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# Line 1  Line 1 
1    #
2    # Copyright (c) 2003-2006 University of Chicago and Fellowship
3    # for Interpretations of Genomes. All Rights Reserved.
4    #
5    # This file is part of the SEED Toolkit.
6    #
7    # The SEED Toolkit is free software. You can redistribute
8    # it and/or modify it under the terms of the SEED Toolkit
9    # Public License.
10    #
11    # You should have received a copy of the SEED Toolkit Public License
12    # along with this program; if not write to the University of Chicago
13    # at info@ci.uchicago.edu or the Fellowship for Interpretation of
14    # Genomes at veronika@thefig.info or download a copy from
15    # http://www.theseed.org/LICENSE.TXT.
16    #
17    
18  package Tracer;  package Tracer;
19    
20          require Exporter;          require Exporter;
21          @ISA = ('Exporter');          @ISA = ('Exporter');
22          @EXPORT = qw(Trace T TSetup QTrace Confess Cluck Assert);      @EXPORT = qw(Trace T TSetup QTrace Confess Cluck Min Max Assert Open OpenDir TICK StandardSetup EmergencyKey ETracing ScriptSetup ScriptFinish Insure ChDir Emergency);
23          @EXPORT_OK = qw(GetFile GetOptions Merge MergeOptions ParseCommand ParseRecord UnEscape);      @EXPORT_OK = qw(GetFile GetOptions Merge MergeOptions ParseCommand ParseRecord UnEscape Escape);
24          use strict;          use strict;
25          use Carp qw(longmess croak);          use Carp qw(longmess croak);
26          use CGI;          use CGI;
27        use Cwd;
28        use FIG_Config;
29        use PageBuilder;
30        use Digest::MD5;
31        use File::Basename;
32        use File::Path;
33        use File::stat;
34        use LWP::UserAgent;
35        use Time::HiRes 'gettimeofday';
36        use URI::Escape;
37    
38  =head1 Tracing and Debugging Helpers  =head1 Tracing and Debugging Helpers
39    
40  =head2 Introduction  =head2 Tracing
41    
42  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
43  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.
44  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,
45  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
46  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
47  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
48  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
49  appear. To generate a trace message, use the following syntax.  appear.
50    
51    =head3 Putting Trace Messages in Your Code
52    
53  C<< Trace($message) if T(errors => 4); >>  To generate a trace message, use the following syntax.
54    
55        Trace($message) if T(errors => 4);
56    
57  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>
58  category is active. Note that the special category C<root> is always active, so  category is active. There is a special category C<main> that is always active, so
59    
60  C<< Trace($message) if T(root => 4); >>      Trace($message) if T(main => 4);
61    
62  will trace if the trace level is 4 or more.  will trace if the trace level is 4 or more.
63    
# Line 34  Line 65 
65  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
66  active and the trace level is 2 or more.  active and the trace level is 2 or more.
67    
68  C<< Trace($message) if T(2); >>      Trace($message) if T(2);
69    
70    In scripts, where no package name is available, the category defaults to C<main>.
71    
72  To set up tracing, you call the C</Setup> method. The method takes as input a trace level, a list  =head3 Custom Tracing
73  of category names, and a set of options. The trace level and list of category names are  
74    Many programs have customized tracing configured using the L</TSetup> method. This is no longer
75    the preferred method, but a knowledge of how custom tracing works can make the more modern
76    L</Emergency Tracing> easier to understand.
77    
78    To set up custom tracing, you call the L</TSetup> method. The method takes as input a trace level,
79    a list of category names, and a destination. The trace level and list of category names are
80  specified as a space-delimited string. Thus  specified as a space-delimited string. Thus
81    
82  C<< TSetup('3 errors Sprout ERDB', 'HTML'); >>      TSetup('3 errors Sprout ERDB', 'TEXT');
83    
84    sets the trace level to 3, activates the C<errors>, C<Sprout>, and C<ERDB> categories, and
85    specifies that messages should be sent to the standard output.
86    
87    To turn on tracing for ALL categories, use an asterisk. The call below sets every category to
88    level 3 and writes the output to the standard error output. This sort of thing might be
89    useful in a CGI environment.
90    
91  sets the trace level to 3, activated the C<errors>, C<Sprout>, and C<ERDB> categories, and      TSetup('3 *', 'WARN');
 specifies that messages should be output as HTML paragraphs. The idea is to make it easier to  
 input tracing configuration on a web form.  
92    
93  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
94  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
95  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
96  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
97  it easier to debug page formatting problems.  it easier to debug page formatting problems.
98    
99    Finally, you can specify that all trace messages be emitted to a file, or the standard output and
100    a file at the same time. To trace to a file, specify the filename with an output character in front
101    of it.
102    
103        TSetup('4 SQL', ">$fileName");
104    
105    To trace to the standard output and a file at the same time, put a C<+> in front of the angle
106    bracket.
107    
108        TSetup('3 *', "+>$fileName");
109    
110  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>.
111  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.
112  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
113  being used out in the field.  being used out in the field.
114    
115    =head3 Trace Levels
116    
117    There is no hard and fast rule on how to use trace levels. The following is therefore only
118    a suggestion.
119    
120    =over 4
121    
122    =item Error 0
123    
124    Message indicates an error that may lead to incorrect results or that has stopped the
125    application entirely.
126    
127    =item Warning 1
128    
129    Message indicates something that is unexpected but that probably did not interfere
130    with program execution.
131    
132    =item Notice 2
133    
134    Message indicates the beginning or end of a major task.
135    
136    =item Information 3
137    
138    Message indicates a subtask. In the FIG system, a subtask generally relates to a single
139    genome. This would be a big loop that is not expected to execute more than 500 times or so.
140    
141    =item Detail 4
142    
143    Message indicates a low-level loop iteration.
144    
145    =back
146    
147    The format of trace messages is important because some utilities analyze trace files.
148    There are three fields-- the time stamp, the category name, and the text.
149    The time stamp is between square brackets and the category name between angle brackets.
150    After the category name there is a colon (C<:>) followed by the message text.
151    If the square brackets or angle brackets are missing, then the trace management
152    utilities assume that they are encountering a set of pre-formatted lines.
153    
154    Note, however, that this formatting is done automatically by the tracing functions. You
155    only need to know about it if you want to parse a trace file.
156    
157    =head3 Emergency Tracing
158    
159    Sometimes, you need a way for tracing to happen automatically without putting parameters
160    in a form or on the command line. Emergency tracing does this. You invoke emergency tracing
161    from the debug form, which is accessed from I<MySeedInstance>C</FIG/Html/SetPassword.html>.
162    Emergency tracing requires you specify a tracing key. For command-line tools, the key is
163    taken from the C<TRACING> environment variable. For web services, the key is taken from
164    a cookie. Either way, the key tells the tracing facility who you are, so that you control
165    the tracing in your environment without stepping on other users.
166    
167    The key can be anything you want. If you don't have a key, the C<SetPassword> page will
168    generate one for you.
169    
170    You can activate and de-activate emergency tracing from the debugging control panel, as
171    well as display the trace file itself.
172    
173    To enable emergency tracing in your code, call
174    
175        ETracing($cgi)
176    
177    from a web script and
178    
179        ETracing()
180    
181    from a command-line script.
182    
183    The web script will look for the tracing key in the cookies, and the command-line
184    script will look for it in the C<TRACING> environment variable. If you are
185    using the L</StandardScript> or L</StandardSetup> methods, emergency tracing
186    will be configured automatically.
187    
188    =head3 Debugging Control Panel
189    
190    The debugging control panel provides several tools to assist in development of
191    SEED and Sprout software. You access the debugging control panel from the URL
192    C</FIG/Html/SetPassword.html> in whichever seed instance you're using. (So,
193    for example, the panel access point for the development NMPDR system is
194    C<http://web-1.nmpdr.org/next/FIG/Html/SetPassword.html>. Contact Bruce to
195    find out what the password is. From this page, you can also specify a tracing
196    key. If you don't specify a key, one will be generated for you.
197    
198    =head4 Emergency Tracing Form
199    
200    At the bottom of the debugging control panel is a form that allows you to
201    specify a trace level and tracing categories. Special and common categories
202    are listed with check boxes. You can hold your mouse over a check box to see
203    what its category does. In general, however, a category name is the same as
204    the name of the package in which the trace message occurs.
205    
206    Additional categories can be entered in an input box, delimited by spaces or commas.
207    
208    The B<Activate> button turns on Emergency tracing at the level you specify with the
209    specified categories active. The B<Terminate> button turns tracing off. The
210    B<Show File> button displays the current contents of the trace file. The tracing
211    form at the bottom of the control panel is designed for emergency tracing, so it
212    will only affect programs that call L</ETracing>, L</StandardScript>,
213    or L</StandardSetup>.
214    
215    =head4 Script Form
216    
217    The top form of the debugging control panel allows you to enter a tiny script and
218    have the output generated in a formatted table. Certain object variables are
219    predefined in the script, including a FIG object (C<$fig>), a CGI object (C<$cgi>),
220    and-- if Sprout is active-- Sprout (C<$sprout>) and SFXlate (C<$sfx>) objects.
221    
222    The last line of the script must be a scalar, but it can be a reference to a hash,
223    a list, a list of lists, and various other combinations. If you select the appropriate
224    data type in the dropdown box, the output will be formatted accordingly. The form
225    also has controls for specifying tracing. These controls override any emergency
226    tracing in effect.
227    
228    =head4 Database Query Forms
229    
230    The forms between the script form and the emergency tracing form allow you to
231    make queries against the database. The FIG query form allows simple queries against
232    a single FIG table. The Sprout query form uses the B<GetAll> method to do a
233    multi-table query against the Sprout database. B<GetAll> is located in the B<ERDB>
234    package, and it takes five parameters.
235    
236        GetAll(\@objectNames, $filterClause, \@parameters, \@fields, $count);
237    
238    Each of the five parameters corresponds to a text box on the query form:
239    
240    =over 4
241    
242    =item Objects
243    
244    Comma-separated list containing the names of the entity and relationship objects to be retrieved.
245    
246    =item Filter
247    
248    WHERE/ORDER BY clause (without the WHERE) to be used to filter and sort the query. The WHERE clause can
249    be parameterized with parameter markers (C<?>). Each field used must be specified in the standard form
250    B<I<objectName>(I<fieldName>)> or B<$I<number>(I<fieldName>)> where I<fieldName> is the name of a
251    field, I<objectName> is the name of the entity or relationship object containing the field, and
252    I<number> is the 1-based position of the object in the object list. Any parameters
253    specified in the filter clause should be specified in the B<Params> field.
254    The fields in a filter clause can come from primary entity relations,
255    relationship relations, or secondary entity relations; however, all of the
256    entities and relationships involved must be included in the list of object names.
257    
258    =item Params
259    
260    List of the parameters to be substituted in for the parameters marks in the filter clause. This
261    is a comma-separated list without any quoting or escaping.
262    
263    =item fields
264    
265    Comma-separated list of the fields to be returned in each element of the list returned. Fields
266    are specified in the same manner as in the filter clause.
267    
268    =item count
269    
270    Maximum number of records to return. If omitted or 0, all available records will be returned.
271    
272    =back
273    
274    B<GetAll> automatically joins together the entities and relationships listed in the object
275    names. This simplifies the coding of the filter clause, but it means that some queries are
276    not possible, since they cannot be expressed in a linear sequence of joins. This is a limitation
277    that has yet to be addressed.
278    
279  =cut  =cut
280    
281  # Declare the configuration variables.  # Declare the configuration variables.
282    
283  my $Destination = "NONE";       # Description of where to send the trace output.  my $Destination = "NONE";       # Description of where to send the trace output.
284  my %Categories = ( root => 1 );  my $TeeFlag = 0;            # TRUE if output is going to a file and to the
285                                # standard output
286    my %Categories = ( main => 1 );
287                                                          # hash of active category names                                                          # hash of active category names
288  my $TraceLevel = 0;                     # trace level; a higher trace level produces more  my $TraceLevel = 0;                     # trace level; a higher trace level produces more
289                                                          # messages                                                          # messages
290  my @Queue = ();                         # queued list of trace messages.  my @Queue = ();                         # queued list of trace messages.
291    my $LastCategory = "main";  # name of the last category interrogated
292    my $SetupCount = 0;         # number of times TSetup called
293    my $AllTrace = 0;           # TRUE if we are tracing all categories.
294    
295  =head2 Public Methods  =head2 Public Methods
296    
# Line 88  Line 312 
312    
313  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
314  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
315  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 ">"
316  the trace messages to a file, you can specify XX special destinations. C<HTML> will  symbol with a C<+> to echo output to a file AND to the standard output. In addition to
317    sending the trace messages to a file, you can specify a special destination. C<HTML> will
318  cause tracing to the standard output with each line formatted as an HTML paragraph. C<TEXT>  cause tracing to the standard output with each line formatted as an HTML paragraph. C<TEXT>
319  will cause tracing to the standard output as ordinary text. C<QUEUE> will cause trace messages  will cause tracing to the standard output as ordinary text. C<ERROR> will cause trace
320  to be stored in a queue for later retrieval by the L</QTrace> method. C<NONE> will cause  messages to be sent to the standard error output as ordinary text. C<QUEUE> will cause trace
321  tracing to be suppressed.  messages to be stored in a queue for later retrieval by the L</QTrace> method. C<WARN> will
322    cause trace messages to be emitted as warnings using the B<warn> directive.  C<NONE> will
323    cause tracing to be suppressed.
324    
325  =back  =back
326    
# Line 106  Line 333 
333          my @categoryData = split /\s+/, $categoryList;          my @categoryData = split /\s+/, $categoryList;
334          # Extract the trace level.          # Extract the trace level.
335          $TraceLevel = shift @categoryData;          $TraceLevel = shift @categoryData;
336          # Build the category hash.      # Presume category-based tracing until we learn otherwise.
337        $AllTrace = 0;
338        # Build the category hash. Note that if we find a "*", we turn on non-category
339        # tracing. We must also clear away any pre-existing data.
340        %Categories = ( main => 1 );
341          for my $category (@categoryData) {          for my $category (@categoryData) {
342                  $Categories{$category} = 1;          if ($category eq '*') {
343                $AllTrace = 1;
344            } else {
345                $Categories{lc $category} = 1;
346            }
347          }          }
348          # Now we need to process the destination information. The most important special          # Now we need to process the destination information. The most important special
349          # case is the single ">", which requires we clear the file first. After doing      # cases are the single ">", which requires we clear the file first, and the
350          # so, we tack on another ">" sign so that future trace messages are appended.      # "+" prefix which indicates a double echo.
351        if ($target =~ m/^\+?>>?/) {
352            if ($target =~ m/^\+/) {
353                $TeeFlag = 1;
354                $target = substr($target, 1);
355            }
356          if ($target =~ m/^>[^>]/) {          if ($target =~ m/^>[^>]/) {
357                  open TRACEFILE, $target;                  open TRACEFILE, $target;
358                  print TRACEFILE Now() . " Tracing initialized.\n";              print TRACEFILE "[" . Now() . "] <Tracer>: Tracing initialized.\n";
359                  close TRACEFILE;                  close TRACEFILE;
360                  $Destination = ">$target";                  $Destination = ">$target";
361          } else {          } else {
362                $Destination = $target;
363            }
364        } else {
365                  $Destination = uc($target);                  $Destination = uc($target);
366          }          }
367        # Increment the setup counter.
368        $SetupCount++;
369  }  }
370    
371  =head3 Now  =head3 StandardSetup
372    
373  C<< my $string = Tracer::Now(); >>  C<< my ($options, @parameters) = StandardSetup(\@categories, \%options, $parmHelp, @ARGV); >>
374    
375  Return a displayable time stamp containing the local time.  This method performs standard command-line parsing and tracing setup. The return
376    values are a hash of the command-line options and a list of the positional
377    parameters. Tracing is automatically set up and the command-line options are
378    validated.
379    
380  =cut  This is a complex method that does a lot of grunt work. The parameters can
381    be more easily understood, however, once they are examined individually.
382    
383  sub Now {  The I<categories> parameter is the most obtuse. It is a reference to a list of
384          my ($sec,$min,$hour,$mday,$mon,$year,$wday,$yday,$isdst) = localtime(time);  special-purpose tracing categories. Most tracing categories are PERL package
385          my $retVal = _p2($mon+1) . "/" . _p2($mday) . "/" . ($year + 1900) . " " .  names. So, for example, if you wanted to turn on tracing inside the B<Sprout>,
386                                   _p2($hour) . ":" . _p2($min) . ":" . _p2($sec);  B<ERDB>, and B<SproutLoad> packages, you would specify the categories
         return $retVal;  
 }  
387    
388  # Pad a number to 2 digits.      ["Sprout", "SproutLoad", "ERDB"]
 sub _p2 {  
         my ($value) = @_;  
         $value = "0$value" if ($value < 10);  
         return $value;  
 }  
389    
390  =head3 LogErrors  This would cause trace messages in the specified three packages to appear in
391    the output. There are two special tracing categories that are automatically
392    handled by this method. In other words, if you used L</TSetup> you would need
393    to include these categories manually, but if you use this method they are turned
394    on automatically.
395    
396  C<< Tracer::LogErrors($fileName); >>  =over 4
397    
398  Route the standard error output to a log file.  =item SQL
399    
400  =over 4  Traces SQL commands and activity.
401    
402  =item fileName  =item Tracer
403    
404  Name of the file to receive the error output.  Traces error messages and call stacks.
405    
406  =back  =back
407    
408  =cut  C<SQL> is only turned on if the C<-sql> option is specified in the command line.
409    The trace level is specified using the C<-trace> command-line option. For example,
410    the following command line for C<TransactFeatures> turns on SQL tracing and runs
411    all tracing at level 3.
412    
413  sub LogErrors {      TransactFeatures -trace=3 -sql register ../xacts IDs.tbl
         # Get the file name.  
         my ($fileName) = @_;  
         # Open the file as the standard error output.  
         open STDERR, '>', $fileName;  
 }  
414    
415  =head3 GetOptions  Standard tracing is output to the standard output and echoed to the file
416    C<trace>I<$$>C<.log> in the FIG temporary directory, where I<$$> is the
417    process ID. You can also specify the C<user> parameter to put a user ID
418    instead of a process ID in the trace file name. So, for example
419    
420  C<< Tracer::GetOptions(\%defaults, \%options); >>  The default trace level is 2. To get all messages, specify a trace level of 4.
421    For a genome-by-genome update, use 3.
422    
423  Merge a specified set of options into a table of defaults. This method takes two hash references      TransactFeatures -trace=3 -sql -user=Bruce register ../xacts IDs.tbl
 as input and uses the data from the second to update the first. If the second does not exist,  
 there will be no effect. An error will be thrown if one of the entries in the second hash does not  
 exist in the first.  
424    
425  Consider the following example.  would send the trace output to C<traceBruce.log> in the temporary directory.
426    
427  C<< my $optionTable = GetOptions({ dbType => 'mySQL', trace => 0 }, $options); >>  The I<options> parameter is a reference to a hash containing the command-line
428    options, their default values, and an explanation of what they mean. Command-line
429    options may be in the form of switches or keywords. In the case of a switch, the
430    option value is 1 if it is specified and 0 if it is not specified. In the case
431    of a keyword, the value is separated from the option name by an equal sign. You
432    can see this last in the command-line example above.
433    
434  In this example, the variable B<$options> is expected to contain at most two options-- B<dbType> and  You can specify a different default trace level by setting C<$options->{trace}>
435  B<trace>. The default database type is C<mySQL> and the default trace level is C<0>. If the value of  prior to calling this method.
 B<$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  
436    
437  C<< {databaseType => 'Oracle'} >>  An example at this point would help. Consider, for example, the command-line utility
438    C<TransactFeatures>. It accepts a list of positional parameters plus the options
439    C<safe>, C<noAlias>, C<start>, and C<tblFiles>. To start up this command, we execute
440    the following code.
441    
442  an error will occur because the B<databaseType> option does not exist.      my ($options, @parameters) = Tracer::StandardSetup(["DocUtils"],
443                            { safe => [0, "use database transactions"],
444                              noAlias => [0, "do not expect aliases in CHANGE transactions"],
445                              start => [' ', "start with this genome"],
446                              tblFiles => [0, "output TBL files containing the corrected IDs"] },
447                            "command transactionDirectory IDfile",
448                          @ARGV);
449    
450    
451    The call to C<ParseCommand> specifies the default values for the options and
452    stores the actual options in a hash that is returned as C<$options>. The
453    positional parameters are returned in C<@parameters>.
454    
455    The following is a sample command line for C<TransactFeatures>.
456    
457        TransactFeatures -trace=2 -noAlias register ../xacts IDs.tbl
458    
459    In this case, C<register>, C<../xacts>, and C<IDs.tbl> are the positional
460    parameters, and would find themselves in I<@parameters> after executing the
461    above code fragment. The tracing would be set to level 2, and the categories
462    would be C<Tracer>, and <DocUtils>. C<Tracer> is standard,
463    and C<DocUtils> was included because it came in within the first parameter
464    to this method. The I<$options> hash would be
465    
466        { trace => 2, sql => 0, safe => 0,
467          noAlias => 1, start => ' ', tblFiles => 0 }
468    
469    Use of C<StandardSetup> in this way provides a simple way of performing
470    standard tracing setup and command-line parsing. Note that the caller is
471    not even aware of the command-line switches C<-trace> and C<-sql>, which
472    are used by this method to control the tracing. If additional tracing features
473    need to be added in the future, they can be processed by this method without
474    upsetting the command-line utilities.
475    
476    If the C<background> option is specified on the command line, then the
477    standard and error outputs will be directed to files in the temporary
478    directory, using the same suffix as the trace file. So, if the command
479    line specified
480    
481        -user=Bruce -background
482    
483    then the trace output would go to C<traceBruce.log>, the standard output to
484    C<outBruce.log>, and the error output to C<errBruce.log>. This is designed to
485    simplify starting a command in the background.
486    
487    The user name is also used as the tracing key for L</Emergency Tracing>.
488    Specifying a value of C<E> for the trace level causes emergency tracing to
489    be used instead of custom tracing. If the user name is not specified,
490    the tracing key is taken from the C<Tracing> environment variable. If there
491    is no value for that variable, the tracing key will be computed from the PID.
492    
493    Finally, if the special option C<-h> is specified, the option names will
494    be traced at level 0 and the program will exit without processing.
495    This provides a limited help capability. For example, if the user enters
496    
497        TransactFeatures -h
498    
499    he would see the following output.
500    
501        TransactFeatures [options] command transactionDirectory IDfile
502            -trace    tracing level (default E)
503            -sql      trace SQL commands
504            -safe     use database transactions
505            -noAlias  do not expect aliases in CHANGE transactions
506            -start    start with this genome
507            -tblFiles output TBL files containing the corrected IDs
508    
509    The caller has the option of modifying the tracing scheme by placing a value
510    for C<trace> in the incoming options hash. The default value can be overridden,
511    or the tracing to the standard output can be turned off by suffixing a minus
512    sign to the trace level. So, for example,
513    
514        { trace => [0, "tracing level (default 0)"],
515           ...
516    
517    would set the default trace level to 0 instead of E, while
518    
519        { trace => ["2-", "tracing level (default 2)"],
520           ...
521    
522    would set the default to 2, but trace only to the log file, not to the
523    standard output.
524    
525    The parameters to this method are as follows.
526    
527  =over 4  =over 4
528    
529  =item defaults  =item categories
530    
531  Table of default option values.  Reference to a list of tracing category names. These should be names of
532    packages whose internal workings will need to be debugged to get the
533    command working.
534    
535  =item options  =item options
536    
537  Table of overrides, if any.  Reference to a hash containing the legal options for the current command mapped
538    to their default values and descriptions. The user can override the defaults
539    by specifying the options as command-line switches prefixed by a hyphen.
540    Tracing-related options may be added to this hash. If the C<-h> option is
541    specified on the command line, the option descriptions will be used to
542    explain the options. To turn off tracing to the standard output, add a
543    minus sign to the value for C<trace> (see above).
544    
545    =item parmHelp
546    
547    A string that vaguely describes the positional parameters. This is used
548    if the user specifies the C<-h> option.
549    
550    =item argv
551    
552    List of command line parameters, including the option switches, which must
553    precede the positional parameters and be prefixed by a hyphen.
554    
555  =item RETURN  =item RETURN
556    
557  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
558    maps the command-line option switches to their values. These will either be the
559    default values or overrides specified on the command line. The remaining
560    elements of the list are the position parameters, in order.
561    
562  =back  =back
563    
564  =cut  =cut
565    
566  sub GetOptions {  sub StandardSetup {
567          # Get the parameters.          # Get the parameters.
568          my ($defaults, $options) = @_;      my ($categories, $options, $parmHelp, @argv) = @_;
569          # Check for overrides.      # Get the default tracing key.
570          if ($options) {      my $tkey = EmergencyKey();
571                  # Loop through the overrides.      # Add the tracing options.
572                  while (my ($option, $setting) = each %{$options}) {      if (! exists $options->{trace}) {
573                          # Insure this override exists.          $options->{trace} = ['E', "tracing level (E for emergency tracing)"];
574                          if (!exists $defaults->{$option}) {      }
575                                  croak "Unrecognized option $option encountered.";      $options->{sql} = [0, "turn on SQL tracing"];
576        $options->{h} = [0, "display command-line options"];
577        $options->{user} = [$tkey, "tracing key"];
578        $options->{background} = [0, "spool standard and error output"];
579        # Create a parsing hash from the options hash. The parsing hash
580        # contains the default values rather than the default value
581        # and the description. While we're at it, we'll memorize the
582        # length of the longest option name.
583        my $longestName = 0;
584        my %parseOptions = ();
585        for my $key (keys %{$options}) {
586            if (length $key > $longestName) {
587                $longestName = length $key;
588            }
589            $parseOptions{$key} = $options->{$key}->[0];
590        }
591        # Parse the command line.
592        my ($retOptions, @retParameters) = ParseCommand(\%parseOptions, @argv);
593        # Get the logfile suffix.
594        my $suffix = $retOptions->{user};
595        # Check for background mode.
596        if ($retOptions->{background}) {
597            my $outFileName = "$FIG_Config::temp/out$suffix.log";
598            my $errFileName = "$FIG_Config::temp/err$suffix.log";
599            open STDOUT, ">$outFileName";
600            open STDERR, ">$errFileName";
601        }
602        # Now we want to set up tracing. First, we need to know if the user
603        # wants emergency tracing.
604        if ($retOptions->{trace} eq 'E') {
605            ETracing($retOptions->{user});
606                          } else {                          } else {
607                                  # Apply the override.          # Here the tracing is controlled from the command line.
608                                  $defaults->{$option} = $setting;          my @cats = @{$categories};
609            if ($retOptions->{sql}) {
610                push @cats, "SQL";
611            }
612            # Add the default categories.
613            push @cats, "Tracer";
614            # Next, we create the category string by joining the categories.
615            my $cats = join(" ", @cats);
616            # Check to determine whether or not the caller wants to turn off tracing
617            # to the standard output.
618            my $traceLevel = $retOptions->{trace};
619            my $textOKFlag = 1;
620            if ($traceLevel =~ /^(.)-/) {
621                $traceLevel = $1;
622                $textOKFlag = 0;
623            }
624            # Now we set up the trace mode.
625            my $traceMode;
626            # Verify that we can open a file in the FIG temporary directory.
627            my $traceFileName = "$FIG_Config::temp/trace$suffix.log";
628            if (open TESTTRACE, ">$traceFileName") {
629                # Here we can trace to a file.
630                $traceMode = ">$traceFileName";
631                if ($textOKFlag) {
632                    # Echo to standard output if the text-OK flag is set.
633                    $traceMode = "+$traceMode";
634                          }                          }
635                # Close the test file.
636                close TESTTRACE;
637            } else {
638                # Here we can't trace to a file. We trace to the standard output if it's
639                # okay, and the error log otherwise.
640                if ($textOKFlag) {
641                    $traceMode = "TEXT";
642                } else {
643                    $traceMode = "WARN";
644                  }                  }
645          }          }
646          # Return the merged table.          # Now set up the tracing.
647          return $defaults;          TSetup("$traceLevel $cats", $traceMode);
648        }
649        # Check for the "h" option. If it is specified, dump the command-line
650        # options and exit the program.
651        if ($retOptions->{h}) {
652            $0 =~ m#[/\\](\w+)(\.pl)?$#i;
653            print "$1 [options] $parmHelp\n";
654            for my $key (sort keys %{$options}) {
655                my $name = Pad($key, $longestName, 0, ' ');
656                my $desc = $options->{$key}->[1];
657                if ($options->{$key}->[0]) {
658                    $desc .= " (default " . $options->{$key}->[0] . ")";
659                }
660                print "  $name $desc\n";
661            }
662            exit(0);
663        }
664        # Return the parsed parameters.
665        return ($retOptions, @retParameters);
666  }  }
667    
668  =head3 MergeOptions  =head3 Setups
669    
670  C<< Tracer::MergeOptions(\%table, \%defaults); >>  C<< my $count = Tracer::Setups(); >>
671    
672  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.
673  second (default) hash, and if a matching key is not found in the first hash, the default  
674  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
675  checking and no return value.  may want to set up tracing if nobody else has done it before us.
676    
677    =cut
678    
679    sub Setups {
680        return $SetupCount;
681    }
682    
683    =head3 Open
684    
685    C<< my $handle = Open($fileHandle, $fileSpec, $message); >>
686    
687    Open a file.
688    
689    The I<$fileSpec> is essentially the second argument of the PERL C<open>
690    function. The mode is specified using Unix-like shell information. So, for
691    example,
692    
693        Open(\*LOGFILE, '>>/usr/spool/news/twitlog', "Could not open twit log.");
694    
695    would open for output appended to the specified file, and
696    
697        Open(\*DATASTREAM, "| sort -u >$outputFile", "Could not open $outputFile.");
698    
699    would open a pipe that sorts the records written and removes duplicates. Note
700    the use of file handle syntax in the Open call. To use anonymous file handles,
701    code as follows.
702    
703        my $logFile = Open(undef, '>>/usr/spool/news/twitlog', "Could not open twit log.");
704    
705    The I<$message> parameter is used if the open fails. If it is set to C<0>, then
706    the open returns TRUE if successful and FALSE if an error occurred. Otherwise, a
707    failed open will throw an exception and the third parameter will be used to construct
708    an error message. If the parameter is omitted, a standard message is constructed
709    using the file spec.
710    
711        Could not open "/usr/spool/news/twitlog"
712    
713    Note that the mode characters are automatically cleaned from the file name.
714    The actual error message from the file system will be captured and appended to the
715    message in any case.
716    
717        Could not open "/usr/spool/news/twitlog": file not found.
718    
719    In some versions of PERL the only error message we get is a number, which
720    corresponds to the C++ C<errno> value.
721    
722        Could not open "/usr/spool/news/twitlog": 6.
723    
724  =over 4  =over 4
725    
726  =item table  =item fileHandle
727    
728  Hash table to be updated with the default values.  File handle. If this parameter is C<undef>, a file handle will be generated
729    and returned as the value of this method.
730    
731  =item defaults  =item fileSpec
732    
733  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.
734    
735    =item message (optional)
736    
737    Error message to use if the open fails. If omitted, a standard error message
738    will be generated. In either case, the error information from the file system
739    is appended to the message. To specify a conditional open that does not throw
740    an error if it fails, use C<0>.
741    
742    =item RETURN
743    
744    Returns the name of the file handle assigned to the file, or C<undef> if the
745    open failed.
746    
747  =back  =back
748    
749  =cut  =cut
750    
751  sub MergeOptions {  sub Open {
752          # Get the parameters.          # Get the parameters.
753          my ($table, $defaults) = @_;      my ($fileHandle, $fileSpec, $message) = @_;
754          # Loop through the defaults.      # Attempt to open the file.
755          while (my ($key, $value) = each %{$defaults}) {      my $rv = open $fileHandle, $fileSpec;
756                  if (!exists $table->{$key}) {      # If the open failed, generate an error message.
757                          $table->{$key} = $value;      if (! $rv) {
758                  }          # Save the system error message.
759          }          my $sysMessage = $!;
760  }          # See if we need a default message.
761            if (!$message) {
762                # Clean any obvious mode characters and leading spaces from the
763                # filename.
764                my ($fileName) = FindNamePart($fileSpec);
765                $message = "Could not open \"$fileName\"";
766            }
767            # Terminate with an error using the supplied message and the
768            # error message from the file system.
769            Confess("$message: $!");
770        }
771        # Return the file handle.
772        return $fileHandle;
773    }
774    
775    =head3 FindNamePart
776    
777    C<< my ($fileName, $start, $len) = Tracer::FindNamePart($fileSpec); >>
778    
779    Extract the portion of a file specification that contains the file name.
780    
781    A file specification is the string passed to an C<open> call. It specifies the file
782    mode and name. In a truly complex situation, it can specify a pipe sequence. This
783    method assumes that the file name is whatever follows the first angle bracket
784    sequence.  So, for example, in the following strings the file name is
785    C</usr/fig/myfile.txt>.
786    
787        >>/usr/fig/myfile.txt
788        </usr/fig/myfile.txt
789        | sort -u > /usr/fig/myfile.txt
790    
791  =head3 Trace  If the method cannot find a file name using its normal methods, it will return the
792    whole incoming string.
793    
794  C<< Trace($message); >>  =over 4
795    
796  Write a trace message to the target location specified in L</TSetup>. If there has not been  =item fileSpec
 any prior call to B<TSetup>.  
797    
798  =over 4  File specification string from which the file name is to be extracted.
799    
800  =item message  =item RETURN
801    
802  Message to write.  Returns a three-element list. The first element contains the file name portion of
803    the specified string, or the whole string if a file name cannot be found via normal
804    methods. The second element contains the start position of the file name portion and
805    the third element contains the length.
806    
807  =back  =back
808    
809  =cut  =cut
810    #: Return Type $;
811  sub Trace {  sub FindNamePart {
812          # Get the parameters.          # Get the parameters.
813          my ($message) = @_;      my ($fileSpec) = @_;
814          # Get the timestamp.      # Default to the whole input string.
815          my $timeStamp = Now();      my ($retVal, $pos, $len) = ($fileSpec, 0, length $fileSpec);
816          # Process according to the destination.      # Parse out the file name if we can.
817          if ($Destination eq "TEXT") {      if ($fileSpec =~ m/(<|>>?)(.+?)(\s*)$/) {
818                  # Write the message to the standard output.          $retVal = $2;
819                  print "$timeStamp $message\n";          $len = length $retVal;
820          } elsif ($Destination eq "QUEUE") {          $pos = (length $fileSpec) - (length $3) - $len;
                 # Push the message into the queue.  
                 push @Queue, "$timeStamp $message";  
         } elsif ($Destination eq "HTML") {  
                 # Convert the message to HTML and write it to the standard output.  
                 my $escapedMessage = CGI::escapeHTML($message);  
                 print "<p>$timeStamp $message</p>\n";  
         } elsif ($Destination =~ m/^>>/) {  
                 # Write the trace message to an output file.  
                 open TRACING, $Destination;  
                 print TRACING "$timeStamp $message\n";  
                 close TRACING;  
821          }          }
822        # Return the result.
823        return ($retVal, $pos, $len);
824  }  }
825    
826  =head3 T  =head3 OpenDir
827    
828  C<< my $switch = T($category, $traceLevel); >>  C<< my @files = OpenDir($dirName, $filtered, $flag); >>
829    
830          or  Open a directory and return all the file names. This function essentially performs
831    the functions of an C<opendir> and C<readdir>. If the I<$filtered> parameter is
832    set to TRUE, all filenames beginning with a period (C<.>), dollar sign (C<$>),
833    or pound sign (C<#>) and all filenames ending with a tilde C<~>) will be
834    filtered out of the return list. If the directory does not open and I<$flag> is not
835    set, an exception is thrown. So, for example,
836    
837  C<< my $switch = T($traceLevel); >>      my @files = OpenDir("/Volumes/fig/contigs", 1);
838    
839  Return TRUE if the trace level is at or above a specified value and the specified category  is effectively the same as
840  is active, else FALSE. If no category is specified, the caller's package name is used.  
841        opendir(TMP, "/Volumes/fig/contigs") || Confess("Could not open /Volumes/fig/contigs.");
842        my @files = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir(TMP);
843    
844    Similarly, the following code
845    
846        my @files = grep { $_ =~ /^\d/ } OpenDir("/Volumes/fig/orgs", 0, 1);
847    
848    Returns the names of all files in C</Volumes/fig/orgs> that begin with digits and
849    automatically returns an empty list if the directory fails to open.
850    
851  =over 4  =over 4
852    
853  =item category  =item dirName
854    
855  Category to which the message belongs. If not specified, the caller's package name is  Name of the directory to open.
 used.  
856    
857  =item traceLevel  =item filtered
858    
859  Relevant tracing level.  TRUE if files whose names begin with a period (C<.>) should be automatically removed
860    from the list, else FALSE.
861    
862  =item RETURN  =item flag
863    
864  TRUE if a message at the specified trace level would appear in the trace, else FALSE.  TRUE if a failure to open is okay, else FALSE
865    
866  =back  =back
867    
868  =cut  =cut
869    #: Return Type @;
870  sub T {  sub OpenDir {
871        # Get the parameters.
872        my ($dirName, $filtered, $flag) = @_;
873          # Declare the return variable.          # Declare the return variable.
874          my $retVal = 0;      my @retVal = ();
875        # Open the directory.
876        if (opendir(my $dirHandle, $dirName)) {
877            # The directory opened successfully. Get the appropriate list according to the
878            # strictures of the filter parameter.
879            if ($filtered) {
880                @retVal = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir $dirHandle;
881            } else {
882                @retVal = readdir $dirHandle;
883            }
884        } elsif (! $flag) {
885            # Here the directory would not open and it's considered an error.
886            Confess("Could not open directory $dirName.");
887        }
888        # Return the result.
889        return @retVal;
890    }
891    
892    =head3 SetLevel
893    
894    C<< Tracer::SetLevel($newLevel); >>
895    
896    Modify the trace level. A higher trace level will cause more messages to appear.
897    
898    =over 4
899    
900    =item newLevel
901    
902    Proposed new trace level.
903    
904    =back
905    
906    =cut
907    
908    sub SetLevel {
909        $TraceLevel = $_[0];
910    }
911    
912    =head3 Now
913    
914    C<< my $string = Tracer::Now(); >>
915    
916    Return a displayable time stamp containing the local time.
917    
918    =cut
919    
920    sub Now {
921        my ($sec,$min,$hour,$mday,$mon,$year,$wday,$yday,$isdst) = localtime(time);
922        my $retVal = _p2($mon+1) . "/" . _p2($mday) . "/" . ($year + 1900) . " " .
923                     _p2($hour) . ":" . _p2($min) . ":" . _p2($sec);
924        return $retVal;
925    }
926    
927    # Pad a number to 2 digits.
928    sub _p2 {
929        my ($value) = @_;
930        $value = "0$value" if ($value < 10);
931        return $value;
932    }
933    
934    =head3 LogErrors
935    
936    C<< Tracer::LogErrors($fileName); >>
937    
938    Route the standard error output to a log file.
939    
940    =over 4
941    
942    =item fileName
943    
944    Name of the file to receive the error output.
945    
946    =back
947    
948    =cut
949    
950    sub LogErrors {
951        # Get the file name.
952        my ($fileName) = @_;
953        # Open the file as the standard error output.
954        open STDERR, '>', $fileName;
955    }
956    
957    =head3 ReadOptions
958    
959    C<< my %options = Tracer::ReadOptions($fileName); >>
960    
961    Read a set of options from a file. Each option is encoded in a line of text that has the
962    format
963    
964    I<optionName>C<=>I<optionValue>C<; >I<comment>
965    
966    The option name must consist entirely of letters, digits, and the punctuation characters
967    C<.> and C<_>, and is case sensitive. Blank lines and lines in which the first nonblank
968    character is a semi-colon will be ignored. The return hash will map each option name to
969    the corresponding option value.
970    
971    =over 4
972    
973    =item fileName
974    
975    Name of the file containing the option data.
976    
977    =item RETURN
978    
979    Returns a hash mapping the option names specified in the file to their corresponding option
980    value.
981    
982    =back
983    
984    =cut
985    
986    sub ReadOptions {
987        # Get the parameters.
988        my ($fileName) = @_;
989        # Open the file.
990        (open CONFIGFILE, "<$fileName") || Confess("Could not open option file $fileName.");
991        # Count the number of records read.
992        my ($records, $comments) = 0;
993        # Create the return hash.
994        my %retVal = ();
995        # Loop through the file, accumulating key-value pairs.
996        while (my $line = <CONFIGFILE>) {
997            # Denote we've read a line.
998            $records++;
999            # Determine the line type.
1000            if ($line =~ /^\s*[\n\r]/) {
1001                # A blank line is a comment.
1002                $comments++;
1003            } elsif ($line =~ /^\s*([A-Za-z0-9_\.]+)=([^;]*);/) {
1004                # Here we have an option assignment.
1005                retVal{$1} = $2;
1006            } elsif ($line =~ /^\s*;/) {
1007                # Here we have a text comment.
1008                $comments++;
1009            } else {
1010                # Here we have an invalid line.
1011                Trace("Invalid option statement in record $records.") if T(0);
1012            }
1013        }
1014        # Return the hash created.
1015        return %retVal;
1016    }
1017    
1018    =head3 GetOptions
1019    
1020    C<< Tracer::GetOptions(\%defaults, \%options); >>
1021    
1022    Merge a specified set of options into a table of defaults. This method takes two hash references
1023    as input and uses the data from the second to update the first. If the second does not exist,
1024    there will be no effect. An error will be thrown if one of the entries in the second hash does not
1025    exist in the first.
1026    
1027    Consider the following example.
1028    
1029    C<< my $optionTable = GetOptions({ dbType => 'mySQL', trace => 0 }, $options); >>
1030    
1031    In this example, the variable B<$options> is expected to contain at most two options-- B<dbType> and
1032    B<trace>. The default database type is C<mySQL> and the default trace level is C<0>. If the value of
1033    B<$options> is C<< {dbType => 'Oracle'} >>, then the database type will be changed to C<Oracle> and
1034    the trace level will remain at 0. If B<$options> is undefined, then the database type and trace level
1035    will remain C<mySQL> and C<0>. If, on the other hand, B<$options> is defined as
1036    
1037    C<< {databaseType => 'Oracle'} >>
1038    
1039    an error will occur because the B<databaseType> option does not exist.
1040    
1041    =over 4
1042    
1043    =item defaults
1044    
1045    Table of default option values.
1046    
1047    =item options
1048    
1049    Table of overrides, if any.
1050    
1051    =item RETURN
1052    
1053    Returns a reference to the default table passed in as the first parameter.
1054    
1055    =back
1056    
1057    =cut
1058    
1059    sub GetOptions {
1060        # Get the parameters.
1061        my ($defaults, $options) = @_;
1062        # Check for overrides.
1063        if ($options) {
1064            # Loop through the overrides.
1065            while (my ($option, $setting) = each %{$options}) {
1066                # Insure this override exists.
1067                if (!exists $defaults->{$option}) {
1068                    croak "Unrecognized option $option encountered.";
1069                } else {
1070                    # Apply the override.
1071                    $defaults->{$option} = $setting;
1072                }
1073            }
1074        }
1075        # Return the merged table.
1076        return $defaults;
1077    }
1078    
1079    =head3 MergeOptions
1080    
1081    C<< Tracer::MergeOptions(\%table, \%defaults); >>
1082    
1083    Merge default values into a hash table. This method looks at the key-value pairs in the
1084    second (default) hash, and if a matching key is not found in the first hash, the default
1085    pair is copied in. The process is similar to L</GetOptions>, but there is no error-
1086    checking and no return value.
1087    
1088    =over 4
1089    
1090    =item table
1091    
1092    Hash table to be updated with the default values.
1093    
1094    =item defaults
1095    
1096    Default values to be merged into the first hash table if they are not already present.
1097    
1098    =back
1099    
1100    =cut
1101    
1102    sub MergeOptions {
1103        # Get the parameters.
1104        my ($table, $defaults) = @_;
1105        # Loop through the defaults.
1106        while (my ($key, $value) = each %{$defaults}) {
1107            if (!exists $table->{$key}) {
1108                $table->{$key} = $value;
1109            }
1110        }
1111    }
1112    
1113    =head3 Trace
1114    
1115    C<< Trace($message); >>
1116    
1117    Write a trace message to the target location specified in L</TSetup>. If there has not been
1118    any prior call to B<TSetup>.
1119    
1120    =over 4
1121    
1122    =item message
1123    
1124    Message to write.
1125    
1126    =back
1127    
1128    =cut
1129    
1130    sub Trace {
1131        # Get the parameters.
1132        my ($message) = @_;
1133        # Get the timestamp.
1134        my $timeStamp = Now();
1135        # Format the message. Note we strip off any line terminators at the end.
1136        my $formatted = "[$timeStamp] <$LastCategory>: " . Strip($message);
1137        # Process according to the destination.
1138        if ($Destination eq "TEXT") {
1139            # Write the message to the standard output.
1140            print "$formatted\n";
1141        } elsif ($Destination eq "ERROR") {
1142            # Write the message to the error output.
1143            print STDERR "$formatted\n";
1144        } elsif ($Destination eq "QUEUE") {
1145            # Push the message into the queue.
1146            push @Queue, "$formatted";
1147        } elsif ($Destination eq "HTML") {
1148            # Convert the message to HTML and write it to the standard output.
1149            my $escapedMessage = CGI::escapeHTML($message);
1150            print "<p>$formatted</p>\n";
1151        } elsif ($Destination eq "WARN") {
1152           # Emit the message as a warning.
1153           warn $message;
1154        } elsif ($Destination =~ m/^>>/) {
1155            # Write the trace message to an output file.
1156            (open TRACING, $Destination) || die "Tracing open for \"$Destination\" failed: $!";
1157            print TRACING "$formatted\n";
1158            close TRACING;
1159            # If the Tee flag is on, echo it to the standard output.
1160            if ($TeeFlag) {
1161                print "$formatted\n";
1162            }
1163        }
1164    }
1165    
1166    =head3 T
1167    
1168    C<< my $switch = T($category, $traceLevel); >>
1169    
1170        or
1171    
1172    C<< my $switch = T($traceLevel); >>
1173    
1174    Return TRUE if the trace level is at or above a specified value and the specified category
1175    is active, else FALSE. If no category is specified, the caller's package name is used.
1176    
1177    =over 4
1178    
1179    =item category
1180    
1181    Category to which the message belongs. If not specified, the caller's package name is
1182    used.
1183    
1184    =item traceLevel
1185    
1186    Relevant tracing level.
1187    
1188    =item RETURN
1189    
1190    TRUE if a message at the specified trace level would appear in the trace, else FALSE.
1191    
1192    =back
1193    
1194    =cut
1195    
1196    sub T {
1197        # Declare the return variable.
1198        my $retVal = 0;
1199          # Only proceed if tracing is turned on.          # Only proceed if tracing is turned on.
1200          if ($Destination ne "NONE") {          if ($Destination ne "NONE") {
1201                  # Get the parameters.                  # Get the parameters.
1202                  my ($category, $traceLevel) = @_;                  my ($category, $traceLevel) = @_;
1203                  if (!defined $traceLevel) {                  if (!defined $traceLevel) {
1204                          # Here we have no category, so we need to get the calling package.                          # Here we have no category, so we need to get the calling package.
1205                # The calling package is normally the first parameter. If it is
1206                # omitted, the first parameter will be the tracelevel. So, the
1207                # first thing we do is shift the so-called category into the
1208                # $traceLevel variable where it belongs.
1209                          $traceLevel = $category;                          $traceLevel = $category;
1210                          my ($package, $fileName, $line) = caller;                          my ($package, $fileName, $line) = caller;
1211                          # If there is no calling package, we default to "root".              # If there is no calling package, we default to "main".
1212                          if (!$package) {                          if (!$package) {
1213                                  $category = "root";                  $category = "main";
1214                } else {
1215                    $category = $package;
1216                }
1217            }
1218            # Save the category name.
1219            $LastCategory = $category;
1220            # Convert it to lower case before we hash it.
1221            $category = lc $category;
1222            # Use the category and tracelevel to compute the result.
1223            if (ref $traceLevel) {
1224                Confess("Bad trace level.");
1225            } elsif (ref $TraceLevel) {
1226                Confess("Bad trace config.");
1227            }
1228            $retVal = ($traceLevel <= $TraceLevel && ($AllTrace || exists $Categories{$category}));
1229        }
1230        # Return the computed result.
1231        return $retVal;
1232    }
1233    
1234    =head3 ParseCommand
1235    
1236    C<< my ($options, @arguments) = Tracer::ParseCommand(\%optionTable, @inputList); >>
1237    
1238    Parse a command line consisting of a list of parameters. The initial parameters may be option
1239    specifiers of the form C<->I<option> or C<->I<option>C<=>I<value>. The options are stripped
1240    off and merged into a table of default options. The remainder of the command line is
1241    returned as a list of positional arguments. For example, consider the following invocation.
1242    
1243    C<< my ($options, @arguments) = ParseCommand({ errors => 0, logFile => 'trace.log'}, @words); >>
1244    
1245    In this case, the list @words will be treated as a command line. There are two options available,
1246    B<errors> and B<logFile>. If @words has the following format
1247    
1248    C<< -logFile=error.log apple orange rutabaga >>
1249    
1250    then at the end of the invocation, C<$options> will be
1251    
1252    C<< { errors => 0, logFile => 'error.log' } >>
1253    
1254    and C<@arguments> will contain
1255    
1256    C<< apple orange rutabaga >>
1257    
1258    The parser allows for some escape sequences. See L</UnEscape> for a description. There is no
1259    support for quote characters.
1260    
1261    =over 4
1262    
1263    =item optionTable
1264    
1265    Table of default options.
1266    
1267    =item inputList
1268    
1269    List of words on the command line.
1270    
1271    =item RETURN
1272    
1273    Returns a reference to the option table and a list of the positional arguments.
1274    
1275    =back
1276    
1277    =cut
1278    
1279    sub ParseCommand {
1280        # Get the parameters.
1281        my ($optionTable, @inputList) = @_;
1282        # Process any options in the input list.
1283        my %overrides = ();
1284        while ((@inputList > 0) && ($inputList[0] =~ /^-/)) {
1285            # Get the current option.
1286            my $arg = shift @inputList;
1287            # Pull out the option name.
1288            $arg =~ /^-([^=]*)/g;
1289            my $name = $1;
1290            # Check for an option value.
1291            if ($arg =~ /\G=(.*)$/g) {
1292                # Here we have a value for the option.
1293                $overrides{$name} = UnEscape($1);
1294            } else {
1295                # Here there is no value, so we use 1.
1296                $overrides{$name} = 1;
1297            }
1298        }
1299        # Merge the options into the defaults.
1300        GetOptions($optionTable, \%overrides);
1301        # Translate the remaining parameters.
1302        my @retVal = ();
1303        for my $inputParm (@inputList) {
1304            push @retVal, UnEscape($inputParm);
1305        }
1306        # Return the results.
1307        return ($optionTable, @retVal);
1308    }
1309    
1310    =head3 Escape
1311    
1312    C<< my $codedString = Tracer::Escape($realString); >>
1313    
1314    Escape a string for use in a command length. Tabs will be replaced by C<\t>, new-lines
1315    replaced by C<\n>, carriage returns will be deleted, and backslashes will be doubled. The
1316    result is to reverse the effect of L</UnEscape>.
1317    
1318    =over 4
1319    
1320    =item realString
1321    
1322    String to escape.
1323    
1324    =item RETURN
1325    
1326    Escaped equivalent of the real string.
1327    
1328    =back
1329    
1330    =cut
1331    
1332    sub Escape {
1333        # Get the parameter.
1334        my ($realString) = @_;
1335        # Initialize the return variable.
1336        my $retVal = "";
1337        # Loop through the parameter string, looking for sequences to escape.
1338        while (length $realString > 0) {
1339            # Look for the first sequence to escape.
1340            if ($realString =~ /^(.*?)([\n\t\r\\])/) {
1341                # Here we found it. The text preceding the sequence is in $1. The sequence
1342                # itself is in $2. First, move the clear text to the return variable.
1343                $retVal .= $1;
1344                # Strip the processed section off the real string.
1345                $realString = substr $realString, (length $2) + (length $1);
1346                # Get the matched character.
1347                my $char = $2;
1348                # If we have a CR, we are done.
1349                if ($char ne "\r") {
1350                    # It's not a CR, so encode the escape sequence.
1351                    $char =~ tr/\t\n/tn/;
1352                    $retVal .= "\\" . $char;
1353                }
1354            } else {
1355                # Here there are no more escape sequences. The rest of the string is
1356                # transferred unmodified.
1357                $retVal .= $realString;
1358                $realString = "";
1359            }
1360        }
1361        # Return the result.
1362        return $retVal;
1363    }
1364    
1365    =head3 UnEscape
1366    
1367    C<< my $realString = Tracer::UnEscape($codedString); >>
1368    
1369    Replace escape sequences with their actual equivalents. C<\t> will be replaced by
1370    a tab, C<\n> by a new-line character, and C<\\> by a backslash. C<\r> codes will
1371    be deleted.
1372    
1373    =over 4
1374    
1375    =item codedString
1376    
1377    String to un-escape.
1378    
1379    =item RETURN
1380    
1381    Returns a copy of the original string with the escape sequences converted to their actual
1382    values.
1383    
1384    =back
1385    
1386    =cut
1387    
1388    sub UnEscape {
1389        # Get the parameter.
1390        my ($codedString) = @_;
1391        # Initialize the return variable.
1392        my $retVal = "";
1393        # Only proceed if the incoming string is nonempty.
1394        if (defined $codedString) {
1395            # Loop through the parameter string, looking for escape sequences. We can't do
1396            # translating because it causes problems with the escaped slash. ("\\t" becomes
1397            # "\<tab>" no matter what we do.)
1398            while (length $codedString > 0) {
1399                # Look for the first escape sequence.
1400                if ($codedString =~ /^(.*?)\\(\\|n|t|r)/) {
1401                    # Here we found it. The text preceding the sequence is in $1. The sequence
1402                    # itself is in $2. First, move the clear text to the return variable.
1403                    $retVal .= $1;
1404                    $codedString = substr $codedString, (2 + length $1);
1405                    # Get the escape value.
1406                    my $char = $2;
1407                    # If we have a "\r", we are done.
1408                    if ($char ne 'r') {
1409                        # Here it's not an 'r', so we convert it.
1410                        $char =~ tr/\\tn/\\\t\n/;
1411                        $retVal .= $char;
1412                    }
1413                } else {
1414                    # Here there are no more escape sequences. The rest of the string is
1415                    # transferred unmodified.
1416                    $retVal .= $codedString;
1417                    $codedString = "";
1418                }
1419            }
1420        }
1421        # Return the result.
1422        return $retVal;
1423    }
1424    
1425    =head3 ParseRecord
1426    
1427    C<< my @fields = Tracer::ParseRecord($line); >>
1428    
1429    Parse a tab-delimited data line. The data line is split into field values. Embedded tab
1430    and new-line characters in the data line must be represented as C<\t> and C<\n>, respectively.
1431    These will automatically be converted.
1432    
1433    =over 4
1434    
1435    =item line
1436    
1437    Line of data containing the tab-delimited fields.
1438    
1439    =item RETURN
1440    
1441    Returns a list of the fields found in the data line.
1442    
1443    =back
1444    
1445    =cut
1446    
1447    sub ParseRecord {
1448        # Get the parameter.
1449        my ($line) = @_;
1450        # Remove the trailing new-line, if any.
1451        chomp $line;
1452        # Split the line read into pieces using the tab character.
1453        my @retVal = split /\t/, $line;
1454        # Trim and fix the escapes in each piece.
1455        for my $value (@retVal) {
1456            # Trim leading whitespace.
1457            $value =~ s/^\s+//;
1458            # Trim trailing whitespace.
1459            $value =~ s/\s+$//;
1460            # Delete the carriage returns.
1461            $value =~ s/\r//g;
1462            # Convert the escapes into their real values.
1463            $value =~ s/\\t/"\t"/ge;
1464            $value =~ s/\\n/"\n"/ge;
1465        }
1466        # Return the result.
1467        return @retVal;
1468    }
1469    
1470    =head3 Merge
1471    
1472    C<< my @mergedList = Tracer::Merge(@inputList); >>
1473    
1474    Sort a list of strings and remove duplicates.
1475    
1476    =over 4
1477    
1478    =item inputList
1479    
1480    List of scalars to sort and merge.
1481    
1482    =item RETURN
1483    
1484    Returns a list containing the same elements sorted in ascending order with duplicates
1485    removed.
1486    
1487    =back
1488    
1489    =cut
1490    
1491    sub Merge {
1492        # Get the input list in sort order.
1493        my @inputList = sort @_;
1494        # Only proceed if the list has at least two elements.
1495        if (@inputList > 1) {
1496            # Now we want to move through the list splicing out duplicates.
1497            my $i = 0;
1498            while ($i < @inputList) {
1499                # Get the current entry.
1500                my $thisEntry = $inputList[$i];
1501                # Find out how many elements duplicate the current entry.
1502                my $j = $i + 1;
1503                my $dup1 = $i + 1;
1504                while ($j < @inputList && $inputList[$j] eq $thisEntry) { $j++; };
1505                # If the number is nonzero, splice out the duplicates found.
1506                if ($j > $dup1) {
1507                    splice @inputList, $dup1, $j - $dup1;
1508                }
1509                # Now the element at position $dup1 is different from the element before it
1510                # at position $i. We push $i forward one position and start again.
1511                $i++;
1512            }
1513        }
1514        # Return the merged list.
1515        return @inputList;
1516    }
1517    
1518    =head3 Percent
1519    
1520    C<< my $percent = Tracer::Percent($number, $base); >>
1521    
1522    Returns the percent of the base represented by the given number. If the base
1523    is zero, returns zero.
1524    
1525    =over 4
1526    
1527    =item number
1528    
1529    Percent numerator.
1530    
1531    =item base
1532    
1533    Percent base.
1534    
1535    =item RETURN
1536    
1537    Returns the percentage of the base represented by the numerator.
1538    
1539    =back
1540    
1541    =cut
1542    
1543    sub Percent {
1544        # Get the parameters.
1545        my ($number, $base) = @_;
1546        # Declare the return variable.
1547        my $retVal = 0;
1548        # Compute the percent.
1549        if ($base != 0) {
1550            $retVal = $number * 100 / $base;
1551        }
1552        # Return the result.
1553        return $retVal;
1554    }
1555    
1556    =head3 GetFile
1557    
1558    C<< my @fileContents = Tracer::GetFile($fileName); >>
1559    
1560        or
1561    
1562    C<< my $fileContents = Tracer::GetFile($fileName); >>
1563    
1564    Return the entire contents of a file. In list context, line-ends are removed and
1565    each line is a list element. In scalar context, line-ends are replaced by C<\n>.
1566    
1567    =over 4
1568    
1569    =item fileName
1570    
1571    Name of the file to read.
1572    
1573    =item RETURN
1574    
1575    In a list context, returns the entire file as a list with the line terminators removed.
1576    In a scalar context, returns the entire file as a string. If an error occurs opening
1577    the file, an empty list will be returned.
1578    
1579    =back
1580    
1581    =cut
1582    
1583    sub GetFile {
1584        # Get the parameters.
1585        my ($fileName) = @_;
1586        # Declare the return variable.
1587        my @retVal = ();
1588        # Open the file for input.
1589        my $handle = Open(undef, "<$fileName");
1590        # Read the whole file into the return variable, stripping off any terminator
1591        # characters.
1592        my $lineCount = 0;
1593        while (my $line = <$handle>) {
1594            $lineCount++;
1595            $line = Strip($line);
1596            push @retVal, $line;
1597        }
1598        # Close it.
1599        close $handle;
1600        my $actualLines = @retVal;
1601        # Return the file's contents in the desired format.
1602        if (wantarray) {
1603            return @retVal;
1604        } else {
1605            return join "\n", @retVal;
1606        }
1607    }
1608    
1609    =head3 PutFile
1610    
1611    C<< Tracer::PutFile($fileName, \@lines); >>
1612    
1613    Write out a file from a list of lines of text.
1614    
1615    =over 4
1616    
1617    =item fileName
1618    
1619    Name of the output file.
1620    
1621    =item lines
1622    
1623    Reference to a list of text lines. The lines will be written to the file in order, with trailing
1624    new-line characters. Alternatively, may be a string, in which case the string will be written without
1625    modification.
1626    
1627    =back
1628    
1629    =cut
1630    
1631    sub PutFile {
1632        # Get the parameters.
1633        my ($fileName, $lines) = @_;
1634        # Open the output file.
1635        my $handle = Open(undef, ">$fileName");
1636        if (ref $lines ne 'ARRAY') {
1637            # Here we have a scalar, so we write it raw.
1638            print $handle $lines;
1639        } else {
1640            # Write the lines one at a time.
1641            for my $line (@{$lines}) {
1642                print $handle "$line\n";
1643            }
1644        }
1645        # Close the output file.
1646        close $handle;
1647    }
1648    
1649    =head3 QTrace
1650    
1651    C<< my $data = QTrace($format); >>
1652    
1653    Return the queued trace data in the specified format.
1654    
1655    =over 4
1656    
1657    =item format
1658    
1659    C<html> to format the data as an HTML list, C<text> to format it as straight text.
1660    
1661    =back
1662    
1663    =cut
1664    
1665    sub QTrace {
1666        # Get the parameter.
1667        my ($format) = @_;
1668        # Create the return variable.
1669        my $retVal = "";
1670        # Only proceed if there is an actual queue.
1671        if (@Queue) {
1672            # Process according to the format.
1673            if ($format =~ m/^HTML$/i) {
1674                # Convert the queue into an HTML list.
1675                $retVal = "<ul>\n";
1676                for my $line (@Queue) {
1677                    my $escapedLine = CGI::escapeHTML($line);
1678                    $retVal .= "<li>$escapedLine</li>\n";
1679                }
1680                $retVal .= "</ul>\n";
1681            } elsif ($format =~ m/^TEXT$/i) {
1682                # Convert the queue into a list of text lines.
1683                $retVal = join("\n", @Queue) . "\n";
1684            }
1685            # Clear the queue.
1686            @Queue = ();
1687        }
1688        # Return the formatted list.
1689        return $retVal;
1690    }
1691    
1692    =head3 Confess
1693    
1694    C<< Confess($message); >>
1695    
1696    Trace the call stack and abort the program with the specified message. When used with
1697    the OR operator and the L</Assert> method, B<Confess> can function as a debugging assert.
1698    So, for example
1699    
1700    C<< Assert($recNum >= 0) || Confess("Invalid record number $recNum."); >>
1701    
1702    Will abort the program with a stack trace if the value of C<$recNum> is negative.
1703    
1704    =over 4
1705    
1706    =item message
1707    
1708    Message to include in the trace.
1709    
1710    =back
1711    
1712    =cut
1713    
1714    sub Confess {
1715        # Get the parameters.
1716        my ($message) = @_;
1717        # Trace the call stack.
1718        Cluck($message);
1719        # Abort the program.
1720        croak(">>> $message");
1721    }
1722    
1723    =head3 Assert
1724    
1725    C<< Assert($condition1, $condition2, ... $conditionN); >>
1726    
1727    Return TRUE if all the conditions are true. This method can be used in conjunction with
1728    the OR operator and the L</Confess> method as a debugging assert.
1729    So, for example
1730    
1731    C<< Assert($recNum >= 0) || Confess("Invalid record number $recNum."); >>
1732    
1733    Will abort the program with a stack trace if the value of C<$recNum> is negative.
1734    
1735    =cut
1736    sub Assert {
1737        my $retVal = 1;
1738        LOOP: for my $condition (@_) {
1739            if (! $condition) {
1740                $retVal = 0;
1741                last LOOP;
1742            }
1743        }
1744        return $retVal;
1745    }
1746    
1747    =head3 Cluck
1748    
1749    C<< Cluck($message); >>
1750    
1751    Trace the call stack. Note that for best results, you should qualify the call with a
1752    trace condition. For example,
1753    
1754    C<< Cluck("Starting record parse.") if T(3); >>
1755    
1756    will only trace the stack if the trace level for the package is 3 or more.
1757    
1758    =over 4
1759    
1760    =item message
1761    
1762    Message to include in the trace.
1763    
1764    =back
1765    
1766    =cut
1767    
1768    sub Cluck {
1769        # Get the parameters.
1770        my ($message) = @_;
1771        # Trace what's happening.
1772        Trace("Stack trace for event: $message");
1773        my $confession = longmess($message);
1774        # Convert the confession to a series of trace messages. Note we skip any
1775        # messages relating to calls into Tracer.
1776        for my $line (split /\s*\n/, $confession) {
1777            Trace($line) if ($line !~ /Tracer\.pm/);
1778        }
1779    }
1780    
1781    =head3 Min
1782    
1783    C<< my $min = Min($value1, $value2, ... $valueN); >>
1784    
1785    Return the minimum argument. The arguments are treated as numbers.
1786    
1787    =over 4
1788    
1789    =item $value1, $value2, ... $valueN
1790    
1791    List of numbers to compare.
1792    
1793    =item RETURN
1794    
1795    Returns the lowest number in the list.
1796    
1797    =back
1798    
1799    =cut
1800    
1801    sub Min {
1802        # Get the parameters. Note that we prime the return value with the first parameter.
1803        my ($retVal, @values) = @_;
1804        # Loop through the remaining parameters, looking for the lowest.
1805        for my $value (@values) {
1806            if ($value < $retVal) {
1807                $retVal = $value;
1808            }
1809        }
1810        # Return the minimum found.
1811        return $retVal;
1812    }
1813    
1814    =head3 Max
1815    
1816    C<< my $max = Max($value1, $value2, ... $valueN); >>
1817    
1818    Return the maximum argument. The arguments are treated as numbers.
1819    
1820    =over 4
1821    
1822    =item $value1, $value2, ... $valueN
1823    
1824    List of numbers to compare.
1825    
1826    =item RETURN
1827    
1828    Returns the highest number in the list.
1829    
1830    =back
1831    
1832    =cut
1833    
1834    sub Max {
1835        # Get the parameters. Note that we prime the return value with the first parameter.
1836        my ($retVal, @values) = @_;
1837        # Loop through the remaining parameters, looking for the highest.
1838        for my $value (@values) {
1839            if ($value > $retVal) {
1840                $retVal = $value;
1841            }
1842        }
1843        # Return the maximum found.
1844        return $retVal;
1845    }
1846    
1847    =head3 AddToListMap
1848    
1849    C<< Tracer::AddToListMap(\%hash, $key, $value1, $value2, ... valueN); >>
1850    
1851    Add a key-value pair to a hash of lists. If no value exists for the key, a singleton list
1852    is created for the key. Otherwise, the new value is pushed onto the list.
1853    
1854    =over 4
1855    
1856    =item hash
1857    
1858    Reference to the target hash.
1859    
1860    =item key
1861    
1862    Key for which the value is to be added.
1863    
1864    =item value1, value2, ... valueN
1865    
1866    List of values to add to the key's value list.
1867    
1868    =back
1869    
1870    =cut
1871    
1872    sub AddToListMap {
1873        # Get the parameters.
1874        my ($hash, $key, @values) = @_;
1875        # Process according to whether or not the key already has a value.
1876        if (! exists $hash->{$key}) {
1877            $hash->{$key} = [@values];
1878        } else {
1879            push @{$hash->{$key}}, @values;
1880        }
1881    }
1882    
1883    =head3 DebugMode
1884    
1885    C<< if (Tracer::DebugMode) { ...code... } >>
1886    
1887    Return TRUE if debug mode has been turned on, else abort.
1888    
1889    Certain CGI scripts are too dangerous to exist in the production
1890    environment. This method provides a simple way to prevent them
1891    from working unless they are explicitly turned on by creating a password
1892    cookie via the B<SetPassword> script.  If debugging mode
1893    is not turned on, an error will occur.
1894    
1895    =cut
1896    
1897    sub DebugMode {
1898        # Declare the return variable.
1899        my $retVal = 0;
1900        # Check the debug configuration.
1901        my $password = CGI::cookie("DebugMode");
1902        my $encrypted = Digest::MD5::md5_hex($password);
1903        if ($encrypted eq "252dec43280e0c0d6a75ffcec486e61d") {
1904            $retVal = 1;
1905        } else {
1906            # Here debug mode is off, so we generate an error.
1907            Confess("Cannot use this facility without logging in.");
1908        }
1909        # Return the determination indicator.
1910        return $retVal;
1911    }
1912    
1913    =head3 Strip
1914    
1915    C<< my $string = Tracer::Strip($line); >>
1916    
1917    Strip all line terminators off a string. This is necessary when dealing with files
1918    that may have been transferred back and forth several times among different
1919    operating environments.
1920    
1921    =over 4
1922    
1923    =item line
1924    
1925    Line of text to be stripped.
1926    
1927    =item RETURN
1928    
1929    The same line of text with all the line-ending characters chopped from the end.
1930    
1931    =back
1932    
1933    =cut
1934    
1935    sub Strip {
1936        # Get a copy of the parameter string.
1937        my ($string) = @_;
1938        my $retVal = (defined $string ? $string : "");
1939        # Strip the line terminator characters.
1940        $retVal =~ s/(\r|\n)+$//g;
1941        # Return the result.
1942        return $retVal;
1943    }
1944    
1945    =head3 Pad
1946    
1947    C<< my $paddedString = Tracer::Pad($string, $len, $left, $padChar); >>
1948    
1949    Pad a string to a specified length. The pad character will be a
1950    space, and the padding will be on the right side unless specified
1951    in the third parameter.
1952    
1953    =over 4
1954    
1955    =item string
1956    
1957    String to be padded.
1958    
1959    =item len
1960    
1961    Desired length of the padded string.
1962    
1963    =item left (optional)
1964    
1965    TRUE if the string is to be left-padded; otherwise it will be padded on the right.
1966    
1967    =item padChar (optional)
1968    
1969    Character to use for padding. The default is a space.
1970    
1971    =item RETURN
1972    
1973    Returns a copy of the original string with the pad character added to the
1974    specified end so that it achieves the desired length.
1975    
1976    =back
1977    
1978    =cut
1979    
1980    sub Pad {
1981        # Get the parameters.
1982        my ($string, $len, $left, $padChar) = @_;
1983        # Compute the padding character.
1984        if (! defined $padChar) {
1985            $padChar = " ";
1986        }
1987        # Compute the number of spaces needed.
1988        my $needed = $len - length $string;
1989        # Copy the string into the return variable.
1990        my $retVal = $string;
1991        # Only proceed if padding is needed.
1992        if ($needed > 0) {
1993            # Create the pad string.
1994            my $pad = $padChar x $needed;
1995            # Affix it to the return value.
1996            if ($left) {
1997                $retVal = $pad . $retVal;
1998            } else {
1999                $retVal .= $pad;
2000            }
2001        }
2002        # Return the result.
2003        return $retVal;
2004    }
2005    
2006    =head3 EOF
2007    
2008    This is a constant that is lexically greater than any useful string.
2009    
2010    =cut
2011    
2012    sub EOF {
2013        return "\xFF\xFF\xFF\xFF\xFF";
2014    }
2015    
2016    =head3 TICK
2017    
2018    C<< my @results = TICK($commandString); >>
2019    
2020    Perform a back-tick operation on a command. If this is a Windows environment, any leading
2021    dot-slash (C<./> will be removed. So, for example, if you were doing
2022    
2023        `./protein.cgi`
2024    
2025    from inside a CGI script, it would work fine in Unix, but would issue an error message
2026    in Windows complaining that C<'.'> is not a valid command. If instead you code
2027    
2028        TICK("./protein.cgi")
2029    
2030    it will work correctly in both environments.
2031    
2032    =over 4
2033    
2034    =item commandString
2035    
2036    The command string to pass to the system.
2037    
2038    =item RETURN
2039    
2040    Returns the standard output from the specified command, as a list.
2041    
2042    =back
2043    
2044    =cut
2045    #: Return Type @;
2046    sub TICK {
2047        # Get the parameters.
2048        my ($commandString) = @_;
2049        # Chop off the dot-slash if this is Windows.
2050        if ($FIG_Config::win_mode) {
2051            $commandString =~ s!^\./!!;
2052        }
2053        # Activate the command and return the result.
2054        return `$commandString`;
2055    }
2056    
2057    =head3 ScriptSetup
2058    
2059    C<< my ($cgi, $varHash) = ScriptSetup($noTrace); >>
2060    
2061    Perform standard tracing and debugging setup for scripts. The value returned is
2062    the CGI object followed by a pre-built variable hash.
2063    
2064    The C<Trace> form parameter is used to determine whether or not tracing is active and
2065    which trace modules (other than C<Tracer> itself) should be turned on. Specifying
2066    the C<CGI> trace module will trace parameter and environment information. Parameters are
2067    traced at level 3 and environment variables at level 4. To trace to a file instead of to
2068    the web page, set C<TF> to 1. At the end of the script, the client should call
2069    L</ScriptFinish> to output the web page.
2070    
2071    In some situations, it is not practical to invoke tracing via form parameters. For this
2072    situation, you can turn on emergency tracing from the debugging control panel.
2073    Tracing will then be turned on automatically for all programs that use the L</ETracing>
2074    method, which includes every program that uses this method or L</StandardSetup>.
2075    
2076    =over 4
2077    
2078    =item noTrace (optional)
2079    
2080    If specified, tracing will be suppressed. This is useful if the script wants to set up
2081    tracing manually.
2082    
2083    =item RETURN
2084    
2085    Returns a two-element list consisting of a CGI query object and a variable hash for
2086    the output page.
2087    
2088    =back
2089    
2090    =cut
2091    
2092    sub ScriptSetup {
2093        # Get the parameters.
2094        my ($noTrace) = @_;
2095        # Get the CGI query object.
2096        my $cgi = CGI->new();
2097        # Set up tracing if it's not suppressed.
2098        ETracing($cgi) unless $noTrace;
2099        # Create the variable hash.
2100        my $varHash = { results => '' };
2101        # Return the query object and variable hash.
2102        return ($cgi, $varHash);
2103    }
2104    
2105    =head3 ETracing
2106    
2107    C<< ETracing($parameter); >>
2108    
2109    Set up emergency tracing. Emergency tracing is tracing that is turned
2110    on automatically for any program that calls this method. The emergency
2111    tracing parameters are stored in a a file identified by a tracing key.
2112    If this method is called with a CGI object, then the tracing key is
2113    taken from a cookie. If it is called with no parameters, then the tracing
2114    key is taken from an environment variable. If it is called with a string,
2115    the tracing key is that string.
2116    
2117    =over 4
2118    
2119    =item parameter
2120    
2121    A parameter from which the tracing key is computed. If it is a scalar,
2122    that scalar is used as the tracing key. If it is a CGI object, the
2123    tracing key is taken from the C<IP> cookie. If it is omitted, the
2124    tracing key is taken from the C<TRACING> environment variable. If it
2125    is a CGI object and emergency tracing is not on, the C<Trace> and
2126    C<TF> parameters will be used to determine the type of tracing.
2127    
2128    =back
2129    
2130    =cut
2131    
2132    sub ETracing {
2133        # Get the parameter.
2134        my ($parameter) = @_;
2135        # Check for CGI mode.
2136        my $cgi = (ref $parameter eq 'CGI' ? $parameter : undef);
2137        # Default to no tracing except errors.
2138        my ($tracing, $dest) = ("0", "WARN");
2139        # Check for emergency tracing.
2140        my $tkey = EmergencyKey($parameter);
2141        my $emergencyFile = EmergencyFileName($tkey);
2142        if (-e $emergencyFile) {
2143            # We have the file. Read in the data.
2144            my @tracing = GetFile($emergencyFile);
2145            # Pull off the time limit.
2146            my $expire = shift @tracing;
2147            # Convert it to seconds.
2148            $expire *= 3600;
2149            # Check the file data.
2150            my $stat = stat($emergencyFile);
2151            my ($now) = gettimeofday;
2152            if ($now - $stat->mtime > $expire) {
2153                # Delete the expired file.
2154                unlink $emergencyFile;
2155            } else {
2156                # Emergency tracing is on. Pull off the destination and
2157                # the trace level;
2158                $dest = shift @tracing;
2159                my $level = shift @tracing;
2160                # Convert the destination to a real tracing destination.
2161                # temp directory.
2162                $dest = EmergencyTracingDest($tkey, $dest);
2163                # Insure Tracer is specified.
2164                my %moduleHash = map { $_ => 1 } @tracing;
2165                $moduleHash{Tracer} = 1;
2166                # Set the trace parameter.
2167                $tracing = join(" ", $level, sort keys %moduleHash);
2168            }
2169        } elsif (defined $cgi) {
2170            # There's no emergency tracing, but we have a CGI object, so check
2171            # for tracing from the form parameters.
2172            if ($cgi->param('Trace')) {
2173                # Here the user has requested tracing via a form.
2174                $dest = ($cgi->param('TF') ? ">$FIG_Config::temp/Trace$$.log" : "QUEUE");
2175                $tracing = $cgi->param('Trace') . " Tracer";
2176            }
2177        }
2178        # Setup the tracing we've determined from all the stuff above.
2179        TSetup($tracing, $dest);
2180        # If we're a web script, trace the parameter and environment data.
2181        if (defined $cgi) {
2182            TraceParms($cgi);
2183        }
2184    }
2185    
2186    =head3 EmergencyFileName
2187    
2188    C<< my $fileName = Tracer::EmergencyFileName($tkey); >>
2189    
2190    Return the emergency tracing file name. This is the file that specifies
2191    the tracing information.
2192    
2193    =over 4
2194    
2195    =item tkey
2196    
2197    Tracing key for the current program.
2198    
2199    =item RETURN
2200    
2201    Returns the name of the file to contain the emergency tracing information.
2202    
2203    =back
2204    
2205    =cut
2206    
2207    sub EmergencyFileName {
2208        # Get the parameters.
2209        my ($tkey) = @_;
2210        # Compute the emergency tracing file name.
2211        return "$FIG_Config::temp/Emergency$tkey.txt";
2212    }
2213    
2214    =head3 EmergencyFileTarget
2215    
2216    C<< my $fileName = Tracer::EmergencyFileTarget($tkey); >>
2217    
2218    Return the emergency tracing target file name. This is the file that receives
2219    the tracing output for file-based tracing.
2220    
2221    =over 4
2222    
2223    =item tkey
2224    
2225    Tracing key for the current program.
2226    
2227    =item RETURN
2228    
2229    Returns the name of the file to contain the trace output.
2230    
2231    =back
2232    
2233    =cut
2234    
2235    sub EmergencyFileTarget {
2236        # Get the parameters.
2237        my ($tkey) = @_;
2238        # Compute the emergency tracing file name.
2239        return "$FIG_Config::temp/trace$tkey.log";
2240    }
2241    
2242    =head3 EmergencyTracingDest
2243    
2244    C<< my $dest = Tracer::EmergencyTracingDest($tkey, $myDest); >>
2245    
2246    This method converts an emergency tracing destination to a real
2247    tracing destination. The main difference is that if the
2248    destination is C<FILE> or C<APPEND>, we convert it to file
2249    output.
2250    
2251    =over 4
2252    
2253    =item tkey
2254    
2255    Tracing key for this environment.
2256    
2257    =item myDest
2258    
2259    Destination from the emergency tracing file.
2260    
2261    =item RETURN
2262    
2263    Returns a destination that can be passed into L</TSetup>.
2264    
2265    =back
2266    
2267    =cut
2268    
2269    sub EmergencyTracingDest {
2270        # Get the parameters.
2271        my ($tkey, $myDest) = @_;
2272        # Declare the return variable.
2273        my $retVal;
2274        # Process according to the destination value.
2275        if ($myDest eq 'FILE') {
2276            $retVal = ">" . EmergencyFileTarget($tkey);
2277        } elsif ($myDest eq 'APPEND') {
2278            $retVal = ">>" . EmergencyFileTarget($tkey);
2279        } else {
2280            $retVal = $myDest;
2281        }
2282        # Return the result.
2283        return $retVal;
2284    }
2285    
2286    =head3 Emergency
2287    
2288    C<< Emergency($key, $hours, $dest, $level, @modules); >>
2289    
2290    Turn on emergency tracing. This method can only be invoked over the web and is
2291    should not be called if debug mode is off. The caller specifies the duration of the
2292    emergency in hours, the desired tracing destination, the trace level,
2293    and a list of the trace modules to activate. For the length of the duration, when a
2294    program in an environment with the specified tracing key active invokes a Sprout
2295    CGI script, tracing will be turned on automatically. See L</TSetup> for more
2296    about tracing setup and L</ETracing> for more about emergency tracing.
2297    
2298    =over 4
2299    
2300    =item tkey
2301    
2302    The tracing key. This is used to identify the control file and the trace file.
2303    
2304    =item hours
2305    
2306    Number of hours to keep emergency tracing alive.
2307    
2308    =item dest
2309    
2310    Tracing destination. If no path information is specified for a file
2311    destination, it is put in the FIG temporary directory.
2312    
2313    =item level
2314    
2315    Tracing level. A higher level means more trace messages.
2316    
2317    =item modules
2318    
2319    A list of the tracing modules to activate.
2320    
2321    =back
2322    
2323    =cut
2324    
2325    sub Emergency {
2326        # Get the parameters.
2327        my ($tkey, $hours, $dest, $level, @modules) = @_;
2328        # Create the emergency file.
2329        my $specFile = EmergencyFileName($tkey);
2330        my $outHandle = Open(undef, ">$specFile");
2331        print $outHandle join("\n", $hours, $dest, $level, @modules, "");
2332    }
2333    
2334    =head3 EmergencyKey
2335    
2336    C<< my $tkey = EmergencyKey($parameter); >>
2337    
2338    Return the Key to be used for emergency tracing. This could be an IP address,
2339     a session ID, or a user name, depending on the environment.
2340    
2341    =over 4
2342    
2343    =item parameter
2344    
2345    Parameter defining the method for finding the tracing key. If it is a scalar,
2346    then it is presumed to be the tracing key itself. If it is a CGI object, then
2347    the tracing key is taken from the C<IP> cookie. Otherwise, the tracing key is
2348    taken from the C<TRACING> environment variable.
2349    
2350    =item RETURN
2351    
2352    Returns the key to be used for labels in emergency tracing.
2353    
2354    =back
2355    
2356    =cut
2357    
2358    sub EmergencyKey {
2359        # Get the parameters.
2360        my ($parameter) = @_;
2361        # Declare the return variable.
2362        my $retVal;
2363        # Determine the parameter type.
2364        if (! defined $parameter) {
2365            # Here we're supposed to check the environment.
2366            $retVal = $ENV{TRACING};
2367        } else {
2368            my $ptype = ref $parameter;
2369            if ($ptype eq 'CGI') {
2370                # Here we were invoked from a web page. Look for a cookie.
2371                $retVal = $parameter->cookie('IP');
2372            } elsif (! $ptype) {
2373                # Here the key was passed in.
2374                $retVal = $parameter;
2375            }
2376        }
2377        # If no luck finding a key, use the PID.
2378        if (! defined $retVal) {
2379            $retVal = $$;
2380        }
2381        # Return the result.
2382        return $retVal;
2383    }
2384    
2385    
2386    =head3 TraceParms
2387    
2388    C<< Tracer::TraceParms($cgi); >>
2389    
2390    Trace the CGI parameters at trace level CGI => 3 and the environment variables
2391    at level CGI => 4.
2392    
2393    =over 4
2394    
2395    =item cgi
2396    
2397    CGI query object containing the parameters to trace.
2398    
2399    =back
2400    
2401    =cut
2402    
2403    sub TraceParms {
2404        # Get the parameters.
2405        my ($cgi) = @_;
2406        if (T(CGI => 3)) {
2407            # Here we want to trace the parameter data.
2408            my @names = $cgi->param;
2409            for my $parmName (sort @names) {
2410                # Note we skip the Trace parameters, which are for our use only.
2411                if ($parmName ne 'Trace' && $parmName ne 'TF') {
2412                    my @values = $cgi->param($parmName);
2413                    Trace("CGI: $parmName = " . join(", ", @values));
2414                }
2415            }
2416            # Display the request method.
2417            my $method = $cgi->request_method();
2418            Trace("Method: $method");
2419        }
2420        if (T(CGI => 4)) {
2421            # Here we want the environment data too.
2422            for my $envName (sort keys %ENV) {
2423                Trace("ENV: $envName = $ENV{$envName}");
2424            }
2425        }
2426    }
2427    
2428    =head3 ScriptFinish
2429    
2430    C<< ScriptFinish($webData, $varHash); >>
2431    
2432    Output a web page at the end of a script. Either the string to be output or the
2433    name of a template file can be specified. If the second parameter is omitted,
2434    it is assumed we have a string to be output; otherwise, it is assumed we have the
2435    name of a template file. The template should have the variable C<DebugData>
2436    specified in any form that invokes a standard script. If debugging mode is turned
2437    on, a form field will be put in that allows the user to enter tracing data.
2438    Trace messages will be placed immediately before the terminal C<BODY> tag in
2439    the output, formatted as a list.
2440    
2441    A typical standard script would loook like the following.
2442    
2443        BEGIN {
2444            # Print the HTML header.
2445            print "CONTENT-TYPE: text/html\n\n";
2446        }
2447        use Tracer;
2448        use CGI;
2449        use FIG;
2450        # ... more uses ...
2451    
2452        my ($cgi, $varHash) = ScriptSetup();
2453        eval {
2454            # ... get data from $cgi, put it in $varHash ...
2455        };
2456        if ($@) {
2457            Trace("Script Error: $@") if T(0);
2458        }
2459        ScriptFinish("Html/MyTemplate.html", $varHash);
2460    
2461    The idea here is that even if the script fails, you'll see trace messages and
2462    useful output.
2463    
2464    =over 4
2465    
2466    =item webData
2467    
2468    A string containing either the full web page to be written to the output or the
2469    name of a template file from which the page is to be constructed. If the name
2470    of a template file is specified, then the second parameter must be present;
2471    otherwise, it must be absent.
2472    
2473    =item varHash (optional)
2474    
2475    If specified, then a reference to a hash mapping variable names for a template
2476    to their values. The template file will be read into memory, and variable markers
2477    will be replaced by data in this hash reference.
2478    
2479    =back
2480    
2481    =cut
2482    
2483    sub ScriptFinish {
2484        # Get the parameters.
2485        my ($webData, $varHash) = @_;
2486        # Check for a template file situation.
2487        my $outputString;
2488        if (defined $varHash) {
2489            # Here we have a template file. We need to determine the template type.
2490            my $template;
2491            if ($FIG_Config::template_url && $webData =~ /\.php$/) {
2492                $template = "$FIG_Config::template_url/$webData";
2493            } else {
2494                $template = "<<$webData";
2495            }
2496            $outputString = PageBuilder::Build($template, $varHash, "Html");
2497                          } else {                          } else {
2498                                  $category = $package;          # Here the user gave us a raw string.
2499            $outputString = $webData;
2500                          }                          }
2501        # Check for trace messages.
2502        if ($Destination ne "NONE" && $TraceLevel > 0) {
2503            # We have trace messages, so we want to put them at the end of the body. This
2504            # is either at the end of the whole string or at the beginning of the BODY
2505            # end-tag.
2506            my $pos = length $outputString;
2507            if ($outputString =~ m#</body>#gi) {
2508                $pos = (pos $outputString) - 7;
2509            }
2510            # If the trace messages were queued, we unroll them. Otherwise, we display the
2511            # destination.
2512            my $traceHtml;
2513            if ($Destination eq "QUEUE") {
2514                $traceHtml = QTrace('Html');
2515            } elsif ($Destination =~ /^>>(.+)$/) {
2516                # Here the tracing output it to a file. We code it as a hyperlink so the user
2517                # can copy the file name into the clipboard easily.
2518                my $actualDest = $1;
2519                $traceHtml = "<p>Tracing output to $actualDest.</p>\n";
2520            } else {
2521                # Here we have one of the special destinations.
2522                $traceHtml = "<P>Tracing output type is $Destination.</p>\n";
2523                  }                  }
2524                  # Use the package and tracelevel to compute the result.          substr $outputString, $pos, 0, $traceHtml;
                 $retVal = ($traceLevel <= $TraceLevel && exists $Categories{$category});  
2525          }          }
2526          # Return the computed result.      # Write the output string.
2527          return $retVal;      print $outputString;
2528  }  }
2529    
2530  =head3 ParseCommand  =head3 Insure
   
 C<< my ($options, @arguments) = Tracer::ParseCommand(\%optionTable, @inputList); >>  
   
 Parse a command line consisting of a list of parameters. The initial parameters may be option  
 specifiers of the form C<->I<option> or C<->I<option>C<=>I<value>. The options are stripped  
 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.  
2531    
2532  C<< my ($options, @arguments) = ParseCommand({ errors => 0, logFile => 'trace.log'}, @words); >>  C<< Insure($dirName); >>
   
 In this case, the list @words will be treated as a command line. There are two options available,  
 B<errors> and B<logFile>. If @words has the following format  
2533    
2534  C<< -logFile=error.log apple orange rutabaga >>  Insure a directory is present.
2535    
2536  then at the end of the invocation, C<$options> will be  =over 4
2537    
2538  C<< { errors => 0, logFile => 'error.log' } >>  =item dirName
2539    
2540  and C<@arguments> will contain  Name of the directory to check. If it does not exist, it will be created.
2541    
2542  C<< apple orange rutabaga >>  =back
2543    
2544  The parser allows for some escape sequences. See L</UnEscape> for a description. There is no  =cut
 support for quote characters.  
2545    
2546  =over 4  sub Insure {
2547        my ($dirName) = @_;
2548        if (! -d $dirName) {
2549            Trace("Creating $dirName directory.") if T(2);
2550            eval { mkpath $dirName; };
2551            if ($@) {
2552                Confess("Error creating $dirName: $@");
2553            }
2554        }
2555    }
2556    
2557  =item optionTable  =head3 ChDir
2558    
2559  Table of default options.  C<< ChDir($dirName); >>
2560    
2561  =item inputList  Change to the specified directory.
2562    
2563  List of words on the command line.  =over 4
2564    
2565  =item RETURN  =item dirName
2566    
2567  Returns a reference to the option table and a list of the positional arguments.  Name of the directory to which we want to change.
2568    
2569  =back  =back
2570    
2571  =cut  =cut
2572    
2573  sub ParseCommand {  sub ChDir {
2574          # Get the parameters.      my ($dirName) = @_;
2575          my ($optionTable, @inputList) = @_;      if (! -d $dirName) {
2576          # Process any options in the input list.          Confess("Cannot change to directory $dirName: no such directory.");
         my %overrides = ();  
         while ((@inputList > 0) && ($inputList[0] =~ /^-/)) {  
                 # Get the current option.  
                 my $arg = shift @inputList;  
                 # Pull out the option name.  
                 $arg =~ /^-([^=]*)/g;  
                 my $name = $1;  
                 # Check for an option value.  
                 if ($arg =~ /\G=(.*)$/g) {  
                         # Here we have a value for the option.  
                         $overrides{$name} = UnEscape($1);  
2577                  } else {                  } else {
2578                          # Here there is no value, so we use 1.          Trace("Changing to directory $dirName.") if T(4);
2579                          $overrides{$name} = 1;          my $okFlag = chdir $dirName;
2580            if (! $okFlag) {
2581                Confess("Error switching to directory $dirName.");
2582                  }                  }
2583          }          }
         # Merge the options into the defaults.  
         GetOptions($optionTable, \%overrides);  
         # Translate the remaining parameters.  
         my @retVal = ();  
         for my $inputParm (@inputList) {  
                 push @retVal, UnEscape($inputParm);  
         }  
         # Return the results.  
         return ($optionTable, @retVal);  
2584  }  }
2585    
2586  =head3 UnEscape  =head3 SendSMS
2587    
2588  C<< my $realString = Tracer::UnEscape($codedString); >>  C<< my $msgID = Tracer::SendSMS($phoneNumber, $msg); >>
2589    
2590    Send a text message to a phone number using Clickatell. The FIG_Config file must contain the
2591    user name, password, and API ID for the relevant account in the hash reference variable
2592    I<$FIG_Config::phone>, using the keys C<user>, C<password>, and C<api_id>. For
2593    example, if the user name is C<BruceTheHumanPet>, the password is C<silly>, and the API ID
2594    is C<2561022>, then the FIG_Config file must contain
2595    
2596        $phone =  { user => 'BruceTheHumanPet',
2597                    password => 'silly',
2598                    api_id => '2561022' };
2599    
2600    The original purpose of this method was to insure Bruce would be notified immediately when the
2601    Sprout Load terminates. Care should be taken if you do not wish Bruce to be notified immediately
2602    when you call this method.
2603    
2604  Replace escape sequences with their actual equivalents. C<\b> will be replaced by a space,  The message ID will be returned if successful, and C<undef> if an error occurs.
 C<\t> by a tab, C<\n> by a new-line character, and C<\\> by a back-slash.  
2605    
2606  =over 4  =over 4
2607    
2608  =item codedString  =item phoneNumber
2609    
2610  String to un-escape.  Phone number to receive the message, in international format. A United States phone number
2611    would be prefixed by "1". A British phone number would be prefixed by "44".
2612    
2613    =item msg
2614    
2615    Message to send to the specified phone.
2616    
2617  =item RETURN  =item RETURN
2618    
2619  Returns a copy of the original string with the escape sequences converted to their actual  Returns the message ID if successful, and C<undef> if the message could not be sent.
 values.  
2620    
2621  =back  =back
2622    
2623  =cut  =cut
2624    
2625  sub UnEscape {  sub SendSMS {
2626          # Get the parameter.      # Get the parameters.
2627          my ($codedString) = @_;      my ($phoneNumber, $msg) = @_;
2628          # Initialize the return variable.      # Declare the return variable. If we do not change it, C<undef> will be returned.
2629          my $retVal = "";      my $retVal;
2630          # Loop through the parameter string, looking for escape sequences. We can't do      # Only proceed if we have phone support.
2631          # translating because it causes problems with the escaped slash. ("\\b" becomes      if (! defined $FIG_Config::phone) {
2632          # "\ " no matter what we do.)          Trace("Phone support not present in FIG_Config.") if T(1);
         while (length $codedString > 0) {  
                 # Look for the first escape sequence.  
                 if ($codedString =~ /^(.*?)\\(\\|b|n|t)/) {  
                         # Here we found it. The text preceding the sequence is in $1. The sequence  
                         # itself is in $2. First, move the clear text to the return variable.  
                         $retVal .= $1;  
                         $codedString = substr $codedString, (2 + length $1);  
                         # Decode the escape sequence.  
                         my $char = $2;  
                         $char =~ tr/\\btn/\\ \t\n/;  
                         $retVal .= $char;  
2633                  } else {                  } else {
2634                          # Here there are no more escape sequences. The rest of the string is          # Get the phone data.
2635                          # transferred unmodified.          my $parms = $FIG_Config::phone;
2636                          $retVal .= $codedString;          # Get the Clickatell URL.
2637                          $codedString = "";          my $url = "http://api.clickatell.com/http/";
2638            # Create the user agent.
2639            my $ua = LWP::UserAgent->new;
2640            # Request a Clickatell session.
2641            my $resp = $ua->post("$url/sendmsg", { user => $parms->{user},
2642                                         password => $parms->{password},
2643                                         api_id => $parms->{api_id},
2644                                         to => $phoneNumber,
2645                                         text => $msg});
2646            # Check for an error.
2647            if (! $resp->is_success) {
2648                Trace("Alert failed.") if T(1);
2649            } else {
2650                # Get the message ID.
2651                my $rstring = $resp->content;
2652                if ($rstring =~ /^ID:\s+(.*)$/) {
2653                    $retVal = $1;
2654                } else {
2655                    Trace("Phone attempt failed with $rstring") if T(1);
2656                }
2657                  }                  }
2658          }          }
2659          # Return the result.          # Return the result.
2660          return $retVal;          return $retVal;
2661  }  }
2662    
2663  =head3 ParseRecord  =head3 CommaFormat
2664    
2665  C<< my @fields = Tracer::ParseRecord($line); >>  C<< my $formatted = Tracer::CommaFormat($number); >>
2666    
2667  Parse a tab-delimited data line. The data line is split into field values. Embedded tab  Insert commas into a number.
 and new-line characters in the data line must be represented as C<\t> and C<\n>, respectively.  
 These will automatically be converted.  
2668    
2669  =over 4  =over 4
2670    
2671  =item line  =item number
2672    
2673  Line of data containing the tab-delimited fields.  A sequence of digits.
2674    
2675  =item RETURN  =item RETURN
2676    
2677  Returns a list of the fields found in the data line.  Returns the same digits with commas strategically inserted.
2678    
2679  =back  =back
2680    
2681  =cut  =cut
2682    
2683  sub ParseRecord {  sub CommaFormat {
2684          # Get the parameter.      # Get the parameters.
2685          my ($line) = @_;      my ($number) = @_;
2686          # Remove the trailing new-line, if any.      # Pad the length up to a multiple of three.
2687          chomp $line;      my $padded = "$number";
2688          # Split the line read into pieces using the tab character.      $padded = " " . $padded while length($padded) % 3 != 0;
2689          my @retVal = split /\t/, $line;      # This is a fancy PERL trick. The parentheses in the SPLIT pattern
2690          # Trim and fix the escapes in each piece.      # cause the delimiters to be included in the output stream. The
2691          for my $value (@retVal) {      # GREP removes the empty strings in between the delimiters.
2692                  # Trim leading whitespace.      my $retVal = join(",", grep { $_ ne '' } split(/(...)/, $padded));
2693                  $value =~ s/^\s+//;      # Clean out the spaces.
2694                  # Trim trailing whitespace.      $retVal =~ s/ //g;
                 $value =~ s/\s+$//;  
                 # Delete the carriage returns.  
                 $value =~ s/\r//g;  
                 # Convert the escapes into their real values.  
                 $value =~ s/\\t/"\t"/ge;  
                 $value =~ s/\\n/"\n"/ge;  
         }  
2695          # Return the result.          # Return the result.
2696          return @retVal;      return $retVal;
2697  }  }
2698    =head3 SetPermissions
2699    
2700  =head3 Merge  C<< Tracer::SetPermissions($dirName, $group, $mask, %otherMasks); >>
2701    
2702  C<< my @mergedList = Tracer::Merge(@inputList); >>  Set the permissions for a directory and all the files and folders inside it.
2703    In addition, the group ownership will be changed to the specified value.
2704    
2705  Sort a list of strings and remove duplicates.  This method is more vulnerable than most to permission and compatability
2706    problems, so it does internal error recovery.
2707    
2708  =over 4  =over 4
2709    
2710  =item inputList  =item dirName
2711    
2712  List of scalars to sort and merge.  Name of the directory to process.
2713    
2714  =item RETURN  =item group
2715    
2716  Returns a list containing the same elements sorted in ascending order with duplicates  Name of the group to be assigned.
2717  removed.  
2718    =item mask
2719    
2720    Permission mask. Bits that are C<1> in this mask will be ORed into the
2721    permission bits of any file or directory that does not already have them
2722    set to 1.
2723    
2724    =item otherMasks
2725    
2726    Map of search patterns to permission masks. If a directory name matches
2727    one of the patterns, that directory and all its members and subdirectories
2728    will be assigned the new pattern. For example, the following would
2729    assign 01664 to most files, but would use 01777 for directories named C<tmp>.
2730    
2731        Tracer::SetPermissions($dirName, 'fig', 01664, '^tmp$' => 01777);
2732    
2733    The list is ordered, so the following would use 0777 for C<tmp1> and
2734    0666 for C<tmp>, C<tmp2>, or C<tmp3>.
2735    
2736        Tracer::SetPermissions($dirName, 'fig', 01664, '^tmp1' => 0777,
2737                                                       '^tmp' => 0666);
2738    
2739    Note that the pattern matches are all case-insensitive, and only directory
2740    names are matched, not file names.
2741    
2742  =back  =back
2743    
2744  =cut  =cut
2745    
2746  sub Merge {  sub SetPermissions {
2747          # Get the input list in sort order.      # Get the parameters.
2748          my @inputList = sort @_;      my ($dirName, $group, $mask, @otherMasks) = @_;
2749          # Only proceed if the list has at least two elements.      # Set up for error recovery.
2750          if (@inputList > 1) {      eval {
2751                  # Now we want to move through the list splicing out duplicates.          # Switch to the specified directory.
2752                  my $i = 0;          ChDir($dirName);
2753                  while ($i < @inputList) {          # Get the group ID.
2754                          # Get the current entry.          my $gid = getgrnam($group);
2755                          my $thisEntry = $inputList[$i];          # Get the mask for tracing.
2756                          # Find out how many elements duplicate the current entry.          my $traceMask = sprintf("%04o", $mask) . "($mask)";
2757                          my $j = $i + 1;          Trace("Fixing permissions for directory $dirName using group $group($gid) and mask $traceMask.") if T(2);
2758                          my $dup1 = $i + 1;          my $fixCount = 0;
2759                          while ($j < @inputList && $inputList[$j] eq $thisEntry) { $j++; };          my $lookCount = 0;
2760                          # If the number is nonzero, splice out the duplicates found.          # @dirs will be a stack of directories to be processed.
2761                          if ($j > $dup1) {          my @dirs = (getcwd());
2762                                  splice @inputList, $dup1, $j - $dup1;          while (scalar(@dirs) > 0) {
2763                # Get the current directory.
2764                my $dir = pop @dirs;
2765                # Check for a match to one of the specified directory names. To do
2766                # that, we need to pull the individual part of the name off of the
2767                # whole path.
2768                my $simpleName = $dir;
2769                if ($dir =~ m!/([^/]+)$!) {
2770                    $simpleName = $1;
2771                }
2772                Trace("Simple directory name for $dir is $simpleName.") if T(4);
2773                # Search for a match.
2774                my $match = 0;
2775                my $i;
2776                for ($i = 0; $i < $#otherMasks && ! $match; $i += 2) {
2777                    my $pattern = $otherMasks[$i];
2778                    if ($simpleName =~ /$pattern/i) {
2779                        $match = 1;
2780                    }
2781                }
2782                # Check for a match. Note we use $i-1 because the loop added 2
2783                # before terminating due to the match.
2784                if ($match && $otherMasks[$i-1] != $mask) {
2785                    # This directory matches one of the incoming patterns, and it's
2786                    # a different mask, so we process it recursively with that mask.
2787                    SetPermissions($dir, $group, $otherMasks[$i-1], @otherMasks);
2788                } else {
2789                    # Here we can process normally. Get all of the non-hidden members.
2790                    my @submems = OpenDir($dir, 1);
2791                    for my $submem (@submems) {
2792                        # Get the full name.
2793                        my $thisMem = "$dir/$submem";
2794                        Trace("Checking member $thisMem.") if T(4);
2795                        $lookCount++;
2796                        if ($lookCount % 1000 == 0) {
2797                            Trace("$lookCount members examined. Current is $thisMem. Mask is $traceMask") if T(3);
2798                        }
2799                        # Fix the group.
2800                        chown -1, $gid, $thisMem;
2801                        # Insure this member is not a symlink.
2802                        if (! -l $thisMem) {
2803                            # Get its info.
2804                            my $fileInfo = stat $thisMem;
2805                            # Only proceed if we got the info. Otherwise, it's a hard link
2806                            # and we want to skip it anyway.
2807                            if ($fileInfo) {
2808                                my $fileMode = $fileInfo->mode;
2809                                if (($fileMode & $mask) != $mask) {
2810                                    # Fix this member.
2811                                    $fileMode |= $mask;
2812                                    chmod $fileMode, $thisMem;
2813                                    $fixCount++;
2814                                }
2815                                # If it's a subdirectory, stack it.
2816                                if (-d $thisMem) {
2817                                    push @dirs, $thisMem;
2818                          }                          }
                         # Now the element at position $dup1 is different from the element before it  
                         # at position $i. We push $i forward one position and start again.  
                         $i++;  
2819                  }                  }
2820          }          }
2821          # Return the merged list.                  }
2822          return @inputList;              }
2823            }
2824            Trace("$lookCount files and directories processed, $fixCount fixed.") if T(2);
2825        };
2826        # Check for an error.
2827        if ($@) {
2828            Confess("SetPermissions error: $@");
2829        }
2830  }  }
2831    
2832  =head3 GetFile  =head3 CompareLists
2833    
2834  C<< my $fileContents = Tracer::GetFile($fileName); >>  C<< my ($inserted, $deleted) = Tracer::CompareLists(\@newList, \@oldList, $keyIndex); >>
2835    
2836  Return the entire contents of a file.  Compare two lists of tuples, and return a hash analyzing the differences. The lists
2837    are presumed to be sorted alphabetically by the value in the $keyIndex column.
2838    The return value contains a list of items that are only in the new list
2839    (inserted) and only in the old list (deleted).
2840    
2841  =over 4  =over 4
2842    
2843  =item fileName  =item newList
2844    
2845  Name of the file to read.  Reference to a list of new tuples.
2846    
2847    =item oldList
2848    
2849    Reference to a list of old tuples.
2850    
2851    =item keyIndex (optional)
2852    
2853    Index into each tuple of its key field. The default is 0.
2854    
2855  =item RETURN  =item RETURN
2856    
2857  Returns the entire file as a single string. If an error occurs, will return  Returns a 2-tuple consisting of a reference to the list of items that are only in the new
2858  an empty string.  list (inserted) followed by a reference to the list of items that are only in the old
2859    list (deleted).
2860    
2861  =back  =back
2862    
2863  =cut  =cut
2864    
2865  sub GetFile {  sub CompareLists {
2866          # Get the parameters.          # Get the parameters.
2867          my ($fileName) = @_;      my ($newList, $oldList, $keyIndex) = @_;
2868          # Declare the return variable.      if (! defined $keyIndex) {
2869          my $retVal = "";          $keyIndex = 0;
2870          # Open the file for input.      }
2871          my $ok = open INPUTFILE, "<$fileName";      # Declare the return variables.
2872          if (!$ok) {      my ($inserted, $deleted) = ([], []);
2873                  # If we had an error, trace it. We will automatically return a null string.      # Loop through the two lists simultaneously.
2874                  Trace(0, "Could not open \"$fileName\" for input.");      my ($newI, $oldI) = (0, 0);
2875          } else {      my ($newN, $oldN) = (scalar @{$newList}, scalar @{$oldList});
2876                  # Read the whole file into the return variable.      while ($newI < $newN || $oldI < $oldN) {
2877                  while (<INPUTFILE>) {          # Get the current object in each list. Note that if one
2878                          $retVal .= $_;          # of the lists is past the end, we'll get undef.
2879            my $newItem = $newList->[$newI];
2880            my $oldItem = $oldList->[$oldI];
2881            if (! defined($newItem) || defined($oldItem) && $newItem->[$keyIndex] gt $oldItem->[$keyIndex]) {
2882                # The old item is not in the new list, so mark it deleted.
2883                push @{$deleted}, $oldItem;
2884                $oldI++;
2885            } elsif (! defined($oldItem) || $oldItem->[$keyIndex] gt $newItem->[$keyIndex]) {
2886                # The new item is not in the old list, so mark it inserted.
2887                push @{$inserted}, $newItem;
2888                $newI++;
2889            } else {
2890                # The item is in both lists, so push forward.
2891                $oldI++;
2892                $newI++;
2893                  }                  }
                 # Close it.  
                 close INPUTFILE;  
2894          }          }
2895          # Return the file's contents.      # Return the result.
2896          return $retVal;      return ($inserted, $deleted);
2897  }  }
2898    
2899  =head3 QTrace  =head3 GetLine
2900    
2901  C<< my $data = QTrace($format); >>  C<< my @data = Tracer::GetLine($handle); >>
2902    
2903  Return the queued trace data in the specified format.  Read a line of data from a tab-delimited file.
2904    
2905  =over 4  =over 4
2906    
2907  =item format  =item handle
2908    
2909  C<html> to format the data as an HTML list, C<text> to format it as straight text.  Open file handle from which to read.
2910    
2911    =item RETURN
2912    
2913    Returns a list of the fields in the record read. The fields are presumed to be
2914    tab-delimited. If we are at the end of the file, then an empty list will be
2915    returned. If an empty line is read, a single list item consisting of a null
2916    string will be returned.
2917    
2918  =back  =back
2919    
2920  =cut  =cut
2921    
2922  sub QTrace {  sub GetLine {
2923          # Get the parameter.      # Get the parameters.
2924          my ($format) = @_;      my ($handle) = @_;
2925          # Create the return variable.      # Declare the return variable.
2926          my $retVal = "";      my @retVal = ();
2927          # Process according to the format.      # Read from the file.
2928          if ($format =~ m/^HTML$/i) {      my $line = <$handle>;
2929                  # Convert the queue into an HTML list.      # Only proceed if we found something.
2930                  $retVal = "<ul>\n";      if (defined $line) {
2931                  for my $line (@Queue) {          # Remove the new-line.
2932                          my $escapedLine = CGI::escapeHTML($line);          chomp $line;
2933                          $retVal .= "<li>$escapedLine</li>\n";          # If the line is empty, return a single empty string; otherwise, parse
2934            # it into fields.
2935            if ($line eq "") {
2936                push @retVal, "";
2937            } else {
2938                push @retVal, split /\t/,$line;
2939                  }                  }
                 $retVal .= "</ul>\n";  
         } elsif ($format =~ m/^TEXT$/i) {  
                 # Convert the queue into a list of text lines.  
                 $retVal = join("\n", @Queue) . "\n";  
2940          }          }
2941          # Clear the queue.      # Return the result.
2942          @Queue = ();      return @retVal;
         # Return the formatted list.  
         return $retVal;  
2943  }  }
2944    
2945  =head3 Confess  =head3 PutLine
2946    
2947  C<< Confess($message); >>  C<< Tracer::PutLine($handle, \@fields); >>
2948    
2949  Trace the call stack and abort the program with the specified message. The stack  Write a line of data to a tab-delimited file. The specified field values will be
2950  trace will only appear if the trace level for this package is 1 or more. When used with  output in tab-separated form, with a trailing new-line.
 the OR operator, this method can function as a debugging assert. So, for example  
2951    
2952  C<< ($recNum >= 0) || Confess("Invalid record number $recNum."); >>  =over 4
2953    
2954  Will abort the program with a stack trace if the value of C<$recNum> is negative.  =item handle
2955    
2956  =over 4  Output file handle.
2957    
2958  =item message  =item fields
2959    
2960  Message to include in the trace.  List of field values.
2961    
2962  =back  =back
2963    
2964  =cut  =cut
2965    
2966  sub Confess {  sub PutLine {
2967          # Get the parameters.          # Get the parameters.
2968          my ($message) = @_;      my ($handle, $fields) = @_;
2969          # Trace the call stack.      # Write the data.
2970          Cluck($message) if T(1);      print $handle join("\t", @{$fields}) . "\n";
         # Abort the program.  
         die $message;  
2971  }  }
2972    
2973  =head3 Cluck  =head3 GenerateURL
2974    
2975  C<< Cluck($message); >>  C<< my $queryUrl = Tracer::GenerateURL($page, %parameters); >>
2976    
2977  Trace the call stack. Note that for best results, you should qualify the call with a  Generate a GET-style URL for the specified page with the specified parameter
2978  trace condition. For example,  names and values. The values will be URL-escaped automatically. So, for
2979    example
2980    
2981  C<< Cluck("Starting record parse.") if T(3); >>      Tracer::GenerateURL("form.cgi", type => 1, string => "\"high pass\" or highway")
2982    
2983  will only trace the stack if the trace level for the package is 3 or more.  would return
2984    
2985        form.cgi?type=1&string=%22high%20pass%22%20or%20highway
2986    
2987  =over 4  =over 4
2988    
2989  =item message  =item page
2990    
2991  Message to include in the trace.  Page URL.
2992    
2993    =item parameters
2994    
2995    Hash mapping parameter names to parameter values.
2996    
2997    =item RETURN
2998    
2999    Returns a GET-style URL that goes to the specified page and passes in the
3000    specified parameters and values.
3001    
3002  =back  =back
3003    
3004  =cut  =cut
3005    
3006  sub Cluck {  sub GenerateURL {
3007          # Get the parameters.          # Get the parameters.
3008          my ($message) = @_;      my ($page, %parameters) = @_;
3009          my $confession = longmess($message);      # Prime the return variable with the page URL.
3010          # Convert the confession to a series of trace messages.      my $retVal = $page;
3011          for my $line (split /\s*\n/, $confession) {      # Loop through the parameters, creating parameter elements in a list.
3012                  Trace($line);      my @parmList = map { "$_=" . uri_escape($parameters{$_}) } keys %parameters;
3013        # If the list is nonempty, tack it on.
3014        if (@parmList) {
3015            $retVal .= "?" . join("&", @parmList);
3016          }          }
3017        # Return the result.
3018        return $retVal;
3019  }  }
3020    
   
3021  1;  1;

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