C<< {databaseType => 'Oracle'} >>
1090    
1091    an error will occur because the B<databaseType> option does not exist.
1092    
1093    =over 4
1094    
1095    =item defaults
1096    
1097    Table of default option values.
1098    
1099    =item options
1100    
1101    Table of overrides, if any.
1102    
1103    =item RETURN
1104    
1105    Returns a reference to the default table passed in as the first parameter.
1106    
1107    =back
1108    
1109    =cut
1110    
1111    sub GetOptions {
1112        # Get the parameters.
1113        my ($defaults, $options) = @_;
1114        # Check for overrides.
1115        if ($options) {
1116            # Loop through the overrides.
1117            while (my ($option, $setting) = each %{$options}) {
1118                # Insure this override exists.
1119                if (!exists $defaults->{$option}) {
1120                    croak "Unrecognized option $option encountered.";
1121                } else {
1122                    # Apply the override.
1123                    $defaults->{$option} = $setting;
1124                }
1125            }
1126        }
1127        # Return the merged table.
1128        return $defaults;
1129    }
1130    
1131    =head3 MergeOptions
1132    
1133    C<< Tracer::MergeOptions(\%table, \%defaults); >>
1134    
1135    Merge default values into a hash table. This method looks at the key-value pairs in the
1136    second (default) hash, and if a matching key is not found in the first hash, the default
1137    pair is copied in. The process is similar to L</GetOptions>, but there is no error-
1138    checking and no return value.
1139    
1140    =over 4
1141    
1142    =item table
1143    
1144    Hash table to be updated with the default values.
1145    
1146    =item defaults
1147    
1148    Default values to be merged into the first hash table if they are not already present.
1149    
1150    =back
1151    
1152    =cut
1153    
1154    sub MergeOptions {
1155        # Get the parameters.
1156        my ($table, $defaults) = @_;
1157        # Loop through the defaults.
1158        while (my ($key, $value) = each %{$defaults}) {
1159            if (!exists $table->{$key}) {
1160                $table->{$key} = $value;
1161            }
1162        }
1163    }
1164    
1165    =head3 Trace
1166    
1167    C<< Trace($message); >>
1168    
1169    Write a trace message to the target location specified in L</TSetup>. If there has not been
1170    any prior call to B<TSetup>.
1171    
1172    =over 4
1173    
1174    =item message
1175    
1176    Message to write.
1177    
1178    =back
1179    
1180    =cut
1181    
1182    sub Trace {
1183        # Get the parameters.
1184        my ($message) = @_;
1185        # Get the timestamp.
1186        my $timeStamp = Now();
1187        # Format the message. Note we strip off any line terminators at the end.
1188        my $formatted = "[$timeStamp] <$LastCategory>: " . Strip($message);
1189        # Process according to the destination.
1190        if ($Destination eq "TEXT") {
1191            # Write the message to the standard output.
1192            print "$formatted\n";
1193        } elsif ($Destination eq "ERROR") {
1194            # Write the message to the error output.
1195            print STDERR "$formatted\n";
1196        } elsif ($Destination eq "QUEUE") {
1197            # Push the message into the queue.
1198            push @Queue, "$formatted";
1199        } elsif ($Destination eq "HTML") {
1200            # Convert the message to HTML and write it to the standard output.
1201            my $escapedMessage = CGI::escapeHTML($message);
1202            print "<p>$formatted</p>\n";
1203        } elsif ($Destination eq "WARN") {
1204           # Emit the message as a warning.
1205           warn $message;
1206        } elsif ($Destination =~ m/^>>/) {
1207            # Write the trace message to an output file.
1208            (open TRACING, $Destination) || die "Tracing open for \"$Destination\" failed: $!";
1209            print TRACING "$formatted\n";
1210            close TRACING;
1211            # If the Tee flag is on, echo it to the standard output.
1212            if ($TeeFlag) {
1213                print "$formatted\n";
1214            }
1215        }
1216    }
1217    
1218    =head3 T
1219    
1220    C<< my $switch = T($category, $traceLevel); >>
1221    
1222        or
1223    
1224    C<< my $switch = T($traceLevel); >>
1225    
1226    Return TRUE if the trace level is at or above a specified value and the specified category
1227    is active, else FALSE. If no category is specified, the caller's package name is used.
1228    
1229    =over 4
1230    
1231    =item category
1232    
1233    Category to which the message belongs. If not specified, the caller's package name is
1234    used.
1235    
1236    =item traceLevel
1237    
1238    Relevant tracing level.
1239    
1240    =item RETURN
1241    
1242    TRUE if a message at the specified trace level would appear in the trace, else FALSE.
1243    
1244    =back
1245    
1246    =cut
1247    
1248    sub T {
1249        # Declare the return variable.
1250        my $retVal = 0;
1251        # Only proceed if tracing is turned on.
1252        if ($Destination ne "NONE") {
1253            # Get the parameters.
1254            my ($category, $traceLevel) = @_;
1255            if (!defined $traceLevel) {
1256                # Here we have no category, so we need to get the calling package.
1257                # The calling package is normally the first parameter. If it is
1258                # omitted, the first parameter will be the tracelevel. So, the
1259                # first thing we do is shift the so-called category into the
1260                # $traceLevel variable where it belongs.
1261                $traceLevel = $category;
1262                my ($package, $fileName, $line) = caller;
1263                # If there is no calling package, we default to "main".
1264                if (!$package) {
1265                    $category = "main";
1266                } else {
1267                    $category = $package;
1268                }
1269            }
1270            # Save the category name.
1271            $LastCategory = $category;
1272            # Convert it to lower case before we hash it.
1273            $category = lc $category;
1274            # Use the category and tracelevel to compute the result.
1275            if (ref $traceLevel) {
1276                Confess("Bad trace level.");
1277            } elsif (ref $TraceLevel) {
1278                Confess("Bad trace config.");
1279            }
1280            $retVal = ($traceLevel <= $TraceLevel && ($AllTrace || exists $Categories{$category}));
1281        }
1282        # Return the computed result.
1283        return $retVal;
1284    }
1285    
1286    =head3 ParseCommand
1287    
1288    C<< my ($options, @arguments) = Tracer::ParseCommand(\%optionTable, @inputList); >>
1289    
1290    Parse a command line consisting of a list of parameters. The initial parameters may be option
1291    specifiers of the form C<->I<option> or C<->I<option>C<=>I<value>. The options are stripped
1292    off and merged into a table of default options. The remainder of the command line is
1293    returned as a list of positional arguments. For example, consider the following invocation.
1294    
1295    C<< my ($options, @arguments) = ParseCommand({ errors => 0, logFile => 'trace.log'}, @words); >>
1296    
1297    In this case, the list @words will be treated as a command line and there are two options available,
1298    B<errors> and B<logFile>. If @words has the following format
1299    
1300    C<< -logFile=error.log apple orange rutabaga >>
1301    
1302    then at the end of the invocation, C<$options> will be
1303    
1304    C<< { errors => 0, logFile => 'error.log' } >>
1305    
1306    and C<@arguments> will contain
1307    
1308    C<< apple orange rutabaga >>
1309    
1310    The parser allows for some escape sequences. See L</UnEscape> for a description. There is no
1311    support for quote characters. Options can be specified with single or double hyphens.
1312    
1313    =over 4
1314    
1315    =item optionTable
1316    
1317    Table of default options.
1318    
1319    =item inputList
1320    
1321    List of words on the command line.
1322    
1323    =item RETURN
1324    
1325    Returns a reference to the option table and a list of the positional arguments.
1326    
1327    =back
1328    
1329    =cut
1330    
1331    sub ParseCommand {
1332        # Get the parameters.
1333        my ($optionTable, @inputList) = @_;
1334        # Process any options in the input list.
1335        my %overrides = ();
1336        while ((@inputList > 0) && ($inputList[0] =~ /^--?/)) {
1337            # Get the current option.
1338            my $arg = shift @inputList;
1339            # Pull out the option name.
1340            $arg =~ /^--?([^=]*)/g;
1341            my $name = $1;
1342            # Check for an option value.
1343            if ($arg =~ /\G=(.*)$/g) {
1344                # Here we have a value for the option.
1345                $overrides{$name} = UnEscape($1);
1346            } else {
1347                # Here there is no value, so we use 1.
1348                $overrides{$name} = 1;
1349            }
1350        }
1351        # Merge the options into the defaults.
1352        GetOptions($optionTable, \%overrides);
1353        # Translate the remaining parameters.
1354        my @retVal = ();
1355        for my $inputParm (@inputList) {
1356            push @retVal, UnEscape($inputParm);
1357        }
1358        # Return the results.
1359        return ($optionTable, @retVal);
1360    }
1361    
1362    =head3 Escape
1363    
1364    C<< my $codedString = Tracer::Escape($realString); >>
1365    
1366    Escape a string for use in a command length. Tabs will be replaced by C<\t>, new-lines
1367    replaced by C<\n>, carriage returns will be deleted, and backslashes will be doubled. The
1368    result is to reverse the effect of L</UnEscape>.
1369    
1370    =over 4
1371    
1372    =item realString
1373    
1374    String to escape.
1375    
1376    =item RETURN
1377    
1378    Escaped equivalent of the real string.
1379    
1380    =back
1381    
1382    =cut
1383    
1384    sub Escape {
1385        # Get the parameter.
1386        my ($realString) = @_;
1387        # Initialize the return variable.
1388        my $retVal = "";
1389        # Loop through the parameter string, looking for sequences to escape.
1390        while (length $realString > 0) {
1391            # Look for the first sequence to escape.
1392            if ($realString =~ /^(.*?)([\n\t\r\\])/) {
1393                # Here we found it. The text preceding the sequence is in $1. The sequence
1394                # itself is in $2. First, move the clear text to the return variable.
1395                $retVal .= $1;
1396                # Strip the processed section off the real string.
1397                $realString = substr $realString, (length $2) + (length $1);
1398                # Get the matched character.
1399                my $char = $2;
1400                # If we have a CR, we are done.
1401                if ($char ne "\r") {
1402                    # It's not a CR, so encode the escape sequence.
1403                    $char =~ tr/\t\n/tn/;
1404                    $retVal .= "\\" . $char;
1405                }
1406            } else {
1407                # Here there are no more escape sequences. The rest of the string is
1408                # transferred unmodified.
1409                $retVal .= $realString;
1410                $realString = "";
1411            }
1412        }
1413        # Return the result.
1414        return $retVal;
1415    }
1416    
1417    =head3 UnEscape
1418    
1419    C<< my $realString = Tracer::UnEscape($codedString); >>
1420    
1421    Replace escape sequences with their actual equivalents. C<\t> will be replaced by
1422    a tab, C<\n> by a new-line character, and C<\\> by a backslash. C<\r> codes will
1423    be deleted.
1424    
1425    =over 4
1426    
1427    =item codedString
1428    
1429    String to un-escape.
1430    
1431    =item RETURN
1432    
1433    Returns a copy of the original string with the escape sequences converted to their actual
1434    values.
1435    
1436    =back
1437    
1438    =cut
1439    
1440    sub UnEscape {
1441        # Get the parameter.
1442        my ($codedString) = @_;
1443        # Initialize the return variable.
1444        my $retVal = "";
1445        # Only proceed if the incoming string is nonempty.
1446        if (defined $codedString) {
1447            # Loop through the parameter string, looking for escape sequences. We can't do
1448            # translating because it causes problems with the escaped slash. ("\\t" becomes
1449            # "\<tab>" no matter what we do.)
1450            while (length $codedString > 0) {
1451                # Look for the first escape sequence.
1452                if ($codedString =~ /^(.*?)\\(\\|n|t|r)/) {
1453                    # Here we found it. The text preceding the sequence is in $1. The sequence
1454                    # itself is in $2. First, move the clear text to the return variable.
1455                    $retVal .= $1;
1456                    $codedString = substr $codedString, (2 + length $1);
1457                    # Get the escape value.
1458                    my $char = $2;
1459                    # If we have a "\r", we are done.
1460                    if ($char ne 'r') {
1461                        # Here it's not an 'r', so we convert it.
1462                        $char =~ tr/\\tn/\\\t\n/;
1463                        $retVal .= $char;
1464                    }
1465                } else {
1466                    # Here there are no more escape sequences. The rest of the string is
1467                    # transferred unmodified.
1468                    $retVal .= $codedString;
1469                    $codedString = "";
1470                }
1471            }
1472        }
1473        # Return the result.
1474        return $retVal;
1475    }
1476    
1477    =head3 ParseRecord
1478    
1479    C<< my @fields = Tracer::ParseRecord($line); >>
1480    
1481    Parse a tab-delimited data line. The data line is split into field values. Embedded tab
1482    and new-line characters in the data line must be represented as C<\t> and C<\n>, respectively.
1483    These will automatically be converted.
1484    
1485    =over 4
1486    
1487    =item line
1488    
1489    Line of data containing the tab-delimited fields.
1490    
1491    =item RETURN
1492    
1493    Returns a list of the fields found in the data line.
1494    
1495    =back
1496    
1497    =cut
1498    
1499    sub ParseRecord {
1500        # Get the parameter.
1501        my ($line) = @_;
1502        # Remove the trailing new-line, if any.
1503        chomp $line;
1504        # Split the line read into pieces using the tab character.
1505        my @retVal = split /\t/, $line;
1506        # Trim and fix the escapes in each piece.
1507        for my $value (@retVal) {
1508            # Trim leading whitespace.
1509            $value =~ s/^\s+//;
1510            # Trim trailing whitespace.
1511            $value =~ s/\s+$//;
1512            # Delete the carriage returns.
1513            $value =~ s/\r//g;
1514            # Convert the escapes into their real values.
1515            $value =~ s/\\t/"\t"/ge;
1516            $value =~ s/\\n/"\n"/ge;
1517        }
1518        # Return the result.
1519        return @retVal;
1520    }
1521    
1522    =head3 Merge
1523    
1524    C<< my @mergedList = Tracer::Merge(@inputList); >>
1525    
1526    Sort a list of strings and remove duplicates.
1527    
1528    =over 4
1529    
1530    =item inputList
1531    
1532    List of scalars to sort and merge.
1533    
1534    =item RETURN
1535    
1536    Returns a list containing the same elements sorted in ascending order with duplicates
1537    removed.
1538    
1539    =back
1540    
1541    =cut
1542    
1543    sub Merge {
1544        # Get the input list in sort order.
1545        my @inputList = sort @_;
1546        # Only proceed if the list has at least two elements.
1547        if (@inputList > 1) {
1548            # Now we want to move through the list splicing out duplicates.
1549            my $i = 0;
1550            while ($i < @inputList) {
1551                # Get the current entry.
1552                my $thisEntry = $inputList[$i];
1553                # Find out how many elements duplicate the current entry.
1554                my $j = $i + 1;
1555                my $dup1 = $i + 1;
1556                while ($j < @inputList && $inputList[$j] eq $thisEntry) { $j++; };
1557                # If the number is nonzero, splice out the duplicates found.
1558                if ($j > $dup1) {
1559                    splice @inputList, $dup1, $j - $dup1;
1560                }
1561                # Now the element at position $dup1 is different from the element before it
1562                # at position $i. We push $i forward one position and start again.
1563                $i++;
1564            }
1565        }
1566        # Return the merged list.
1567        return @inputList;
1568    }
1569    
1570    =head3 Percent
1571    
1572    C<< my $percent = Tracer::Percent($number, $base); >>
1573    
1574    Returns the percent of the base represented by the given number. If the base
1575    is zero, returns zero.
1576    
1577    =over 4
1578    
1579    =item number
1580    
1581    Percent numerator.
1582    
1583    =item base
1584    
1585    Percent base.
1586    
1587    =item RETURN
1588    
1589    Returns the percentage of the base represented by the numerator.
1590    
1591    =back
1592    
1593    =cut
1594    
1595    sub Percent {
1596        # Get the parameters.
1597        my ($number, $base) = @_;
1598        # Declare the return variable.
1599        my $retVal = 0;
1600        # Compute the percent.
1601        if ($base != 0) {
1602            $retVal = $number * 100 / $base;
1603        }
1604        # Return the result.
1605        return $retVal;
1606    }
1607    
1608    =head3 GetFile
1609    
1610    C<< my @fileContents = Tracer::GetFile($fileName); >>
1611    
1612        or
1613    
1614    C<< my $fileContents = Tracer::GetFile($fileName); >>
1615    
1616    Return the entire contents of a file. In list context, line-ends are removed and
1617    each line is a list element. In scalar context, line-ends are replaced by C<\n>.
1618    
1619    =over 4
1620    
1621    =item fileName
1622    
1623    Name of the file to read.
1624    
1625    =item RETURN
1626    
1627    In a list context, returns the entire file as a list with the line terminators removed.
1628    In a scalar context, returns the entire file as a string. If an error occurs opening
1629    the file, an empty list will be returned.
1630    
1631    =back
1632    
1633    =cut
1634    
1635    sub GetFile {
1636        # Get the parameters.
1637        my ($fileName) = @_;
1638        # Declare the return variable.
1639        my @retVal = ();
1640        # Open the file for input.
1641        my $handle = Open(undef, "<$fileName");
1642        # Read the whole file into the return variable, stripping off any terminator
1643        # characters.
1644        my $lineCount = 0;
1645        while (my $line = <$handle>) {
1646            $lineCount++;
1647            $line = Strip($line);
1648            push @retVal, $line;
1649        }
1650        # Close it.
1651        close $handle;
1652        my $actualLines = @retVal;
1653        Trace("$actualLines lines read from file $fileName.") if T(File => 2);
1654        # Return the file's contents in the desired format.
1655        if (wantarray) {
1656            return @retVal;
1657        } else {
1658            return join "\n", @retVal;
1659        }
1660    }
1661    
1662    =head3 PutFile
1663    
1664    C<< Tracer::PutFile($fileName, \@lines); >>
1665    
1666    Write out a file from a list of lines of text.
1667    
1668    =over 4
1669    
1670    =item fileName
1671    
1672    Name of the output file.
1673    
1674    =item lines
1675    
1676    Reference to a list of text lines. The lines will be written to the file in order, with trailing
1677    new-line characters. Alternatively, may be a string, in which case the string will be written without
1678    modification.
1679    
1680    =back
1681    
1682    =cut
1683    
1684    sub PutFile {
1685        # Get the parameters.
1686        my ($fileName, $lines) = @_;
1687        # Open the output file.
1688        my $handle = Open(undef, ">$fileName");
1689        # Count the lines written.
1690        if (ref $lines ne 'ARRAY') {
1691            # Here we have a scalar, so we write it raw.
1692            print $handle $lines;
1693            Trace("Scalar put to file $fileName.") if T(File => 3);
1694        } else {
1695            # Write the lines one at a time.
1696            my $count = 0;
1697            for my $line (@{$lines}) {
1698                print $handle "$line\n";
1699                $count++;
1700            }
1701            Trace("$count lines put to file $fileName.") if T(File => 3);
1702        }
1703        # Close the output file.
1704        close $handle;
1705    }
1706    
1707    =head3 QTrace
1708    
1709    C<< my $data = QTrace($format); >>
1710    
1711    Return the queued trace data in the specified format.
1712    
1713    =over 4
1714    
1715    =item format
1716    
1717    C<html> to format the data as an HTML list, C<text> to format it as straight text.
1718    
1719    =back
1720    
1721    =cut
1722    
1723    sub QTrace {
1724        # Get the parameter.
1725        my ($format) = @_;
1726        # Create the return variable.
1727        my $retVal = "";
1728        # Only proceed if there is an actual queue.
1729        if (@Queue) {
1730            # Process according to the format.
1731            if ($format =~ m/^HTML$/i) {
1732                # Convert the queue into an HTML list.
1733                $retVal = "<ul>\n";
1734                for my $line (@Queue) {
1735                    my $escapedLine = CGI::escapeHTML($line);
1736                    $retVal .= "<li>$escapedLine</li>\n";
1737                }
1738                $retVal .= "</ul>\n";
1739            } elsif ($format =~ m/^TEXT$/i) {
1740                # Convert the queue into a list of text lines.
1741                $retVal = join("\n", @Queue) . "\n";
1742            }
1743            # Clear the queue.
1744            @Queue = ();
1745        }
1746        # Return the formatted list.
1747        return $retVal;
1748    }
1749    
1750    =head3 Confess
1751    
1752    C<< Confess($message); >>
1753    
1754    Trace the call stack and abort the program with the specified message. When used with
1755    the OR operator and the L</Assert> method, B<Confess> can function as a debugging assert.
1756    So, for example
1757    
1758    C<< Assert($recNum >= 0) || Confess("Invalid record number $recNum."); >>
1759    
1760    Will abort the program with a stack trace if the value of C<$recNum> is negative.
1761    
1762    =over 4
1763    
1764    =item message
1765    
1766    Message to include in the trace.
1767    
1768    =back
1769    
1770    =cut
1771    
1772    sub Confess {
1773        # Get the parameters.
1774        my ($message) = @_;
1775        # Trace the call stack.
1776        Cluck($message);
1777        # Abort the program.
1778        croak(">>> $message");
1779    }
1780    
1781    =head3 Assert
1782    
1783    C<< Assert($condition1, $condition2, ... $conditionN); >>
1784    
1785    Return TRUE if all the conditions are true. This method can be used in conjunction with
1786    the OR operator and the L</Confess> method as a debugging assert.
1787    So, for example
1788    
1789    C<< Assert($recNum >= 0) || Confess("Invalid record number $recNum."); >>
1790    
1791    Will abort the program with a stack trace if the value of C<$recNum> is negative.
1792    
1793    =cut
1794    sub Assert {
1795        my $retVal = 1;
1796        LOOP: for my $condition (@_) {
1797            if (! $condition) {
1798                $retVal = 0;
1799                last LOOP;
1800            }
1801        }
1802        return $retVal;
1803    }
1804    
1805    =head3 Cluck
1806    
1807    C<< Cluck($message); >>
1808    
1809    Trace the call stack. Note that for best results, you should qualify the call with a
1810    trace condition. For example,
1811    
1812    C<< Cluck("Starting record parse.") if T(3); >>
1813    
1814    will only trace the stack if the trace level for the package is 3 or more.
1815    
1816    =over 4
1817    
1818    =item message
1819    
1820    Message to include in the trace.
1821    
1822    =back
1823    
1824    =cut
1825    
1826    sub Cluck {
1827        # Get the parameters.
1828        my ($message) = @_;
1829        # Trace what's happening.
1830        Trace("Stack trace for event: $message");
1831        my $confession = longmess($message);
1832        # Convert the confession to a series of trace messages. Note we skip any
1833        # messages relating to calls into Tracer.
1834        for my $line (split /\s*\n/, $confession) {
1835            Trace($line) if ($line !~ /Tracer\.pm/);
1836        }
1837    }
1838    
1839    =head3 Min
1840    
1841    C<< my $min = Min($value1, $value2, ... $valueN); >>
1842    
1843    Return the minimum argument. The arguments are treated as numbers.
1844    
1845    =over 4
1846    
1847    =item $value1, $value2, ... $valueN
1848    
1849    List of numbers to compare.
1850    
1851    =item RETURN
1852    
1853    Returns the lowest number in the list.
1854    
1855    =back
1856    
1857    =cut
1858    
1859    sub Min {
1860        # Get the parameters. Note that we prime the return value with the first parameter.
1861        my ($retVal, @values) = @_;
1862        # Loop through the remaining parameters, looking for the lowest.
1863        for my $value (@values) {
1864            if ($value < $retVal) {
1865                $retVal = $value;
1866            }
1867        }
1868        # Return the minimum found.
1869        return $retVal;
1870    }
1871    
1872    =head3 Max
1873    
1874    C<< my $max = Max($value1, $value2, ... $valueN); >>
1875    
1876    Return the maximum argument. The arguments are treated as numbers.
1877    
1878    =over 4
1879    
1880    =item $value1, $value2, ... $valueN
1881    
1882    List of numbers to compare.
1883    
1884    =item RETURN
1885    
1886    Returns the highest number in the list.
1887    
1888    =back
1889    
1890  =cut  =cut
1891    
1892  sub Trace {  sub Max {
1893        # Get the parameters. Note that we prime the return value with the first parameter.
1894        my ($retVal, @values) = @_;
1895        # Loop through the remaining parameters, looking for the highest.
1896        for my $value (@values) {
1897            if ($value > $retVal) {
1898                $retVal = $value;
1899            }
1900        }
1901        # Return the maximum found.
1902        return $retVal;
1903    }
1904    
1905    =head3 AddToListMap
1906    
1907    C<< Tracer::AddToListMap(\%hash, $key, $value1, $value2, ... valueN); >>
1908    
1909    Add a key-value pair to a hash of lists. If no value exists for the key, a singleton list
1910    is created for the key. Otherwise, the new value is pushed onto the list.
1911    
1912    =over 4
1913    
1914    =item hash
1915    
1916    Reference to the target hash.
1917    
1918    =item key
1919    
1920    Key for which the value is to be added.
1921    
1922    =item value1, value2, ... valueN
1923    
1924    List of values to add to the key's value list.
1925    
1926    =back
1927    
1928    =cut
1929    
1930    sub AddToListMap {
1931          # Get the parameters.          # Get the parameters.
1932          my ($message) = @_;      my ($hash, $key, @values) = @_;
1933          # Get the timestamp.      # Process according to whether or not the key already has a value.
1934          my $timeStamp = Now();      if (! exists $hash->{$key}) {
1935          # Format the message. Note we strip off any line terminators at the end.          $hash->{$key} = [@values];
1936          my $formatted = "$timeStamp <$LastCategory>: " . Strip($message);      } else {
1937          # Process according to the destination.          push @{$hash->{$key}}, @values;
         if ($Destination eq "TEXT") {  
                 # Write the message to the standard output.  
                 print "$formatted\n";  
         } elsif ($Destination eq "ERROR") {  
                 # Write the message to the error output.  
                 print STDERR "$formatted\n";  
         } elsif ($Destination eq "QUEUE") {  
                 # Push the message into the queue.  
                 push @Queue, "$formatted";  
         } elsif ($Destination eq "HTML") {  
                 # Convert the message to HTML and write it to the standard output.  
                 my $escapedMessage = CGI::escapeHTML($message);  
                 print "<p>$formatted</p>\n";  
     } elsif ($Destination eq "WARN") {  
        # Emit the message as a warning.  
        warn $message;  
         } elsif ($Destination =~ m/^>>/) {  
                 # Write the trace message to an output file.  
                 open TRACING, $Destination;  
                 print TRACING "$formatted\n";  
                 close TRACING;  
1938          }          }
1939  }  }
1940    
1941  =head3 T  =head3 DebugMode
1942    
1943  C<< my $switch = T($category, $traceLevel); >>  C<< if (Tracer::DebugMode) { ...code... } >>
1944    
1945          or  Return TRUE if debug mode has been turned on, else abort.
1946    
1947  C<< my $switch = T($traceLevel); >>  Certain CGI scripts are too dangerous to exist in the production
1948    environment. This method provides a simple way to prevent them
1949    from working unless they are explicitly turned on by creating a password
1950    cookie via the B<SetPassword> script.  If debugging mode
1951    is not turned on, an error will occur.
1952    
1953  Return TRUE if the trace level is at or above a specified value and the specified category  =cut
1954  is active, else FALSE. If no category is specified, the caller's package name is used.  
1955    sub DebugMode {
1956        # Declare the return variable.
1957        my $retVal = 0;
1958        # Check the debug configuration.
1959        my $password = CGI::cookie("DebugMode");
1960        my $encrypted = Digest::MD5::md5_hex($password);
1961        if ($encrypted eq "252dec43280e0c0d6a75ffcec486e61d") {
1962            $retVal = 1;
1963        } else {
1964            # Here debug mode is off, so we generate an error.
1965            Confess("Cannot use this facility without logging in.");
1966        }
1967        # Return the determination indicator.
1968        return $retVal;
1969    }
1970    
1971    =head3 Strip
1972    
1973    C<< my $string = Tracer::Strip($line); >>
1974    
1975    Strip all line terminators off a string. This is necessary when dealing with files
1976    that may have been transferred back and forth several times among different
1977    operating environments.
1978    
1979  =over 4  =over 4
1980    
1981  =item category  =item line
1982    
1983  Category to which the message belongs. If not specified, the caller's package name is  Line of text to be stripped.
1984  used.  
1985    =item RETURN
1986    
1987    The same line of text with all the line-ending characters chopped from the end.
1988    
1989    =back
1990    
1991    =cut
1992    
1993    sub Strip {
1994        # Get a copy of the parameter string.
1995        my ($string) = @_;
1996        my $retVal = (defined $string ? $string : "");
1997        # Strip the line terminator characters.
1998        $retVal =~ s/(\r|\n)+$//g;
1999        # Return the result.
2000        return $retVal;
2001    }
2002    
2003    =head3 Pad
2004    
2005    C<< my $paddedString = Tracer::Pad($string, $len, $left, $padChar); >>
2006    
2007    Pad a string to a specified length. The pad character will be a
2008    space, and the padding will be on the right side unless specified
2009    in the third parameter.
2010    
2011    =over 4
2012    
2013    =item string
2014    
2015    String to be padded.
2016    
2017    =item len
2018    
2019    Desired length of the padded string.
2020    
2021    =item left (optional)
2022    
2023    TRUE if the string is to be left-padded; otherwise it will be padded on the right.
2024    
2025    =item padChar (optional)
2026    
2027    Character to use for padding. The default is a space.
2028    
2029    =item RETURN
2030    
2031    Returns a copy of the original string with the pad character added to the
2032    specified end so that it achieves the desired length.
2033    
2034    =back
2035    
2036    =cut
2037    
2038    sub Pad {
2039        # Get the parameters.
2040        my ($string, $len, $left, $padChar) = @_;
2041        # Compute the padding character.
2042        if (! defined $padChar) {
2043            $padChar = " ";
2044        }
2045        # Compute the number of spaces needed.
2046        my $needed = $len - length $string;
2047        # Copy the string into the return variable.
2048        my $retVal = $string;
2049        # Only proceed if padding is needed.
2050        if ($needed > 0) {
2051            # Create the pad string.
2052            my $pad = $padChar x $needed;
2053            # Affix it to the return value.
2054            if ($left) {
2055                $retVal = $pad . $retVal;
2056            } else {
2057                $retVal .= $pad;
2058            }
2059        }
2060        # Return the result.
2061        return $retVal;
2062    }
2063    
2064    =head3 EOF
2065    
2066    This is a constant that is lexically greater than any useful string.
2067    
2068    =cut
2069    
2070    sub EOF {
2071        return "\xFF\xFF\xFF\xFF\xFF";
2072    }
2073    
2074    =head3 TICK
2075    
2076    C<< my @results = TICK($commandString); >>
2077    
2078    Perform a back-tick operation on a command. If this is a Windows environment, any leading
2079    dot-slash (C<./> will be removed. So, for example, if you were doing
2080    
2081        `./protein.cgi`
2082    
2083    from inside a CGI script, it would work fine in Unix, but would issue an error message
2084    in Windows complaining that C<'.'> is not a valid command. If instead you code
2085    
2086        TICK("./protein.cgi")
2087    
2088    it will work correctly in both environments.
2089    
2090    =over 4
2091    
2092    =item commandString
2093    
2094    The command string to pass to the system.
2095    
2096    =item RETURN
2097    
2098    Returns the standard output from the specified command, as a list.
2099    
2100    =back
2101    
2102    =cut
2103    #: Return Type @;
2104    sub TICK {
2105        # Get the parameters.
2106        my ($commandString) = @_;
2107        # Chop off the dot-slash if this is Windows.
2108        if ($FIG_Config::win_mode) {
2109            $commandString =~ s!^\./!!;
2110        }
2111        # Activate the command and return the result.
2112        return `$commandString`;
2113    }
2114    
2115    =head3 ScriptSetup
2116    
2117    C<< my ($cgi, $varHash) = ScriptSetup($noTrace); >>
2118    
2119    Perform standard tracing and debugging setup for scripts. The value returned is
2120    the CGI object followed by a pre-built variable hash. At the end of the script,
2121    the client should call L</ScriptFinish> to output the web page.
2122    
2123    This method calls L</ETracing> to configure tracing, which allows the tracing
2124    to be configured via the emergency tracing form on the debugging control panel.
2125    Tracing will then be turned on automatically for all programs that use the L</ETracing>
2126    method, which includes every program that uses this method or L</StandardSetup>.
2127    
2128    =over 4
2129    
2130    =item noTrace (optional)
2131    
2132    If specified, tracing will be suppressed. This is useful if the script wants to set up
2133    tracing manually.
2134    
2135    =item RETURN
2136    
2137    Returns a two-element list consisting of a CGI query object and a variable hash for
2138    the output page.
2139    
2140    =back
2141    
2142    =cut
2143    
2144    sub ScriptSetup {
2145        # Get the parameters.
2146        my ($noTrace) = @_;
2147        # Get the CGI query object.
2148        my $cgi = CGI->new();
2149        # Set up tracing if it's not suppressed.
2150        ETracing($cgi) unless $noTrace;
2151        # Create the variable hash.
2152        my $varHash = { results => '' };
2153        # Return the query object and variable hash.
2154        return ($cgi, $varHash);
2155    }
2156    
2157    =head3 ETracing
2158    
2159    C<< ETracing($parameter); >>
2160    
2161    Set up emergency tracing. Emergency tracing is tracing that is turned
2162    on automatically for any program that calls this method. The emergency
2163    tracing parameters are stored in a a file identified by a tracing key.
2164    If this method is called with a CGI object, then the tracing key is
2165    taken from a cookie. If it is called with no parameters, then the tracing
2166    key is taken from an environment variable. If it is called with a string,
2167    the tracing key is that string.
2168    
2169    =over 4
2170    
2171    =item parameter
2172    
2173    A parameter from which the tracing key is computed. If it is a scalar,
2174    that scalar is used as the tracing key. If it is a CGI object, the
2175    tracing key is taken from the C<IP> cookie. If it is omitted, the
2176    tracing key is taken from the C<TRACING> environment variable. If it
2177    is a CGI object and emergency tracing is not on, the C<Trace> and
2178    C<TF> parameters will be used to determine the type of tracing.
2179    
2180    =back
2181    
2182    =cut
2183    
2184    sub ETracing {
2185        # Get the parameter.
2186        my ($parameter) = @_;
2187        # Check for CGI mode.
2188        my $cgi = (ref $parameter eq 'CGI' ? $parameter : undef);
2189        # Default to no tracing except errors.
2190        my ($tracing, $dest) = ("0", "WARN");
2191        # Check for emergency tracing.
2192        my $tkey = EmergencyKey($parameter);
2193        my $emergencyFile = EmergencyFileName($tkey);
2194        if (-e $emergencyFile) {
2195            # We have the file. Read in the data.
2196            my @tracing = GetFile($emergencyFile);
2197            # Pull off the time limit.
2198            my $expire = shift @tracing;
2199            # Convert it to seconds.
2200            $expire *= 3600;
2201            # Check the file data.
2202            my $stat = stat($emergencyFile);
2203            my ($now) = gettimeofday;
2204            if ($now - $stat->mtime > $expire) {
2205                # Delete the expired file.
2206                unlink $emergencyFile;
2207            } else {
2208                # Emergency tracing is on. Pull off the destination and
2209                # the trace level;
2210                $dest = shift @tracing;
2211                my $level = shift @tracing;
2212                # Convert the destination to a real tracing destination.
2213                # temp directory.
2214                $dest = EmergencyTracingDest($tkey, $dest);
2215                # Insure Tracer is specified.
2216                my %moduleHash = map { $_ => 1 } @tracing;
2217                $moduleHash{Tracer} = 1;
2218                # Set the trace parameter.
2219                $tracing = join(" ", $level, sort keys %moduleHash);
2220            }
2221        } elsif (defined $cgi) {
2222            # There's no emergency tracing, but we have a CGI object, so check
2223            # for tracing from the form parameters.
2224            if ($cgi->param('Trace')) {
2225                # Here the user has requested tracing via a form.
2226                $dest = ($cgi->param('TF') ? ">$FIG_Config::temp/Trace$$.log" : "QUEUE");
2227                $tracing = $cgi->param('Trace') . " Tracer";
2228            }
2229        }
2230        # Setup the tracing we've determined from all the stuff above.
2231        TSetup($tracing, $dest);
2232        # If we're a web script, trace the parameter and environment data.
2233        if (defined $cgi) {
2234            TraceParms($cgi);
2235        }
2236    }
2237    
2238    =head3 EmergencyFileName
2239    
2240    C<< my $fileName = Tracer::EmergencyFileName($tkey); >>
2241    
2242    Return the emergency tracing file name. This is the file that specifies
2243    the tracing information.
2244    
2245    =over 4
2246    
2247  =item traceLevel  =item tkey
2248    
2249  Relevant tracing level.  Tracing key for the current program.
2250    
2251  =item RETURN  =item RETURN
2252    
2253  TRUE if a message at the specified trace level would appear in the trace, else FALSE.  Returns the name of the file to contain the emergency tracing information.
2254    
2255  =back  =back
2256    
2257  =cut  =cut
2258    
2259  sub T {  sub EmergencyFileName {
         # Declare the return variable.  
         my $retVal = 0;  
         # Only proceed if tracing is turned on.  
         if ($Destination ne "NONE") {  
2260                  # Get the parameters.                  # Get the parameters.
2261                  my ($category, $traceLevel) = @_;      my ($tkey) = @_;
2262                  if (!defined $traceLevel) {      # Compute the emergency tracing file name.
2263                          # Here we have no category, so we need to get the calling package.      return "$FIG_Config::temp/Emergency$tkey.txt";
                         $traceLevel = $category;  
                         my ($package, $fileName, $line) = caller;  
             # If there is no calling package, we default to "main".  
                         if (!$package) {  
                 $category = "main";  
                         } else {  
                                 $category = $package;  
                         }  
                 }  
         # Save the category name.  
         $LastCategory = $category;  
                 # Use the category and tracelevel to compute the result.  
                 $retVal = ($traceLevel <= $TraceLevel && exists $Categories{$category});  
     }  
         # Return the computed result.  
     return $retVal;  
2264  }  }
2265    
2266  =head3 ParseCommand  =head3 EmergencyFileTarget
2267    
2268  C<< my ($options, @arguments) = Tracer::ParseCommand(\%optionTable, @inputList); >>  C<< my $fileName = Tracer::EmergencyFileTarget($tkey); >>
2269    
2270  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
2271  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.  
2272    
2273  C<< my ($options, @arguments) = ParseCommand({ errors => 0, logFile => 'trace.log'}, @words); >>  =over 4
2274    
2275  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  
2276    
2277  C<< -logFile=error.log apple orange rutabaga >>  Tracing key for the current program.
2278    
2279  then at the end of the invocation, C<$options> will be  =item RETURN
2280    
2281  C<< { errors => 0, logFile => 'error.log' } >>  Returns the name of the file to contain the trace output.
2282    
2283  and C<@arguments> will contain  =back
2284    
2285  C<< apple orange rutabaga >>  =cut
2286    
2287  The parser allows for some escape sequences. See L</UnEscape> for a description. There is no  sub EmergencyFileTarget {
2288  support for quote characters.      # Get the parameters.
2289        my ($tkey) = @_;
2290        # Compute the emergency tracing file name.
2291        return "$FIG_Config::temp/trace$tkey.log";
2292    }
2293    
2294    =head3 EmergencyTracingDest
2295    
2296    C<< my $dest = Tracer::EmergencyTracingDest($tkey, $myDest); >>
2297    
2298    This method converts an emergency tracing destination to a real
2299    tracing destination. The main difference is that if the
2300    destination is C<FILE> or C<APPEND>, we convert it to file
2301    output. If the destination is C<DUAL>, we convert it to file
2302    and standard output.
2303    
2304  =over 4  =over 4
2305    
2306  =item optionTable  =item tkey
2307    
2308  Table of default options.  Tracing key for this environment.
2309    
2310  =item inputList  =item myDest
2311    
2312  List of words on the command line.  Destination from the emergency tracing file.
2313    
2314  =item RETURN  =item RETURN
2315    
2316  Returns a reference to the option table and a list of the positional arguments.  Returns a destination that can be passed into L</TSetup>.
2317    
2318  =back  =back
2319    
2320  =cut  =cut
2321    
2322  sub ParseCommand {  sub EmergencyTracingDest {
2323          # Get the parameters.          # Get the parameters.
2324          my ($optionTable, @inputList) = @_;      my ($tkey, $myDest) = @_;
2325          # Process any options in the input list.      # Declare the return variable.
2326          my %overrides = ();      my $retVal;
2327          while ((@inputList > 0) && ($inputList[0] =~ /^-/)) {      # Process according to the destination value.
2328                  # Get the current option.      if ($myDest eq 'FILE') {
2329                  my $arg = shift @inputList;          $retVal = ">" . EmergencyFileTarget($tkey);
2330                  # Pull out the option name.      } elsif ($myDest eq 'APPEND') {
2331                  $arg =~ /^-([^=]*)/g;          $retVal = ">>" . EmergencyFileTarget($tkey);
2332                  my $name = $1;      } elsif ($myDest eq 'DUAL') {
2333                  # 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;  
                 }  
         }  
         # Merge the options into the defaults.  
         GetOptions($optionTable, \%overrides);  
         # Translate the remaining parameters.  
         my @retVal = ();  
         for my $inputParm (@inputList) {  
                 push @retVal, UnEscape($inputParm);  
2334          }          }
2335          # Return the results.      # Return the result.
2336          return ($optionTable, @retVal);      return $retVal;
2337  }  }
2338    
2339  =head3 Escape  =head3 Emergency
2340    
2341  C<< my $codedString = Tracer::Escape($realString); >>  C<< Emergency($key, $hours, $dest, $level, @modules); >>
2342    
2343  Escape a string for use in a command length. Spaces will be replaced by C<\b>,  Turn on emergency tracing. This method is normally invoked over the web from
2344  tabs replaced by C<\t>, new-lines replaced by C<\n>, and backslashes will be  a debugging console, but it can also be called by the C<trace.pl> script.
2345  doubled. The effect is to exactly reverse the effect of L</UnEscape>.  The caller specifies the duration of the emergency in hours, the desired tracing
2346    destination, the trace level, and a list of the trace modules to activate.
2347    For the length of the duration, when a program in an environment with the
2348    specified tracing key active invokes a Sprout CGI script, tracing will be
2349    turned on automatically. See L</TSetup> for more about tracing setup and
2350    L</ETracing> for more about emergency tracing.
2351    
2352  =over 4  =over 4
2353    
2354  =item realString  =item tkey
2355    
2356  String to escape.  The tracing key. This is used to identify the control file and the trace file.
2357    
2358  =item RETURN  =item hours
2359    
2360  Escaped equivalent of the real string.  Number of hours to keep emergency tracing alive.
2361    
2362    =item dest
2363    
2364    Tracing destination. If no path information is specified for a file
2365    destination, it is put in the FIG temporary directory.
2366    
2367    =item level
2368    
2369    Tracing level. A higher level means more trace messages.
2370    
2371    =item modules
2372    
2373    A list of the tracing modules to activate.
2374    
2375  =back  =back
2376    
2377  =cut  =cut
2378    
2379  sub Escape {  sub Emergency {
2380          # Get the parameter.      # Get the parameters.
2381          my ($realString) = @_;      my ($tkey, $hours, $dest, $level, @modules) = @_;
2382          # Initialize the return variable.      # Create the emergency file.
2383          my $retVal = "";      my $specFile = EmergencyFileName($tkey);
2384          # Loop through the parameter string, looking for sequences to escape.      my $outHandle = Open(undef, ">$specFile");
2385          while (length $realString > 0) {      print $outHandle join("\n", $hours, $dest, $level, @modules, "");
                 # Look for the first sequence to escape.  
                 if ($realString =~ /^(.*?)([ \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;  
                         $realString = substr $realString, (length $2 + length $1);  
                         # Encode the escape sequence.  
                         my $char = $2;  
                         $char =~ tr/ \t\n/btn/;  
                         $retVal .= "\\" . $char;  
                 } else {  
                         # Here there are no more escape sequences. The rest of the string is  
                         # transferred unmodified.  
                         $retVal .= $realString;  
                         $realString = "";  
                 }  
         }  
         # Return the result.  
         return $retVal;  
2386  }  }
2387    
2388  =head3 UnEscape  =head3 EmergencyKey
2389    
2390  C<< my $realString = Tracer::UnEscape($codedString); >>  C<< my $tkey = EmergencyKey($parameter); >>
2391    
2392  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,
2393  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.
2394    
2395  =over 4  =over 4
2396    
2397  =item codedString  =item parameter
2398    
2399  String to un-escape.  Parameter defining the method for finding the tracing key. If it is a scalar,
2400    then it is presumed to be the tracing key itself. If it is a CGI object, then
2401    the tracing key is taken from the C<IP> cookie. Otherwise, the tracing key is
2402    taken from the C<TRACING> environment variable.
2403    
2404  =item RETURN  =item RETURN
2405    
2406  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.
 values.  
2407    
2408  =back  =back
2409    
2410  =cut  =cut
2411    
2412  sub UnEscape {  sub EmergencyKey {
2413          # Get the parameter.      # Get the parameters.
2414          my ($codedString) = @_;      my ($parameter) = @_;
2415          # Initialize the return variable.      # Declare the return variable.
2416          my $retVal = "";      my $retVal;
2417          # Only proceed if the incoming string is nonempty.      # Determine the parameter type.
2418          if (defined $codedString) {      if (! defined $parameter) {
2419                  # Loop through the parameter string, looking for escape sequences. We can't do          # Here we're supposed to check the environment.
2420                  # translating because it causes problems with the escaped slash. ("\\b" becomes          $retVal = $ENV{TRACING};
                 # "\ " no matter what we do.)  
                 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;  
2421                          } else {                          } else {
2422                                  # Here there are no more escape sequences. The rest of the string is          my $ptype = ref $parameter;
2423                                  # transferred unmodified.          if ($ptype eq 'CGI') {
2424                                  $retVal .= $codedString;              # Here we were invoked from a web page. Look for a cookie.
2425                                  $codedString = "";              $retVal = $parameter->cookie('IP');
2426            } elsif (! $ptype) {
2427                # Here the key was passed in.
2428                $retVal = $parameter;
2429                          }                          }
2430                  }                  }
2431        # If no luck finding a key, use the PID.
2432        if (! defined $retVal) {
2433            $retVal = $$;
2434          }          }
2435          # Return the result.          # Return the result.
2436          return $retVal;          return $retVal;
2437  }  }
2438    
 =head3 ParseRecord  
   
 C<< my @fields = Tracer::ParseRecord($line); >>  
2439    
2440  Parse a tab-delimited data line. The data line is split into field values. Embedded tab  =head3 TraceParms
 and new-line characters in the data line must be represented as C<\t> and C<\n>, respectively.  
 These will automatically be converted.  
2441    
2442  =over 4  C<< Tracer::TraceParms($cgi); >>
2443    
2444  =item line  Trace the CGI parameters at trace level CGI => 3 and the environment variables
2445    at level CGI => 4.
2446    
2447  Line of data containing the tab-delimited fields.  =over 4
2448    
2449  =item RETURN  =item cgi
2450    
2451  Returns a list of the fields found in the data line.  CGI query object containing the parameters to trace.
2452    
2453  =back  =back
2454    
2455  =cut  =cut
2456    
2457  sub ParseRecord {  sub TraceParms {
2458          # Get the parameter.      # Get the parameters.
2459          my ($line) = @_;      my ($cgi) = @_;
2460          # Remove the trailing new-line, if any.      if (T(CGI => 3)) {
2461          chomp $line;          # Here we want to trace the parameter data.
2462          # Split the line read into pieces using the tab character.          my @names = $cgi->param;
2463          my @retVal = split /\t/, $line;          for my $parmName (sort @names) {
2464          # Trim and fix the escapes in each piece.              # Note we skip the Trace parameters, which are for our use only.
2465          for my $value (@retVal) {              if ($parmName ne 'Trace' && $parmName ne 'TF') {
2466                  # Trim leading whitespace.                  my @values = $cgi->param($parmName);
2467                  $value =~ s/^\s+//;                  Trace("CGI: $parmName = " . join(", ", @values));
2468                  # Trim trailing whitespace.              }
2469                  $value =~ s/\s+$//;          }
2470                  # Delete the carriage returns.          # Display the request method.
2471                  $value =~ s/\r//g;          my $method = $cgi->request_method();
2472                  # Convert the escapes into their real values.          Trace("Method: $method");
2473                  $value =~ s/\\t/"\t"/ge;      }
2474                  $value =~ s/\\n/"\n"/ge;      if (T(CGI => 4)) {
2475            # Here we want the environment data too.
2476            for my $envName (sort keys %ENV) {
2477                Trace("ENV: $envName = $ENV{$envName}");
2478            }
2479          }          }
         # Return the result.  
         return @retVal;  
2480  }  }
2481    
2482  =head3 Merge  =head3 ScriptFinish
2483    
2484  C<< my @mergedList = Tracer::Merge(@inputList); >>  C<< ScriptFinish($webData, $varHash); >>
2485    
2486  Sort a list of strings and remove duplicates.  Output a web page at the end of a script. Either the string to be output or the
2487    name of a template file can be specified. If the second parameter is omitted,
2488    it is assumed we have a string to be output; otherwise, it is assumed we have the
2489    name of a template file. The template should have the variable C<DebugData>
2490    specified in any form that invokes a standard script. If debugging mode is turned
2491    on, a form field will be put in that allows the user to enter tracing data.
2492    Trace messages will be placed immediately before the terminal C<BODY> tag in
2493    the output, formatted as a list.
2494    
2495    A typical standard script would loook like the following.
2496    
2497        BEGIN {
2498            # Print the HTML header.
2499            print "CONTENT-TYPE: text/html\n\n";
2500        }
2501        use Tracer;
2502        use CGI;
2503        use FIG;
2504        # ... more uses ...
2505    
2506        my ($cgi, $varHash) = ScriptSetup();
2507        eval {
2508            # ... get data from $cgi, put it in $varHash ...
2509        };
2510        if ($@) {
2511            Trace("Script Error: $@") if T(0);
2512        }
2513        ScriptFinish("Html/MyTemplate.html", $varHash);
2514    
2515    The idea here is that even if the script fails, you'll see trace messages and
2516    useful output.
2517    
2518  =over 4  =over 4
2519    
2520  =item inputList  =item webData
2521    
2522  List of scalars to sort and merge.  A string containing either the full web page to be written to the output or the
2523    name of a template file from which the page is to be constructed. If the name
2524    of a template file is specified, then the second parameter must be present;
2525    otherwise, it must be absent.
2526    
2527  =item RETURN  =item varHash (optional)
2528    
2529  Returns a list containing the same elements sorted in ascending order with duplicates  If specified, then a reference to a hash mapping variable names for a template
2530  removed.  to their values. The template file will be read into memory, and variable markers
2531    will be replaced by data in this hash reference.
2532    
2533  =back  =back
2534    
2535  =cut  =cut
2536    
2537  sub Merge {  sub ScriptFinish {
2538          # Get the input list in sort order.      # Get the parameters.
2539          my @inputList = sort @_;      my ($webData, $varHash) = @_;
2540          # Only proceed if the list has at least two elements.      # Check for a template file situation.
2541          if (@inputList > 1) {      my $outputString;
2542                  # Now we want to move through the list splicing out duplicates.      if (defined $varHash) {
2543                  my $i = 0;          # Here we have a template file. We need to determine the template type.
2544                  while ($i < @inputList) {          my $template;
2545                          # Get the current entry.          if ($FIG_Config::template_url && $webData =~ /\.php$/) {
2546                          my $thisEntry = $inputList[$i];              $template = "$FIG_Config::template_url/$webData";
2547                          # Find out how many elements duplicate the current entry.          } else {
2548                          my $j = $i + 1;              $template = "<<$webData";
                         my $dup1 = $i + 1;  
                         while ($j < @inputList && $inputList[$j] eq $thisEntry) { $j++; };  
                         # If the number is nonzero, splice out the duplicates found.  
                         if ($j > $dup1) {  
                                 splice @inputList, $dup1, $j - $dup1;  
2549                          }                          }
2550                          # Now the element at position $dup1 is different from the element before it          $outputString = PageBuilder::Build($template, $varHash, "Html");
2551                          # at position $i. We push $i forward one position and start again.      } else {
2552                          $i++;          # Here the user gave us a raw string.
2553            $outputString = $webData;
2554        }
2555        # Check for trace messages.
2556        if ($Destination ne "NONE" && $TraceLevel > 0) {
2557            # We have trace messages, so we want to put them at the end of the body. This
2558            # is either at the end of the whole string or at the beginning of the BODY
2559            # end-tag.
2560            my $pos = length $outputString;
2561            if ($outputString =~ m#</body>#gi) {
2562                $pos = (pos $outputString) - 7;
2563            }
2564            # If the trace messages were queued, we unroll them. Otherwise, we display the
2565            # destination.
2566            my $traceHtml;
2567            if ($Destination eq "QUEUE") {
2568                $traceHtml = QTrace('Html');
2569            } elsif ($Destination =~ /^>>(.+)$/) {
2570                # Here the tracing output it to a file. We code it as a hyperlink so the user
2571                # can copy the file name into the clipboard easily.
2572                my $actualDest = $1;
2573                $traceHtml = "<p>Tracing output to $actualDest.</p>\n";
2574            } else {
2575                # Here we have one of the special destinations.
2576                $traceHtml = "<P>Tracing output type is $Destination.</p>\n";
2577                  }                  }
2578            substr $outputString, $pos, 0, $traceHtml;
2579          }          }
2580          # Return the merged list.      # Write the output string.
2581          return @inputList;      print $outputString;
2582  }  }
2583    
2584  =head3 GetFile  =head3 Insure
2585    
2586  C<< my @fileContents = Tracer::GetFile($fileName); >>  C<< Insure($dirName); >>
2587    
2588  Return the entire contents of a file.  Insure a directory is present.
2589    
2590  =over 4  =over 4
2591    
2592  =item fileName  =item dirName
   
 Name of the file to read.  
   
 =item RETURN  
2593    
2594  In a list context, returns the entire file as a list with the line terminators removed.  Name of the directory to check. If it does not exist, it will be created.
 In a scalar context, returns the entire file as a string.  
2595    
2596  =back  =back
2597    
2598  =cut  =cut
2599    
2600  sub GetFile {  sub Insure {
2601          # Get the parameters.      my ($dirName) = @_;
2602          my ($fileName) = @_;      if (! -d $dirName) {
2603          # Declare the return variable.          Trace("Creating $dirName directory.") if T(File => 2);
2604          my @retVal = ();          eval { mkpath $dirName; };
2605          # Open the file for input.          if ($@) {
2606          my $ok = open INPUTFILE, "<$fileName";              Confess("Error creating $dirName: $@");
         if (!$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 any terminator  
         # characters.  
         my $lineCount = 0;  
                 while (my $line = <INPUTFILE>) {  
             $lineCount++;  
             $line = Strip($line);  
                         push @retVal, $line;  
2607                  }                  }
                 # Close it.  
                 close INPUTFILE;  
         my $actualLines = @retVal;  
         Trace("$lineCount lines read from $fileName. $actualLines processed.") if T(3);  
         }  
         # Return the file's contents in the desired format.  
     if (wantarray) {  
             return @retVal;  
     } else {  
         return join "\n", @retVal;  
2608      }      }
2609  }  }
2610    
2611  =head3 QTrace  =head3 ChDir
2612    
2613  C<< my $data = QTrace($format); >>  C<< ChDir($dirName); >>
2614    
2615  Return the queued trace data in the specified format.  Change to the specified directory.
2616    
2617  =over 4  =over 4
2618    
2619  =item format  =item dirName
2620    
2621  C<html> to format the data as an HTML list, C<text> to format it as straight text.  Name of the directory to which we want to change.
2622    
2623  =back  =back
2624    
2625  =cut  =cut
2626    
2627  sub QTrace {  sub ChDir {
2628          # Get the parameter.      my ($dirName) = @_;
2629          my ($format) = @_;      if (! -d $dirName) {
2630          # Create the return variable.          Confess("Cannot change to directory $dirName: no such directory.");
2631          my $retVal = "";      } else {
2632          # Process according to the format.          Trace("Changing to directory $dirName.") if T(File => 4);
2633          if ($format =~ m/^HTML$/i) {          my $okFlag = chdir $dirName;
2634                  # Convert the queue into an HTML list.          if (! $okFlag) {
2635                  $retVal = "<ul>\n";              Confess("Error switching to directory $dirName.");
                 for my $line (@Queue) {  
                         my $escapedLine = CGI::escapeHTML($line);  
                         $retVal .= "<li>$escapedLine</li>\n";  
2636                  }                  }
                 $retVal .= "</ul>\n";  
         } elsif ($format =~ m/^TEXT$/i) {  
                 # Convert the queue into a list of text lines.  
                 $retVal = join("\n", @Queue) . "\n";  
2637          }          }
         # Clear the queue.  
         @Queue = ();  
         # Return the formatted list.  
         return $retVal;  
2638  }  }
2639    
2640  =head3 Confess  =head3 SendSMS
2641    
2642  C<< Confess($message); >>  C<< my $msgID = Tracer::SendSMS($phoneNumber, $msg); >>
2643    
2644  Trace the call stack and abort the program with the specified message. The stack  Send a text message to a phone number using Clickatell. The FIG_Config file must contain the
2645  trace will only appear if the trace level for this package is 1 or more. When used with  user name, password, and API ID for the relevant account in the hash reference variable
2646  the OR operator and the L</Assert> method, B<Confess> can function as a debugging assert.  I<$FIG_Config::phone>, using the keys C<user>, C<password>, and C<api_id>. For
2647  So, for example  example, if the user name is C<BruceTheHumanPet>, the password is C<silly>, and the API ID
2648    is C<2561022>, then the FIG_Config file must contain
2649    
2650  C<< Assert($recNum >= 0) || Confess("Invalid record number $recNum."); >>      $phone =  { user => 'BruceTheHumanPet',
2651                    password => 'silly',
2652                    api_id => '2561022' };
2653    
2654  Will abort the program with a stack trace if the value of C<$recNum> is negative.  The original purpose of this method was to insure Bruce would be notified immediately when the
2655    Sprout Load terminates. Care should be taken if you do not wish Bruce to be notified immediately
2656    when you call this method.
2657    
2658    The message ID will be returned if successful, and C<undef> if an error occurs.
2659    
2660  =over 4  =over 4
2661    
2662  =item message  =item phoneNumber
2663    
2664  Message to include in the trace.  Phone number to receive the message, in international format. A United States phone number
2665    would be prefixed by "1". A British phone number would be prefixed by "44".
2666    
2667    =item msg
2668    
2669    Message to send to the specified phone.
2670    
2671    =item RETURN
2672    
2673    Returns the message ID if successful, and C<undef> if the message could not be sent.
2674    
2675  =back  =back
2676    
2677  =cut  =cut
2678    
2679  sub Confess {  sub SendSMS {
2680          # Get the parameters.          # Get the parameters.
2681          my ($message) = @_;      my ($phoneNumber, $msg) = @_;
2682          # Trace the call stack.      # Declare the return variable. If we do not change it, C<undef> will be returned.
2683          Cluck($message) if T(1);      my $retVal;
2684          # Abort the program.      # Only proceed if we have phone support.
2685          croak(">>> $message");      if (! defined $FIG_Config::phone) {
2686            Trace("Phone support not present in FIG_Config.") if T(1);
2687        } else {
2688            # Get the phone data.
2689            my $parms = $FIG_Config::phone;
2690            # Get the Clickatell URL.
2691            my $url = "http://api.clickatell.com/http/";
2692            # Create the user agent.
2693            my $ua = LWP::UserAgent->new;
2694            # Request a Clickatell session.
2695            my $resp = $ua->post("$url/sendmsg", { user => $parms->{user},
2696                                         password => $parms->{password},
2697                                         api_id => $parms->{api_id},
2698                                         to => $phoneNumber,
2699                                         text => $msg});
2700            # Check for an error.
2701            if (! $resp->is_success) {
2702                Trace("Alert failed.") if T(1);
2703            } else {
2704                # Get the message ID.
2705                my $rstring = $resp->content;
2706                if ($rstring =~ /^ID:\s+(.*)$/) {
2707                    $retVal = $1;
2708                } else {
2709                    Trace("Phone attempt failed with $rstring") if T(1);
2710                }
2711            }
2712        }
2713        # Return the result.
2714        return $retVal;
2715  }  }
2716    
2717  =head3 Assert  =head3 CommaFormat
2718    
2719  C<< Assert($condition1, $condition2, ... $conditionN); >>  C<< my $formatted = Tracer::CommaFormat($number); >>
2720    
2721  Return TRUE if all the conditions are true. This method can be used in conjunction with  Insert commas into a number.
 the OR operator and the L</Confess> method, B<Assert> can function as a debugging assert.  
 So, for example  
2722    
2723  C<< Assert($recNum >= 0) || Confess("Invalid record number $recNum."); >>  =over 4
2724    
2725  Will abort the program with a stack trace if the value of C<$recNum> is negative.  =item number
2726    
2727    A sequence of digits.
2728    
2729    =item RETURN
2730    
2731    Returns the same digits with commas strategically inserted.
2732    
2733    =back
2734    
2735  =cut  =cut
2736  sub Assert {  
2737      my $retVal = 1;  sub CommaFormat {
2738      LOOP: for my $condition (@_) {      # Get the parameters.
2739          if (! $condition) {      my ($number) = @_;
2740              $retVal = 0;      # Pad the length up to a multiple of three.
2741              last LOOP;      my $padded = "$number";
2742          }      $padded = " " . $padded while length($padded) % 3 != 0;
2743      }      # This is a fancy PERL trick. The parentheses in the SPLIT pattern
2744        # cause the delimiters to be included in the output stream. The
2745        # GREP removes the empty strings in between the delimiters.
2746        my $retVal = join(",", grep { $_ ne '' } split(/(...)/, $padded));
2747        # Clean out the spaces.
2748        $retVal =~ s/ //g;
2749        # Return the result.
2750      return $retVal;      return $retVal;
2751  }  }
2752    =head3 SetPermissions
2753    
2754  =head3 Cluck  C<< Tracer::SetPermissions($dirName, $group, $mask, %otherMasks); >>
2755    
2756  C<< Cluck($message); >>  Set the permissions for a directory and all the files and folders inside it.
2757    In addition, the group ownership will be changed to the specified value.
2758    
2759  Trace the call stack. Note that for best results, you should qualify the call with a  This method is more vulnerable than most to permission and compatability
2760  trace condition. For example,  problems, so it does internal error recovery.
2761    
2762  C<< Cluck("Starting record parse.") if T(3); >>  =over 4
2763    
2764  will only trace the stack if the trace level for the package is 3 or more.  =item dirName
2765    
2766  =over 4  Name of the directory to process.
2767    
2768  =item message  =item group
2769    
2770  Message to include in the trace.  Name of the group to be assigned.
2771    
2772    =item mask
2773    
2774    Permission mask. Bits that are C<1> in this mask will be ORed into the
2775    permission bits of any file or directory that does not already have them
2776    set to 1.
2777    
2778    =item otherMasks
2779    
2780    Map of search patterns to permission masks. If a directory name matches
2781    one of the patterns, that directory and all its members and subdirectories
2782    will be assigned the new pattern. For example, the following would
2783    assign 01664 to most files, but would use 01777 for directories named C<tmp>.
2784    
2785        Tracer::SetPermissions($dirName, 'fig', 01664, '^tmp$' => 01777);
2786    
2787    The list is ordered, so the following would use 0777 for C<tmp1> and
2788    0666 for C<tmp>, C<tmp2>, or C<tmp3>.
2789    
2790        Tracer::SetPermissions($dirName, 'fig', 01664, '^tmp1' => 0777,
2791                                                       '^tmp' => 0666);
2792    
2793    Note that the pattern matches are all case-insensitive, and only directory
2794    names are matched, not file names.
2795    
2796  =back  =back
2797    
2798  =cut  =cut
2799    
2800  sub Cluck {  sub SetPermissions {
2801          # Get the parameters.          # Get the parameters.
2802          my ($message) = @_;      my ($dirName, $group, $mask, @otherMasks) = @_;
2803      # Trace what's happening.      # Set up for error recovery.
2804      Trace("Stack trace for event: $message");      eval {
2805          my $confession = longmess($message);          # Switch to the specified directory.
2806          # Convert the confession to a series of trace messages. Note we skip any          ChDir($dirName);
2807      # messages relating to calls into Tracer.          # Get the group ID.
2808          for my $line (split /\s*\n/, $confession) {          my $gid = getgrnam($group);
2809                  Trace($line) if ($line !~ /Tracer\.pm/);          # Get the mask for tracing.
2810            my $traceMask = sprintf("%04o", $mask) . "($mask)";
2811            Trace("Fixing permissions for directory $dirName using group $group($gid) and mask $traceMask.") if T(File => 2);
2812            my $fixCount = 0;
2813            my $lookCount = 0;
2814            # @dirs will be a stack of directories to be processed.
2815            my @dirs = (getcwd());
2816            while (scalar(@dirs) > 0) {
2817                # Get the current directory.
2818                my $dir = pop @dirs;
2819                # Check for a match to one of the specified directory names. To do
2820                # that, we need to pull the individual part of the name off of the
2821                # whole path.
2822                my $simpleName = $dir;
2823                if ($dir =~ m!/([^/]+)$!) {
2824                    $simpleName = $1;
2825                }
2826                Trace("Simple directory name for $dir is $simpleName.") if T(File => 4);
2827                # Search for a match.
2828                my $match = 0;
2829                my $i;
2830                for ($i = 0; $i < $#otherMasks && ! $match; $i += 2) {
2831                    my $pattern = $otherMasks[$i];
2832                    if ($simpleName =~ /$pattern/i) {
2833                        $match = 1;
2834                    }
2835                }
2836                # Check for a match. Note we use $i-1 because the loop added 2
2837                # before terminating due to the match.
2838                if ($match && $otherMasks[$i-1] != $mask) {
2839                    # This directory matches one of the incoming patterns, and it's
2840                    # a different mask, so we process it recursively with that mask.
2841                    SetPermissions($dir, $group, $otherMasks[$i-1], @otherMasks);
2842                } else {
2843                    # Here we can process normally. Get all of the non-hidden members.
2844                    my @submems = OpenDir($dir, 1);
2845                    for my $submem (@submems) {
2846                        # Get the full name.
2847                        my $thisMem = "$dir/$submem";
2848                        Trace("Checking member $thisMem.") if T(4);
2849                        $lookCount++;
2850                        if ($lookCount % 1000 == 0) {
2851                            Trace("$lookCount members examined. Current is $thisMem. Mask is $traceMask") if T(File => 3);
2852                        }
2853                        # Fix the group.
2854                        chown -1, $gid, $thisMem;
2855                        # Insure this member is not a symlink.
2856                        if (! -l $thisMem) {
2857                            # Get its info.
2858                            my $fileInfo = stat $thisMem;
2859                            # Only proceed if we got the info. Otherwise, it's a hard link
2860                            # and we want to skip it anyway.
2861                            if ($fileInfo) {
2862                                my $fileMode = $fileInfo->mode;
2863                                if (($fileMode & $mask) != $mask) {
2864                                    # Fix this member.
2865                                    $fileMode |= $mask;
2866                                    chmod $fileMode, $thisMem;
2867                                    $fixCount++;
2868                                }
2869                                # If it's a subdirectory, stack it.
2870                                if (-d $thisMem) {
2871                                    push @dirs, $thisMem;
2872                                }
2873                            }
2874                        }
2875                    }
2876                }
2877            }
2878            Trace("$lookCount files and directories processed, $fixCount fixed.") if T(File => 2);
2879        };
2880        # Check for an error.
2881        if ($@) {
2882            Confess("SetPermissions error: $@");
2883          }          }
2884  }  }
2885    
2886  =head3 Min  =head3 CompareLists
2887    
2888  C<< my $min = Min($value1, $value2, ... $valueN); >>  C<< my ($inserted, $deleted) = Tracer::CompareLists(\@newList, \@oldList, $keyIndex); >>
2889    
2890  Return the minimum argument. The arguments are treated as numbers.  Compare two lists of tuples, and return a hash analyzing the differences. The lists
2891    are presumed to be sorted alphabetically by the value in the $keyIndex column.
2892    The return value contains a list of items that are only in the new list
2893    (inserted) and only in the old list (deleted).
2894    
2895  =over 4  =over 4
2896    
2897  =item $value1, $value2, ... $valueN  =item newList
2898    
2899  List of numbers to compare.  Reference to a list of new tuples.
2900    
2901    =item oldList
2902    
2903    Reference to a list of old tuples.
2904    
2905    =item keyIndex (optional)
2906    
2907    Index into each tuple of its key field. The default is 0.
2908    
2909  =item RETURN  =item RETURN
2910    
2911  Returns the lowest number in the list.  Returns a 2-tuple consisting of a reference to the list of items that are only in the new
2912    list (inserted) followed by a reference to the list of items that are only in the old
2913    list (deleted).
2914    
2915  =back  =back
2916    
2917  =cut  =cut
2918    
2919  sub Min {  sub CompareLists {
2920          # Get the parameters. Note that we prime the return value with the first parameter.      # Get the parameters.
2921          my ($retVal, @values) = @_;      my ($newList, $oldList, $keyIndex) = @_;
2922          # Loop through the remaining parameters, looking for the lowest.      if (! defined $keyIndex) {
2923          for my $value (@values) {          $keyIndex = 0;
2924                  if ($value < $retVal) {      }
2925                          $retVal = $value;      # Declare the return variables.
2926        my ($inserted, $deleted) = ([], []);
2927        # Loop through the two lists simultaneously.
2928        my ($newI, $oldI) = (0, 0);
2929        my ($newN, $oldN) = (scalar @{$newList}, scalar @{$oldList});
2930        while ($newI < $newN || $oldI < $oldN) {
2931            # Get the current object in each list. Note that if one
2932            # of the lists is past the end, we'll get undef.
2933            my $newItem = $newList->[$newI];
2934            my $oldItem = $oldList->[$oldI];
2935            if (! defined($newItem) || defined($oldItem) && $newItem->[$keyIndex] gt $oldItem->[$keyIndex]) {
2936                # The old item is not in the new list, so mark it deleted.
2937                push @{$deleted}, $oldItem;
2938                $oldI++;
2939            } elsif (! defined($oldItem) || $oldItem->[$keyIndex] gt $newItem->[$keyIndex]) {
2940                # The new item is not in the old list, so mark it inserted.
2941                push @{$inserted}, $newItem;
2942                $newI++;
2943            } else {
2944                # The item is in both lists, so push forward.
2945                $oldI++;
2946                $newI++;
2947                  }                  }
2948          }          }
2949          # Return the minimum found.      # Return the result.
2950          return $retVal;      return ($inserted, $deleted);
2951  }  }
2952    
2953  =head3 Max  =head3 GetLine
2954    
2955  C<< my $max = Max($value1, $value2, ... $valueN); >>  C<< my @data = Tracer::GetLine($handle); >>
2956    
2957  Return the maximum argument. The arguments are treated as numbers.  Read a line of data from a tab-delimited file.
2958    
2959  =over 4  =over 4
2960    
2961  =item $value1, $value2, ... $valueN  =item handle
2962    
2963  List of numbers to compare.  Open file handle from which to read.
2964    
2965  =item RETURN  =item RETURN
2966    
2967  Returns the highest number in the list.  Returns a list of the fields in the record read. The fields are presumed to be
2968    tab-delimited. If we are at the end of the file, then an empty list will be
2969    returned. If an empty line is read, a single list item consisting of a null
2970    string will be returned.
2971    
2972  =back  =back
2973    
2974  =cut  =cut
2975    
2976  sub Max {  sub GetLine {
2977          # Get the parameters. Note that we prime the return value with the first parameter.      # Get the parameters.
2978          my ($retVal, @values) = @_;      my ($handle) = @_;
2979          # Loop through the remaining parameters, looking for the highest.      # Declare the return variable.
2980          for my $value (@values) {      my @retVal = ();
2981                  if ($value > $retVal) {      Trace("File position is " . tell($handle) . ". EOF flag is " . eof($handle) . ".") if T(File => 4);
2982                          $retVal = $value;      # Read from the file.
2983        my $line = <$handle>;
2984        # Only proceed if we found something.
2985        if (defined $line) {
2986            # Remove the new-line. We are a bit over-cautious here because the file may be coming in via an
2987            # upload control and have a nonstandard EOL combination.
2988            $line =~ s/(\r|\n)+$//;
2989            # Here we do some fancy tracing to help in debugging complicated EOL marks.
2990            if (T(File => 4)) {
2991                my $escapedLine = $line;
2992                $escapedLine =~ s/\n/\\n/g;
2993                $escapedLine =~ s/\r/\\r/g;
2994                $escapedLine =~ s/\t/\\t/g;
2995                Trace("Line read: -->$escapedLine<--");
2996            }
2997            # If the line is empty, return a single empty string; otherwise, parse
2998            # it into fields.
2999            if ($line eq "") {
3000                push @retVal, "";
3001            } else {
3002                push @retVal, split /\t/,$line;
3003                  }                  }
3004        } else {
3005            # Trace the reason the read failed.
3006            Trace("End of file: $!") if T(File => 3);
3007          }          }
3008          # Return the maximum found.      # Return the result.
3009          return $retVal;      return @retVal;
3010  }  }
3011    
3012  =head3 AddToListMap  =head3 PutLine
3013    
3014  C<< Tracer::AddToListMap(\%hash, $key, $value); >>  C<< Tracer::PutLine($handle, \@fields, $eol); >>
3015    
3016  Add a key-value pair to a hash of lists. If no value exists for the key, a singleton list  Write a line of data to a tab-delimited file. The specified field values will be
3017  is created for the key. Otherwise, the new value is pushed onto the list.  output in tab-separated form, with a trailing new-line.
3018    
3019  =over 4  =over 4
3020    
3021  =item hash  =item handle
3022    
3023  Reference to the target hash.  Output file handle.
3024    
3025  =item key  =item fields
3026    
3027  Key for which the value is to be added.  List of field values.
3028    
3029  =item value  =item eol (optional)
3030    
3031  Value to add to the key's value list.  End-of-line character (default is "\n").
3032    
3033  =back  =back
3034    
3035  =cut  =cut
3036    
3037  sub AddToListMap {  sub PutLine {
3038      # Get the parameters.      # Get the parameters.
3039      my ($hash, $key, $value) = @_;      my ($handle, $fields, $eol) = @_;
3040      # Process according to whether or not the key already has a value.      # Write the data.
3041      if (! exists $hash->{$key}) {      print $handle join("\t", @{$fields}) . ($eol || "\n");
         $hash->{$key} = [$value];  
     } else {  
         push @{$hash->{$key}}, $value;  
     }  
3042  }  }
3043    
3044  =head3 DebugMode  =head3 GenerateURL
   
 C<< if (Tracer::DebugMode) { ...code... } >>  
3045    
3046  Return TRUE if debug mode has been turned on in FIG_Config, else output  C<< my $queryUrl = Tracer::GenerateURL($page, %parameters); >>
 an error page and return FALSE.  
3047    
3048  Certain CGI scripts are too dangerous to exist in the production  Generate a GET-style URL for the specified page with the specified parameter
3049  environment. This method provides a simple way to prevent them  names and values. The values will be URL-escaped automatically. So, for
3050  from working unless they are explicitly turned on in the configuration  example
 file by setting C<$FIG_Config::debug_mode> to 1. If debugging mode  
 is not turned on, an error web page will be output.  
3051    
3052  =cut      Tracer::GenerateURL("form.cgi", type => 1, string => "\"high pass\" or highway")
3053    
3054  sub DebugMode {  would return
         # Declare the return variable.  
         my $retVal;  
         # Check the debug configuration.  
         if ($FIG_Config::debug_mode) {  
                 $retVal = 1;  
         } else {  
                 # Here debug mode is off, so we generate an error page.  
         my $pageString = PageBuilder::Build("<Html/ErrorPage.html", {}, "Html");  
                 print $pageString;  
         }  
         # Return the determination indicator.  
         return $retVal;  
 }  
3055    
3056  =head3 Strip      form.cgi?type=1;string=%22high%20pass%22%20or%20highway
3057    
3058  C<< my $string = Tracer::Strip($line); >>  =over 4
3059    
3060  Strip all line terminators off a string. This is necessary when dealing with files  =item page
 that may have been transferred back and forth several times among different  
 operating environments.  
3061    
3062  =over 4  Page URL.
3063    
3064  =item line  =item parameters
3065    
3066  Line of text to be stripped.  Hash mapping parameter names to parameter values.
3067    
3068  =item RETURN  =item RETURN
3069    
3070  The same line of text with all the line-ending characters chopped from the end.  Returns a GET-style URL that goes to the specified page and passes in the
3071    specified parameters and values.
3072    
3073  =back  =back
3074    
3075  =cut  =cut
3076    
3077  sub Strip {  sub GenerateURL {
3078          # Get a copy of the parameter string.      # Get the parameters.
3079          my ($string) = @_;      my ($page, %parameters) = @_;
3080          my $retVal = $string;      # Prime the return variable with the page URL.
3081      # Strip the line terminator characters.      my $retVal = $page;
3082      $retVal =~ s/(\r|\n)+$//g;      # Loop through the parameters, creating parameter elements in a list.
3083        my @parmList = map { "$_=" . uri_escape($parameters{$_}) } keys %parameters;
3084        # If the list is nonempty, tack it on.
3085        if (@parmList) {
3086            $retVal .= "?" . join(";", @parmList);
3087        }
3088          # Return the result.          # Return the result.
3089          return $retVal;          return $retVal;
3090  }  }
3091    
3092  =head3 Pad  =head3 ApplyURL
3093    
3094  C<< my $paddedString = Tracer::Pad($string, $len, $left, $padChar); >>  C<< Tracer::ApplyURL($table, $target, $url); >>
3095    
3096  Pad a string to a specified length. The pad character will be a  Run through a two-dimensional table (or more accurately, a list of lists), converting the
3097  space, and the padding will be on the right side unless specified  I<$target> column to HTML text having a hyperlink to a URL in the I<$url> column. The
3098  in the third parameter.  URL column will be deleted by this process and the target column will be HTML-escaped.
3099    
3100    This provides a simple way to process the results of a database query into something
3101    displayable by combining a URL with text.
3102    
3103  =over 4  =over 4
3104    
3105  =item string  =item table
3106    
3107  String to be padded.  Reference to a list of lists. The elements in the containing list will be updated by
3108    this method.
3109    
3110  =item len  =item target
3111    
3112  Desired length of the padded string.  The index of the column to be converted into HTML.
3113    
3114  =item left (optional)  =item url
3115    
3116  TRUE if the string is to be left-padded; otherwise it will be padded on the right.  The index of the column containing the URL. Note that the URL must have a recognizable
3117    C<http:> at the beginning.
3118    
3119  =item padChar (optional)  =back
3120    
3121    =cut
3122    
3123    sub ApplyURL {
3124        # Get the parameters.
3125        my ($table, $target, $url) = @_;
3126        # Loop through the table.
3127        for my $row (@{$table}) {
3128            # Apply the URL to the target cell.
3129            $row->[$target] = CombineURL($row->[$target], $row->[$url]);
3130            # Delete the URL from the row.
3131            delete $row->[$url];
3132        }
3133    }
3134    
3135    =head3 CombineURL
3136    
3137    C<< my $combinedHtml = Tracer::CombineURL($text, $url); >>
3138    
3139    This method will convert the specified text into HTML hyperlinked to the specified
3140    URL. The hyperlinking will only take place if the URL looks legitimate: that is, it
3141    is defined and begins with an C<http:> header.
3142    
3143    =over 4
3144    
3145    =item text
3146    
3147    Text to return. This will be HTML-escaped automatically.
3148    
3149    =item url
3150    
3151    A URL to be hyperlinked to the text. If it does not look like a URL, then the text
3152    will be returned without any hyperlinking.
3153    
3154  =item RETURN  =item RETURN
3155    
3156  Returns a copy of the original string with the spaces added to the specified end so  Returns the original text, HTML-escaped, with the URL hyperlinked to it. If the URL
3157  that it achieves the desired length.  doesn't look right, the HTML-escaped text will be returned without any further
3158    modification.
3159    
3160  =back  =back
3161    
3162  =cut  =cut
3163    
3164  sub Pad {  sub CombineURL {
3165          # Get the parameters.          # Get the parameters.
3166          my ($string, $len, $left, $padChar) = @_;      my ($text, $url) = @_;
3167          # Compute the padding character.      # Declare the return variable.
3168          if (! defined $padChar) {      my $retVal = CGI::escapeHTML($text);
3169                  $padChar = " ";      # Verify the URL.
3170          }      if (defined($url) && $url =~ m!http://!i) {
3171          # Compute the number of spaces needed.          # It's good, so we apply it to the text.
3172          my $needed = $len - length $string;          $retVal = "<a href=\"$url\">$retVal</a>";
         # Copy the string into the return variable.  
         my $retVal = $string;  
         # Only proceed if padding is needed.  
         if ($needed > 0) {  
                 # Create the pad string.  
                 my $pad = $padChar x $needed;  
                 # Affix it to the return value.  
                 if ($left) {  
                         $retVal = $pad . $retVal;  
                 } else {  
                         $retVal .= $pad;  
                 }  
3173          }          }
3174          # Return the result.          # Return the result.
3175          return $retVal;          return $retVal;

Legend:
Removed from v.1.9  
changed lines
  Added in v.1.84

MCS Webmaster
ViewVC Help
Powered by ViewVC 1.0.3