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# Line 1  Line 1 
1    #
2    # Copyright (c) 2003-2006 University of Chicago and Fellowship
3    # for Interpretations of Genomes. All Rights Reserved.
4    #
5    # This file is part of the SEED Toolkit.
6    #
7    # The SEED Toolkit is free software. You can redistribute
8    # it and/or modify it under the terms of the SEED Toolkit
9    # Public License.
10    #
11    # You should have received a copy of the SEED Toolkit Public License
12    # along with this program; if not write to the University of Chicago
13    # at info@ci.uchicago.edu or the Fellowship for Interpretation of
14    # Genomes at veronika@thefig.info or download a copy from
15    # http://www.theseed.org/LICENSE.TXT.
16    #
17    
18  package Tracer;  package Tracer;
19    
20          require Exporter;          require Exporter;
21          @ISA = ('Exporter');          @ISA = ('Exporter');
22          @EXPORT = qw(Trace T TSetup QTrace Confess Cluck Min Max Assert);      @EXPORT = qw(Trace T TSetup QTrace Confess Cluck Min Max Assert Open OpenDir TICK StandardSetup EmergencyKey ETracing ScriptSetup ScriptFinish Insure ChDir Emergency);
23          @EXPORT_OK = qw(GetFile GetOptions Merge MergeOptions ParseCommand ParseRecord UnEscape Escape);          @EXPORT_OK = qw(GetFile GetOptions Merge MergeOptions ParseCommand ParseRecord UnEscape Escape);
24          use strict;          use strict;
25          use Carp qw(longmess croak);          use Carp qw(longmess croak);
26          use CGI;          use CGI;
27        use Cwd;
28          use FIG_Config;          use FIG_Config;
29      use PageBuilder;      use PageBuilder;
30        use Digest::MD5;
31        use File::Basename;
32        use File::Path;
33        use File::stat;
34        use LWP::UserAgent;
35        use Time::HiRes 'gettimeofday';
36        use URI::Escape;
37        use Time::Local;
38    
39  =head1 Tracing and Debugging Helpers  =head1 Tracing and Debugging Helpers
40    
41  =head2 Introduction  =head2 Tracing
42    
43  This package provides simple tracing for debugging and reporting purposes. To use it simply call the  This package provides simple tracing for debugging and reporting purposes. To use it simply call the
44  L</TSetup> method to set the options and call L</Trace> to write out trace messages. Each trace  L</TSetup> or L</ETracing> method to set the options and call L</Trace> to write out trace messages.
45  message has a I<trace level> and I<category> associated with it. In addition, the tracing package itself  L</TSetup> and L</ETracing> both establish a I<trace level> and a list of I<categories>. Similarly,
46  has a list of categories and a single trace level set by the B<TSetup> method. Only messages whose trace  each trace message has a I<trace level> and I<category> associated with it. Only messages whose trace
47  level is less than or equal to this package's trace level and whose category is activated will  level is less than or equal to the setup trace level and whose category is activated will
48  be written. Thus, a higher trace level on a message indicates that the message  be written. Thus, a higher trace level on a message indicates that the message
49  is less likely to be seen. A higher trace level passed to B<Setup> means more trace messages will  is less likely to be seen, while a higher trace level passed to B<TSetup> means more trace messages will
50  appear. To generate a trace message, use the following syntax.  appear.
51    
52    =head3 Putting Trace Messages in Your Code
53    
54  C<< Trace($message) if T(errors => 4); >>  To generate a trace message, use the following syntax.
55    
56        Trace($message) if T(errors => 4);
57    
58  This statement will produce a trace message if the trace level is 4 or more and the C<errors>  This statement will produce a trace message if the trace level is 4 or more and the C<errors>
59  category is active. Note that the special category C<main> is always active, so  category is active. There is a special category C<main> that is always active, so
60    
61  C<< Trace($message) if T(main => 4); >>      Trace($message) if T(main => 4);
62    
63  will trace if the trace level is 4 or more.  will trace if the trace level is 4 or more.
64    
# Line 36  Line 66 
66  following call is made in the B<Sprout> package, it will appear if the C<Sprout> category is  following call is made in the B<Sprout> package, it will appear if the C<Sprout> category is
67  active and the trace level is 2 or more.  active and the trace level is 2 or more.
68    
69  C<< Trace($message) if T(2); >>      Trace($message) if T(2);
70    
71    In scripts, where no package name is available, the category defaults to C<main>.
72    
73  To set up tracing, you call the C</Setup> method. The method takes as input a trace level, a list  =head3 Custom Tracing
74  of category names, and a set of options. The trace level and list of category names are  
75    Many programs have customized tracing configured using the L</TSetup> method. This is no longer
76    the preferred method, but a knowledge of how custom tracing works can make the more modern
77    L</Emergency Tracing> easier to understand.
78    
79    To set up custom tracing, you call the L</TSetup> method. The method takes as input a trace level,
80    a list of category names, and a destination. The trace level and list of category names are
81  specified as a space-delimited string. Thus  specified as a space-delimited string. Thus
82    
83  C<< TSetup('3 errors Sprout ERDB', 'HTML'); >>      TSetup('3 errors Sprout ERDB', 'TEXT');
84    
85  sets the trace level to 3, activates the C<errors>, C<Sprout>, and C<ERDB> categories, and  sets the trace level to 3, activates the C<errors>, C<Sprout>, and C<ERDB> categories, and
86  specifies that messages should be output as HTML paragraphs. The parameters are formatted  specifies that messages should be sent to the standard output.
87  to make it easier to input tracing configuration on a web form.  
88    To turn on tracing for ALL categories, use an asterisk. The call below sets every category to
89    level 3 and writes the output to the standard error output. This sort of thing might be
90    useful in a CGI environment.
91    
92        TSetup('3 *', 'WARN');
93    
94  In addition to HTML and file output for trace messages, you can specify that the trace messages  In addition standard error and file output for trace messages, you can specify that the trace messages
95  be queued. The messages can then be retrieved by calling the L</QTrace> method. This approach  be queued. The messages can then be retrieved by calling the L</QTrace> method. This approach
96  is useful if you are building a web page. Instead of having the trace messages interspersed with  is useful if you are building a web page. Instead of having the trace messages interspersed with
97  the page output, they can be gathered together and displayed at the end of the page. This makes  the page output, they can be gathered together and displayed at the end of the page. This makes
98  it easier to debug page formatting problems.  it easier to debug page formatting problems.
99    
100  Finally, you can specify that all trace messages be emitted as warnings.  Finally, you can specify that all trace messages be emitted to a file, or the standard output and
101    a file at the same time. To trace to a file, specify the filename with an output character in front
102    of it.
103    
104        TSetup('4 SQL', ">$fileName");
105    
106    To trace to the standard output and a file at the same time, put a C<+> in front of the angle
107    bracket.
108    
109        TSetup('3 *', "+>$fileName");
110    
111  The flexibility of tracing makes it superior to simple use of directives like C<die> and C<warn>.  The flexibility of tracing makes it superior to simple use of directives like C<die> and C<warn>.
112  Tracer calls can be left in the code with minimal overhead and then turned on only when needed.  Tracer calls can be left in the code with minimal overhead and then turned on only when needed.
113  Thus, debugging information is available and easily retrieved even when the application is  Thus, debugging information is available and easily retrieved even when the application is
114  being used out in the field.  being used out in the field.
115    
116    =head3 Trace Levels
117    
118    There is no hard and fast rule on how to use trace levels. The following is therefore only
119    a suggestion.
120    
121    =over 4
122    
123    =item Error 0
124    
125    Message indicates an error that may lead to incorrect results or that has stopped the
126    application entirely.
127    
128    =item Warning 1
129    
130    Message indicates something that is unexpected but that probably did not interfere
131    with program execution.
132    
133    =item Notice 2
134    
135    Message indicates the beginning or end of a major task.
136    
137    =item Information 3
138    
139    Message indicates a subtask. In the FIG system, a subtask generally relates to a single
140    genome. This would be a big loop that is not expected to execute more than 500 times or so.
141    
142    =item Detail 4
143    
144    Message indicates a low-level loop iteration.
145    
146    =back
147    
148    The format of trace messages is important because some utilities analyze trace files.
149    There are three fields-- the time stamp, the category name, and the text.
150    The time stamp is between square brackets and the category name between angle brackets.
151    After the category name there is a colon (C<:>) followed by the message text.
152    If the square brackets or angle brackets are missing, then the trace management
153    utilities assume that they are encountering a set of pre-formatted lines.
154    
155    Note, however, that this formatting is done automatically by the tracing functions. You
156    only need to know about it if you want to parse a trace file.
157    
158    =head3 Emergency Tracing
159    
160    Sometimes, you need a way for tracing to happen automatically without putting parameters
161    in a form or on the command line. Emergency tracing does this. You invoke emergency tracing
162    from the debug form, which is accessed from I<MySeedInstance>C</FIG/Html/SetPassword.html>.
163    Emergency tracing requires you specify a tracing key. For command-line tools, the key is
164    taken from the C<TRACING> environment variable. For web services, the key is taken from
165    a cookie. Either way, the key tells the tracing facility who you are, so that you control
166    the tracing in your environment without stepping on other users.
167    
168    The key can be anything you want. If you don't have a key, the C<SetPassword> page will
169    generate one for you.
170    
171    You can activate and de-activate emergency tracing from the debugging control panel, as
172    well as display the trace file itself.
173    
174    To enable emergency tracing in your code, call
175    
176        ETracing($cgi)
177    
178    from a web script and
179    
180        ETracing()
181    
182    from a command-line script.
183    
184    The web script will look for the tracing key in the cookies, and the command-line
185    script will look for it in the C<TRACING> environment variable. If you are
186    using the L</StandardScript> or L</StandardSetup> methods, emergency tracing
187    will be configured automatically.
188    
189    =head3 Debugging Control Panel
190    
191    The debugging control panel provides several tools to assist in development of
192    SEED and Sprout software. You access the debugging control panel from the URL
193    C</FIG/Html/SetPassword.html> in whichever seed instance you're using. (So,
194    for example, the panel access point for the development NMPDR system is
195    C<http://web-1.nmpdr.org/next/FIG/Html/SetPassword.html>. Contact Bruce to
196    find out what the password is. From this page, you can also specify a tracing
197    key. If you don't specify a key, one will be generated for you.
198    
199    =head4 Emergency Tracing Form
200    
201    At the bottom of the debugging control panel is a form that allows you to
202    specify a trace level and tracing categories. Special and common categories
203    are listed with check boxes. You can hold your mouse over a check box to see
204    what its category does. In general, however, a category name is the same as
205    the name of the package in which the trace message occurs.
206    
207    Additional categories can be entered in an input box, delimited by spaces or commas.
208    
209    The B<Activate> button turns on Emergency tracing at the level you specify with the
210    specified categories active. The B<Terminate> button turns tracing off. The
211    B<Show File> button displays the current contents of the trace file. The tracing
212    form at the bottom of the control panel is designed for emergency tracing, so it
213    will only affect programs that call L</ETracing>, L</StandardScript>,
214    or L</StandardSetup>.
215    
216    =head4 Script Form
217    
218    The top form of the debugging control panel allows you to enter a tiny script and
219    have the output generated in a formatted table. Certain object variables are
220    predefined in the script, including a FIG object (C<$fig>), a CGI object (C<$cgi>),
221    and-- if Sprout is active-- Sprout (C<$sprout>) and SFXlate (C<$sfx>) objects.
222    
223    The last line of the script must be a scalar, but it can be a reference to a hash,
224    a list, a list of lists, and various other combinations. If you select the appropriate
225    data type in the dropdown box, the output will be formatted accordingly. The form
226    also has controls for specifying tracing. These controls override any emergency
227    tracing in effect.
228    
229    =head4 Database Query Forms
230    
231    The forms between the script form and the emergency tracing form allow you to
232    make queries against the database. The FIG query form allows simple queries against
233    a single FIG table. The Sprout query form uses the B<GetAll> method to do a
234    multi-table query against the Sprout database. B<GetAll> is located in the B<ERDB>
235    package, and it takes five parameters.
236    
237        GetAll(\@objectNames, $filterClause, \@parameters, \@fields, $count);
238    
239    Each of the five parameters corresponds to a text box on the query form:
240    
241    =over 4
242    
243    =item Objects
244    
245    Comma-separated list containing the names of the entity and relationship objects to be retrieved.
246    
247    =item Filter
248    
249    WHERE/ORDER BY clause (without the WHERE) to be used to filter and sort the query. The WHERE clause can
250    be parameterized with parameter markers (C<?>). Each field used must be specified in the standard form
251    B<I<objectName>(I<fieldName>)> or B<$I<number>(I<fieldName>)> where I<fieldName> is the name of a
252    field, I<objectName> is the name of the entity or relationship object containing the field, and
253    I<number> is the 1-based position of the object in the object list. Any parameters
254    specified in the filter clause should be specified in the B<Params> field.
255    The fields in a filter clause can come from primary entity relations,
256    relationship relations, or secondary entity relations; however, all of the
257    entities and relationships involved must be included in the list of object names.
258    
259    =item Params
260    
261    List of the parameters to be substituted in for the parameters marks in the filter clause. This
262    is a comma-separated list without any quoting or escaping.
263    
264    =item fields
265    
266    Comma-separated list of the fields to be returned in each element of the list returned. Fields
267    are specified in the same manner as in the filter clause.
268    
269    =item count
270    
271    Maximum number of records to return. If omitted or 0, all available records will be returned.
272    
273    =back
274    
275    B<GetAll> automatically joins together the entities and relationships listed in the object
276    names. This simplifies the coding of the filter clause, but it means that some queries are
277    not possible, since they cannot be expressed in a linear sequence of joins. This is a limitation
278    that has yet to be addressed.
279    
280  =cut  =cut
281    
282  # Declare the configuration variables.  # Declare the configuration variables.
283    
284  my $Destination = "NONE";       # Description of where to send the trace output.  my $Destination = "NONE";       # Description of where to send the trace output.
285    my $TeeFlag = 0;            # TRUE if output is going to a file and to the
286                                # standard output
287  my %Categories = ( main => 1 );  my %Categories = ( main => 1 );
288                                                          # hash of active category names                                                          # hash of active category names
289  my $TraceLevel = 0;                     # trace level; a higher trace level produces more  my $TraceLevel = 0;                     # trace level; a higher trace level produces more
290                                                          # messages                                                          # messages
291  my @Queue = ();                         # queued list of trace messages.  my @Queue = ();                         # queued list of trace messages.
292  my $LastCategory = "main";  # name of the last category interrogated  my $LastCategory = "main";  # name of the last category interrogated
293    my $SetupCount = 0;         # number of times TSetup called
294    my $AllTrace = 0;           # TRUE if we are tracing all categories.
295    
296  =head2 Public Methods  =head2 Public Methods
297    
# Line 93  Line 313 
313    
314  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
315  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
316  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 ">"
317  the trace messages to a file, you can specify a special destination. C<HTML> will cause  symbol with a C<+> to echo output to a file AND to the standard output. In addition to
318  tracing to the standard output with each line formatted as an HTML paragraph. C<TEXT>  sending the trace messages to a file, you can specify a special destination. C<HTML> will
319    cause tracing to the standard output with each line formatted as an HTML paragraph. C<TEXT>
320  will cause tracing to the standard output as ordinary text. C<ERROR> will cause trace  will cause tracing to the standard output as ordinary text. C<ERROR> will cause trace
321  messages to be sent to the standard error output as ordinary text. C<QUEUE> will cause trace  messages to be sent to the standard error output as ordinary text. C<QUEUE> will cause trace
322  messages to be stored in a queue for later retrieval by the L</QTrace> method. C<WARN> will  messages to be stored in a queue for later retrieval by the L</QTrace> method. C<WARN> will
# Line 113  Line 334 
334          my @categoryData = split /\s+/, $categoryList;          my @categoryData = split /\s+/, $categoryList;
335          # Extract the trace level.          # Extract the trace level.
336          $TraceLevel = shift @categoryData;          $TraceLevel = shift @categoryData;
337          # Build the category hash.      # Presume category-based tracing until we learn otherwise.
338        $AllTrace = 0;
339        # Build the category hash. Note that if we find a "*", we turn on non-category
340        # tracing. We must also clear away any pre-existing data.
341        %Categories = ( main => 1 );
342          for my $category (@categoryData) {          for my $category (@categoryData) {
343                  $Categories{$category} = 1;          if ($category eq '*') {
344                $AllTrace = 1;
345            } else {
346                $Categories{lc $category} = 1;
347            }
348          }          }
349          # Now we need to process the destination information. The most important special          # Now we need to process the destination information. The most important special
350          # case is the single ">", which requires we clear the file first. After doing      # cases are the single ">", which requires we clear the file first, and the
351          # so, we tack on another ">" sign so that future trace messages are appended.      # "+" prefix which indicates a double echo.
352        if ($target =~ m/^\+?>>?/) {
353            if ($target =~ m/^\+/) {
354                $TeeFlag = 1;
355                $target = substr($target, 1);
356            }
357          if ($target =~ m/^>[^>]/) {          if ($target =~ m/^>[^>]/) {
358                  open TRACEFILE, $target;                  open TRACEFILE, $target;
359                  print TRACEFILE Now() . " Tracing initialized.\n";              print TRACEFILE "[" . Now() . "] <Tracer>: Tracing initialized.\n";
360                  close TRACEFILE;                  close TRACEFILE;
361                  $Destination = ">$target";                  $Destination = ">$target";
362          } else {          } else {
363                $Destination = $target;
364            }
365        } else {
366                  $Destination = uc($target);                  $Destination = uc($target);
367          }          }
368        # Increment the setup counter.
369        $SetupCount++;
370  }  }
371    
372  =head3 SetLevel  =head3 StandardSetup
373    
374  C<< Tracer::SetLevel($newLevel); >>  C<< my ($options, @parameters) = StandardSetup(\@categories, \%options, $parmHelp, @ARGV); >>
375    
376  Modify the trace level. A higher trace level will cause more messages to appear.  This method performs standard command-line parsing and tracing setup. The return
377    values are a hash of the command-line options and a list of the positional
378    parameters. Tracing is automatically set up and the command-line options are
379    validated.
380    
381    This is a complex method that does a lot of grunt work. The parameters can
382    be more easily understood, however, once they are examined individually.
383    
384    The I<categories> parameter is the most obtuse. It is a reference to a list of
385    special-purpose tracing categories. Most tracing categories are PERL package
386    names. So, for example, if you wanted to turn on tracing inside the B<Sprout>,
387    B<ERDB>, and B<SproutLoad> packages, you would specify the categories
388    
389        ["Sprout", "SproutLoad", "ERDB"]
390    
391    This would cause trace messages in the specified three packages to appear in
392    the output. There are two special tracing categories that are automatically
393    handled by this method. In other words, if you used L</TSetup> you would need
394    to include these categories manually, but if you use this method they are turned
395    on automatically.
396    
397  =over 4  =over 4
398    
399  =item newLevel  =item SQL
400    
401  Proposed new trace level.  Traces SQL commands and activity.
402    
403    =item Tracer
404    
405    Traces error messages and call stacks.
406    
407  =back  =back
408    
409  =cut  C<SQL> is only turned on if the C<-sql> option is specified in the command line.
410    The trace level is specified using the C<-trace> command-line option. For example,
411    the following command line for C<TransactFeatures> turns on SQL tracing and runs
412    all tracing at level 3.
413    
414  sub SetLevel {      TransactFeatures -trace=3 -sql register ../xacts IDs.tbl
     $TraceLevel = $_[0];  
 }  
415    
416  =head3 Now  Standard tracing is output to the standard output and echoed to the file
417    C<trace>I<$$>C<.log> in the FIG temporary directory, where I<$$> is the
418    process ID. You can also specify the C<user> parameter to put a user ID
419    instead of a process ID in the trace file name. So, for example
420    
421  C<< my $string = Tracer::Now(); >>  The default trace level is 2. To get all messages, specify a trace level of 4.
422    For a genome-by-genome update, use 3.
423    
424  Return a displayable time stamp containing the local time.      TransactFeatures -trace=3 -sql -user=Bruce register ../xacts IDs.tbl
425    
426  =cut  would send the trace output to C<traceBruce.log> in the temporary directory.
427    
428  sub Now {  The I<options> parameter is a reference to a hash containing the command-line
429          my ($sec,$min,$hour,$mday,$mon,$year,$wday,$yday,$isdst) = localtime(time);  options, their default values, and an explanation of what they mean. Command-line
430          my $retVal = _p2($mon+1) . "/" . _p2($mday) . "/" . ($year + 1900) . " " .  options may be in the form of switches or keywords. In the case of a switch, the
431                                   _p2($hour) . ":" . _p2($min) . ":" . _p2($sec);  option value is 1 if it is specified and 0 if it is not specified. In the case
432          return $retVal;  of a keyword, the value is separated from the option name by an equal sign. You
433  }  can see this last in the command-line example above.
434    
435  # Pad a number to 2 digits.  You can specify a different default trace level by setting C<$options->{trace}>
436  sub _p2 {  prior to calling this method.
         my ($value) = @_;  
         $value = "0$value" if ($value < 10);  
         return $value;  
 }  
437    
438  =head3 LogErrors  An example at this point would help. Consider, for example, the command-line utility
439    C<TransactFeatures>. It accepts a list of positional parameters plus the options
440    C<safe>, C<noAlias>, C<start>, and C<tblFiles>. To start up this command, we execute
441    the following code.
442    
443  C<< Tracer::LogErrors($fileName); >>      my ($options, @parameters) = Tracer::StandardSetup(["DocUtils"],
444                            { safe => [0, "use database transactions"],
445                              noAlias => [0, "do not expect aliases in CHANGE transactions"],
446                              start => [' ', "start with this genome"],
447                              tblFiles => [0, "output TBL files containing the corrected IDs"] },
448                            "command transactionDirectory IDfile",
449                          @ARGV);
450    
 Route the standard error output to a log file.  
451    
452  =over 4  The call to C<ParseCommand> specifies the default values for the options and
453    stores the actual options in a hash that is returned as C<$options>. The
454    positional parameters are returned in C<@parameters>.
455    
456  =item fileName  The following is a sample command line for C<TransactFeatures>.
457    
458  Name of the file to receive the error output.      TransactFeatures -trace=2 -noAlias register ../xacts IDs.tbl
459    
460  =back  In this case, C<register>, C<../xacts>, and C<IDs.tbl> are the positional
461    parameters, and would find themselves in I<@parameters> after executing the
462    above code fragment. The tracing would be set to level 2, and the categories
463    would be C<Tracer>, and <DocUtils>. C<Tracer> is standard,
464    and C<DocUtils> was included because it came in within the first parameter
465    to this method. The I<$options> hash would be
466    
467  =cut      { trace => 2, sql => 0, safe => 0,
468          noAlias => 1, start => ' ', tblFiles => 0 }
469    
470  sub LogErrors {  Use of C<StandardSetup> in this way provides a simple way of performing
471          # Get the file name.  standard tracing setup and command-line parsing. Note that the caller is
472          my ($fileName) = @_;  not even aware of the command-line switches C<-trace> and C<-sql>, which
473          # Open the file as the standard error output.  are used by this method to control the tracing. If additional tracing features
474          open STDERR, '>', $fileName;  need to be added in the future, they can be processed by this method without
475  }  upsetting the command-line utilities.
476    
477  =head3 ReadOptions  If the C<background> option is specified on the command line, then the
478    standard and error outputs will be directed to files in the temporary
479    directory, using the same suffix as the trace file. So, if the command
480    line specified
481    
482  C<< my %options = Tracer::ReadOptions($fileName); >>      -user=Bruce -background
483    
484  Read a set of options from a file. Each option is encoded in a line of text that has the  then the trace output would go to C<traceBruce.log>, the standard output to
485  format  C<outBruce.log>, and the error output to C<errBruce.log>. This is designed to
486    simplify starting a command in the background.
487    
488  I<optionName>C<=>I<optionValue>C<; >I<comment>  The user name is also used as the tracing key for L</Emergency Tracing>.
489    Specifying a value of C<E> for the trace level causes emergency tracing to
490    be used instead of custom tracing. If the user name is not specified,
491    the tracing key is taken from the C<Tracing> environment variable. If there
492    is no value for that variable, the tracing key will be computed from the PID.
493    
494  The option name must consist entirely of letters, digits, and the punctuation characters  Finally, if the special option C<-h> is specified, the option names will
495  C<.> and C<_>, and is case sensitive. Blank lines and lines in which the first nonblank  be traced at level 0 and the program will exit without processing.
496  character is a semi-colon will be ignored. The return hash will map each option name to  This provides a limited help capability. For example, if the user enters
497  the corresponding option value.  
498        TransactFeatures -h
499    
500    he would see the following output.
501    
502        TransactFeatures [options] command transactionDirectory IDfile
503            -trace    tracing level (default E)
504            -sql      trace SQL commands
505            -safe     use database transactions
506            -noAlias  do not expect aliases in CHANGE transactions
507            -start    start with this genome
508            -tblFiles output TBL files containing the corrected IDs
509    
510    The caller has the option of modifying the tracing scheme by placing a value
511    for C<trace> in the incoming options hash. The default value can be overridden,
512    or the tracing to the standard output can be turned off by suffixing a minus
513    sign to the trace level. So, for example,
514    
515        { trace => [0, "tracing level (default 0)"],
516           ...
517    
518    would set the default trace level to 0 instead of E, while
519    
520        { trace => ["2-", "tracing level (default 2)"],
521           ...
522    
523    would set the default to 2, but trace only to the log file, not to the
524    standard output.
525    
526    The parameters to this method are as follows.
527    
528  =over 4  =over 4
529    
530  =item fileName  =item categories
531    
532  Name of the file containing the option data.  Reference to a list of tracing category names. These should be names of
533    packages whose internal workings will need to be debugged to get the
534    command working.
535    
536    =item options
537    
538    Reference to a hash containing the legal options for the current command mapped
539    to their default values and descriptions. The user can override the defaults
540    by specifying the options as command-line switches prefixed by a hyphen.
541    Tracing-related options may be added to this hash. If the C<-h> option is
542    specified on the command line, the option descriptions will be used to
543    explain the options. To turn off tracing to the standard output, add a
544    minus sign to the value for C<trace> (see above).
545    
546    =item parmHelp
547    
548    A string that vaguely describes the positional parameters. This is used
549    if the user specifies the C<-h> option.
550    
551    =item argv
552    
553    List of command line parameters, including the option switches, which must
554    precede the positional parameters and be prefixed by a hyphen.
555    
556  =item RETURN  =item RETURN
557    
558  Returns a hash mapping the option names specified in the file to their corresponding option  Returns a list. The first element of the list is the reference to a hash that
559  value.  maps the command-line option switches to their values. These will either be the
560    default values or overrides specified on the command line. The remaining
561    elements of the list are the position parameters, in order.
562    
563  =back  =back
564    
565  =cut  =cut
566    
567  sub ReadOptions {  sub StandardSetup {
568          # Get the parameters.          # Get the parameters.
569          my ($fileName) = @_;      my ($categories, $options, $parmHelp, @argv) = @_;
570          # Open the file.      # Get the default tracing key.
571          (open CONFIGFILE, "<$fileName") || Confess("Could not open option file $fileName.");      my $tkey = EmergencyKey();
572          # Count the number of records read.      # Add the tracing options.
573          my ($records, $comments) = 0;      if (! exists $options->{trace}) {
574          # Create the return hash.          $options->{trace} = ['E', "tracing level (E for emergency tracing)"];
575          my %retVal = ();      }
576          # Loop through the file, accumulating key-value pairs.      $options->{sql} = [0, "turn on SQL tracing"];
577          while (my $line = <CONFIGFILE>) {      $options->{h} = [0, "display command-line options"];
578                  # Denote we've read a line.      $options->{user} = [$tkey, "tracing key"];
579                  $records++;      $options->{background} = [0, "spool standard and error output"];
580                  # Determine the line type.      # Create a parsing hash from the options hash. The parsing hash
581                  if ($line =~ /^\s*[\n\r]/) {      # contains the default values rather than the default value
582                          # A blank line is a comment.      # and the description. While we're at it, we'll memorize the
583                          $comments++;      # length of the longest option name.
584                  } elsif ($line =~ /^\s*([A-Za-z0-9_\.]+)=([^;]*);/) {      my $longestName = 0;
585                          # Here we have an option assignment.      my %parseOptions = ();
586                          retVal{$1} = $2;      for my $key (keys %{$options}) {
587                  } elsif ($line =~ /^\s*;/) {          if (length $key > $longestName) {
588                          # Here we have a text comment.              $longestName = length $key;
589                          $comments++;          }
590            $parseOptions{$key} = $options->{$key}->[0];
591        }
592        # Parse the command line.
593        my ($retOptions, @retParameters) = ParseCommand(\%parseOptions, @argv);
594        # Get the logfile suffix.
595        my $suffix = $retOptions->{user};
596        # Check for background mode.
597        if ($retOptions->{background}) {
598            my $outFileName = "$FIG_Config::temp/out$suffix.log";
599            my $errFileName = "$FIG_Config::temp/err$suffix.log";
600            open STDOUT, ">$outFileName";
601            open STDERR, ">$errFileName";
602        }
603        # Now we want to set up tracing. First, we need to know if the user
604        # wants emergency tracing.
605        if ($retOptions->{trace} eq 'E') {
606            ETracing($retOptions->{user});
607                  } else {                  } else {
608                          # Here we have an invalid line.          # Here the tracing is controlled from the command line.
609                          Trace("Invalid option statement in record $records.") if T(0);          my @cats = @{$categories};
610            if ($retOptions->{sql}) {
611                push @cats, "SQL";
612            }
613            # Add the default categories.
614            push @cats, "Tracer";
615            # Next, we create the category string by joining the categories.
616            my $cats = join(" ", @cats);
617            # Check to determine whether or not the caller wants to turn off tracing
618            # to the standard output.
619            my $traceLevel = $retOptions->{trace};
620            my $textOKFlag = 1;
621            if ($traceLevel =~ /^(.)-/) {
622                $traceLevel = $1;
623                $textOKFlag = 0;
624            }
625            # Now we set up the trace mode.
626            my $traceMode;
627            # Verify that we can open a file in the FIG temporary directory.
628            my $traceFileName = "$FIG_Config::temp/trace$suffix.log";
629            if (open TESTTRACE, ">$traceFileName") {
630                # Here we can trace to a file.
631                $traceMode = ">$traceFileName";
632                if ($textOKFlag) {
633                    # Echo to standard output if the text-OK flag is set.
634                    $traceMode = "+$traceMode";
635                  }                  }
636                # Close the test file.
637                close TESTTRACE;
638            } else {
639                # Here we can't trace to a file. We trace to the standard output if it's
640                # okay, and the error log otherwise.
641                if ($textOKFlag) {
642                    $traceMode = "TEXT";
643                } else {
644                    $traceMode = "WARN";
645          }          }
646          # Return the hash created.          }
647          return %retVal;          # Now set up the tracing.
648            TSetup("$traceLevel $cats", $traceMode);
649        }
650        # Check for the "h" option. If it is specified, dump the command-line
651        # options and exit the program.
652        if ($retOptions->{h}) {
653            $0 =~ m#[/\\](\w+)(\.pl)?$#i;
654            print "$1 [options] $parmHelp\n";
655            for my $key (sort keys %{$options}) {
656                my $name = Pad($key, $longestName, 0, ' ');
657                my $desc = $options->{$key}->[1];
658                if ($options->{$key}->[0]) {
659                    $desc .= " (default " . $options->{$key}->[0] . ")";
660                }
661                print "  $name $desc\n";
662            }
663            exit(0);
664        }
665        # Return the parsed parameters.
666        return ($retOptions, @retParameters);
667  }  }
668    
669  =head3 GetOptions  =head3 Setups
670    
671  C<< Tracer::GetOptions(\%defaults, \%options); >>  C<< my $count = Tracer::Setups(); >>
672    
673  Merge a specified set of options into a table of defaults. This method takes two hash references  Return the number of times L</TSetup> has been called.
 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.  
674    
675  Consider the following example.  This method allows for the creation of conditional tracing setups where, for example, we
676    may want to set up tracing if nobody else has done it before us.
677    
678  C<< my $optionTable = GetOptions({ dbType => 'mySQL', trace => 0 }, $options); >>  =cut
679    
680  In this example, the variable B<$options> is expected to contain at most two options-- B<dbType> and  sub Setups {
681  B<trace>. The default database type is C<mySQL> and the default trace level is C<0>. If the value of      return $SetupCount;
682  B<$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  
683    
684  C<< {databaseType => 'Oracle'} >>  =head3 Open
685    
686  an error will occur because the B<databaseType> option does not exist.  C<< my $handle = Open($fileHandle, $fileSpec, $message); >>
687    
688  =over 4  Open a file.
689    
690  =item defaults  The I<$fileSpec> is essentially the second argument of the PERL C<open>
691    function. The mode is specified using Unix-like shell information. So, for
692    example,
693    
694  Table of default option values.      Open(\*LOGFILE, '>>/usr/spool/news/twitlog', "Could not open twit log.");
695    
696  =item options  would open for output appended to the specified file, and
697    
698  Table of overrides, if any.      Open(\*DATASTREAM, "| sort -u >$outputFile", "Could not open $outputFile.");
699    
700  =item RETURN  would open a pipe that sorts the records written and removes duplicates. Note
701    the use of file handle syntax in the Open call. To use anonymous file handles,
702    code as follows.
703    
704  Returns a reference to the default table passed in as the first parameter.      my $logFile = Open(undef, '>>/usr/spool/news/twitlog', "Could not open twit log.");
705    
706  =back  The I<$message> parameter is used if the open fails. If it is set to C<0>, then
707    the open returns TRUE if successful and FALSE if an error occurred. Otherwise, a
708    failed open will throw an exception and the third parameter will be used to construct
709    an error message. If the parameter is omitted, a standard message is constructed
710    using the file spec.
711    
712  =cut      Could not open "/usr/spool/news/twitlog"
713    
714  sub GetOptions {  Note that the mode characters are automatically cleaned from the file name.
715          # Get the parameters.  The actual error message from the file system will be captured and appended to the
716          my ($defaults, $options) = @_;  message in any case.
         # Check for overrides.  
         if ($options) {  
                 # Loop through the overrides.  
                 while (my ($option, $setting) = each %{$options}) {  
                         # Insure this override exists.  
                         if (!exists $defaults->{$option}) {  
                                 croak "Unrecognized option $option encountered.";  
                         } else {  
                                 # Apply the override.  
                                 $defaults->{$option} = $setting;  
                         }  
                 }  
         }  
         # Return the merged table.  
         return $defaults;  
 }  
717    
718  =head3 MergeOptions      Could not open "/usr/spool/news/twitlog": file not found.
719    
720  C<< Tracer::MergeOptions(\%table, \%defaults); >>  In some versions of PERL the only error message we get is a number, which
721    corresponds to the C++ C<errno> value.
722    
723  Merge default values into a hash table. This method looks at the key-value pairs in the      Could not open "/usr/spool/news/twitlog": 6.
 second (default) hash, and if a matching key is not found in the first hash, the default  
 pair is copied in. The process is similar to L</GetOptions>, but there is no error-  
 checking and no return value.  
724    
725  =over 4  =over 4
726    
727  =item table  =item fileHandle
728    
729  Hash table to be updated with the default values.  File handle. If this parameter is C<undef>, a file handle will be generated
730    and returned as the value of this method.
731    
732  =item defaults  =item fileSpec
733    
734  Default values to be merged into the first hash table if they are not already present.  File name and mode, as per the PERL C<open> function.
735    
736    =item message (optional)
737    
738    Error message to use if the open fails. If omitted, a standard error message
739    will be generated. In either case, the error information from the file system
740    is appended to the message. To specify a conditional open that does not throw
741    an error if it fails, use C<0>.
742    
743    =item RETURN
744    
745    Returns the name of the file handle assigned to the file, or C<undef> if the
746    open failed.
747    
748  =back  =back
749    
750  =cut  =cut
751    
752  sub MergeOptions {  sub Open {
753          # Get the parameters.          # Get the parameters.
754          my ($table, $defaults) = @_;      my ($fileHandle, $fileSpec, $message) = @_;
755          # Loop through the defaults.      # Attempt to open the file.
756          while (my ($key, $value) = each %{$defaults}) {      my $rv = open $fileHandle, $fileSpec;
757                  if (!exists $table->{$key}) {      # If the open failed, generate an error message.
758                          $table->{$key} = $value;      if (! $rv) {
759            # Save the system error message.
760            my $sysMessage = $!;
761            # See if we need a default message.
762            if (!$message) {
763                # Clean any obvious mode characters and leading spaces from the
764                # filename.
765                my ($fileName) = FindNamePart($fileSpec);
766                $message = "Could not open \"$fileName\"";
767                  }                  }
768            # Terminate with an error using the supplied message and the
769            # error message from the file system.
770            Confess("$message: $!");
771          }          }
772        # Return the file handle.
773        return $fileHandle;
774  }  }
775    
776  =head3 Trace  =head3 FindNamePart
777    
778  C<< Trace($message); >>  C<< my ($fileName, $start, $len) = Tracer::FindNamePart($fileSpec); >>
779    
780  Write a trace message to the target location specified in L</TSetup>. If there has not been  Extract the portion of a file specification that contains the file name.
781  any prior call to B<TSetup>.  
782    A file specification is the string passed to an C<open> call. It specifies the file
783    mode and name. In a truly complex situation, it can specify a pipe sequence. This
784    method assumes that the file name is whatever follows the first angle bracket
785    sequence.  So, for example, in the following strings the file name is
786    C</usr/fig/myfile.txt>.
787    
788        >>/usr/fig/myfile.txt
789        </usr/fig/myfile.txt
790        | sort -u > /usr/fig/myfile.txt
791    
792    If the method cannot find a file name using its normal methods, it will return the
793    whole incoming string.
794    
795  =over 4  =over 4
796    
797  =item message  =item fileSpec
798    
799  Message to write.  File specification string from which the file name is to be extracted.
800    
801    =item RETURN
802    
803    Returns a three-element list. The first element contains the file name portion of
804    the specified string, or the whole string if a file name cannot be found via normal
805    methods. The second element contains the start position of the file name portion and
806    the third element contains the length.
807    
808  =back  =back
809    
810  =cut  =cut
811    #: Return Type $;
812    sub FindNamePart {
813        # Get the parameters.
814        my ($fileSpec) = @_;
815        # Default to the whole input string.
816        my ($retVal, $pos, $len) = ($fileSpec, 0, length $fileSpec);
817        # Parse out the file name if we can.
818        if ($fileSpec =~ m/(<|>>?)(.+?)(\s*)$/) {
819            $retVal = $2;
820            $len = length $retVal;
821            $pos = (length $fileSpec) - (length $3) - $len;
822        }
823        # Return the result.
824        return ($retVal, $pos, $len);
825    }
826    
827    =head3 OpenDir
828    
829    C<< my @files = OpenDir($dirName, $filtered, $flag); >>
830    
831    Open a directory and return all the file names. This function essentially performs
832    the functions of an C<opendir> and C<readdir>. If the I<$filtered> parameter is
833    set to TRUE, all filenames beginning with a period (C<.>), dollar sign (C<$>),
834    or pound sign (C<#>) and all filenames ending with a tilde C<~>) will be
835    filtered out of the return list. If the directory does not open and I<$flag> is not
836    set, an exception is thrown. So, for example,
837    
838        my @files = OpenDir("/Volumes/fig/contigs", 1);
839    
840    is effectively the same as
841    
842        opendir(TMP, "/Volumes/fig/contigs") || Confess("Could not open /Volumes/fig/contigs.");
843        my @files = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir(TMP);
844    
845    Similarly, the following code
846    
847        my @files = grep { $_ =~ /^\d/ } OpenDir("/Volumes/fig/orgs", 0, 1);
848    
849    Returns the names of all files in C</Volumes/fig/orgs> that begin with digits and
850    automatically returns an empty list if the directory fails to open.
851    
852    =over 4
853    
854    =item dirName
855    
856    Name of the directory to open.
857    
858    =item filtered
859    
860    TRUE if files whose names begin with a period (C<.>) should be automatically removed
861    from the list, else FALSE.
862    
863    =item flag
864    
865    TRUE if a failure to open is okay, else FALSE
866    
867    =back
868    
869    =cut
870    #: Return Type @;
871    sub OpenDir {
872        # Get the parameters.
873        my ($dirName, $filtered, $flag) = @_;
874        # Declare the return variable.
875        my @retVal = ();
876        # Open the directory.
877        if (opendir(my $dirHandle, $dirName)) {
878            # The directory opened successfully. Get the appropriate list according to the
879            # strictures of the filter parameter.
880            if ($filtered) {
881                @retVal = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir $dirHandle;
882            } else {
883                @retVal = readdir $dirHandle;
884            }
885        } elsif (! $flag) {
886            # Here the directory would not open and it's considered an error.
887            Confess("Could not open directory $dirName.");
888        }
889        # Return the result.
890        return @retVal;
891    }
892    
893    =head3 SetLevel
894    
895    C<< Tracer::SetLevel($newLevel); >>
896    
897    Modify the trace level. A higher trace level will cause more messages to appear.
898    
899    =over 4
900    
901    =item newLevel
902    
903    Proposed new trace level.
904    
905    =back
906    
907    =cut
908    
909    sub SetLevel {
910        $TraceLevel = $_[0];
911    }
912    
913    =head3 Now
914    
915    C<< my $string = Tracer::Now(); >>
916    
917    Return a displayable time stamp containing the local time.
918    
919    =cut
920    
921    sub Now {
922        my ($sec,$min,$hour,$mday,$mon,$year,$wday,$yday,$isdst) = localtime(time);
923        my $retVal = _p2($mon+1) . "/" . _p2($mday) . "/" . ($year + 1900) . " " .
924                     _p2($hour) . ":" . _p2($min) . ":" . _p2($sec);
925        return $retVal;
926    }
927    
928    # Pad a number to 2 digits.
929    sub _p2 {
930        my ($value) = @_;
931        $value = "0$value" if ($value < 10);
932        return $value;
933    }
934    
935    =head3 ParseTraceDate
936    
937    C<< my $time = Tracer::ParseTraceDate($dateString); >>
938    
939    Convert a date from the trace file into a PERL timestamp.
940    
941    =over 4
942    
943    =item dateString
944    
945    The date string from the trace file. The format of the string is determined by the
946    L</Now> method.
947    
948    =item RETURN
949    
950    Returns a PERL time, that is, a number of seconds since the epoch, or C<undef> if
951    the time string is invalid.
952    
953    =cut
954    
955    sub ParseTraceDate {
956        # Get the parameters.
957        my ($dateString) = @_;
958        # Declare the return variable.
959        my $retVal;
960        # Parse the date.
961        if ($dateString =~ m#(\d+)/(\d+)/(\d+)\s+(\d+):(\d+):(\d+)#) {
962            # Create a time object.
963            $retVal = timelocal($6, $5, $4, $3, $2, $1);
964        }
965        # Return the result.
966        return $retVal;
967    }
968    
969    =head3 LogErrors
970    
971    C<< Tracer::LogErrors($fileName); >>
972    
973    Route the standard error output to a log file.
974    
975    =over 4
976    
977    =item fileName
978    
979    Name of the file to receive the error output.
980    
981    =back
982    
983    =cut
984    
985    sub LogErrors {
986        # Get the file name.
987        my ($fileName) = @_;
988        # Open the file as the standard error output.
989        open STDERR, '>', $fileName;
990    }
991    
992    =head3 ReadOptions
993    
994    C<< my %options = Tracer::ReadOptions($fileName); >>
995    
996    Read a set of options from a file. Each option is encoded in a line of text that has the
997    format
998    
999    I<optionName>C<=>I<optionValue>C<; >I<comment>
1000    
1001    The option name must consist entirely of letters, digits, and the punctuation characters
1002    C<.> and C<_>, and is case sensitive. Blank lines and lines in which the first nonblank
1003    character is a semi-colon will be ignored. The return hash will map each option name to
1004    the corresponding option value.
1005    
1006    =over 4
1007    
1008    =item fileName
1009    
1010    Name of the file containing the option data.
1011    
1012    =item RETURN
1013    
1014    Returns a hash mapping the option names specified in the file to their corresponding option
1015    value.
1016    
1017    =back
1018    
1019    =cut
1020    
1021    sub ReadOptions {
1022        # Get the parameters.
1023        my ($fileName) = @_;
1024        # Open the file.
1025        (open CONFIGFILE, "<$fileName") || Confess("Could not open option file $fileName.");
1026        # Count the number of records read.
1027        my ($records, $comments) = 0;
1028        # Create the return hash.
1029        my %retVal = ();
1030        # Loop through the file, accumulating key-value pairs.
1031        while (my $line = <CONFIGFILE>) {
1032            # Denote we've read a line.
1033            $records++;
1034            # Determine the line type.
1035            if ($line =~ /^\s*[\n\r]/) {
1036                # A blank line is a comment.
1037                $comments++;
1038            } elsif ($line =~ /^\s*([A-Za-z0-9_\.]+)=([^;]*);/) {
1039                # Here we have an option assignment.
1040                retVal{$1} = $2;
1041            } elsif ($line =~ /^\s*;/) {
1042                # Here we have a text comment.
1043                $comments++;
1044            } else {
1045                # Here we have an invalid line.
1046                Trace("Invalid option statement in record $records.") if T(0);
1047            }
1048        }
1049        # Return the hash created.
1050        return %retVal;
1051    }
1052    
1053    =head3 GetOptions
1054    
1055    C<< Tracer::GetOptions(\%defaults, \%options); >>
1056    
1057    Merge a specified set of options into a table of defaults. This method takes two hash references
1058    as input and uses the data from the second to update the first. If the second does not exist,
1059    there will be no effect. An error will be thrown if one of the entries in the second hash does not
1060    exist in the first.
1061    
1062    Consider the following example.
1063    
1064    C<< my $optionTable = GetOptions({ dbType => 'mySQL', trace => 0 }, $options); >>
1065    
1066    In this example, the variable B<$options> is expected to contain at most two options-- B<dbType> and
1067    B<trace>. The default database type is C<mySQL> and the default trace level is C<0>. If the value of
1068    B<$options> is C<< {dbType => 'Oracle'} >>, then the database type will be changed to C<Oracle> and
1069    the trace level will remain at 0. If B<$options> is undefined, then the database type and trace level
1070    will remain C<mySQL> and C<0>. If, on the other hand, B<$options> is defined as
1071    
1072    C<< {databaseType => 'Oracle'} >>
1073    
1074    an error will occur because the B<databaseType> option does not exist.
1075    
1076    =over 4
1077    
1078    =item defaults
1079    
1080    Table of default option values.
1081    
1082    =item options
1083    
1084    Table of overrides, if any.
1085    
1086    =item RETURN
1087    
1088    Returns a reference to the default table passed in as the first parameter.
1089    
1090    =back
1091    
1092    =cut
1093    
1094    sub GetOptions {
1095        # Get the parameters.
1096        my ($defaults, $options) = @_;
1097        # Check for overrides.
1098        if ($options) {
1099            # Loop through the overrides.
1100            while (my ($option, $setting) = each %{$options}) {
1101                # Insure this override exists.
1102                if (!exists $defaults->{$option}) {
1103                    croak "Unrecognized option $option encountered.";
1104                } else {
1105                    # Apply the override.
1106                    $defaults->{$option} = $setting;
1107                }
1108            }
1109        }
1110        # Return the merged table.
1111        return $defaults;
1112    }
1113    
1114    =head3 MergeOptions
1115    
1116    C<< Tracer::MergeOptions(\%table, \%defaults); >>
1117    
1118    Merge default values into a hash table. This method looks at the key-value pairs in the
1119    second (default) hash, and if a matching key is not found in the first hash, the default
1120    pair is copied in. The process is similar to L</GetOptions>, but there is no error-
1121    checking and no return value.
1122    
1123    =over 4
1124    
1125    =item table
1126    
1127    Hash table to be updated with the default values.
1128    
1129    =item defaults
1130    
1131    Default values to be merged into the first hash table if they are not already present.
1132    
1133    =back
1134    
1135    =cut
1136    
1137    sub MergeOptions {
1138        # Get the parameters.
1139        my ($table, $defaults) = @_;
1140        # Loop through the defaults.
1141        while (my ($key, $value) = each %{$defaults}) {
1142            if (!exists $table->{$key}) {
1143                $table->{$key} = $value;
1144            }
1145        }
1146    }
1147    
1148    =head3 Trace
1149    
1150    C<< Trace($message); >>
1151    
1152    Write a trace message to the target location specified in L</TSetup>. If there has not been
1153    any prior call to B<TSetup>.
1154    
1155    =over 4
1156    
1157    =item message
1158    
1159    Message to write.
1160    
1161    =back
1162    
1163    =cut
1164    
1165    sub Trace {
1166        # Get the parameters.
1167        my ($message) = @_;
1168        # Get the timestamp.
1169        my $timeStamp = Now();
1170        # Format the message. Note we strip off any line terminators at the end.
1171        my $formatted = "[$timeStamp] <$LastCategory>: " . Strip($message);
1172        # Process according to the destination.
1173        if ($Destination eq "TEXT") {
1174            # Write the message to the standard output.
1175            print "$formatted\n";
1176        } elsif ($Destination eq "ERROR") {
1177            # Write the message to the error output.
1178            print STDERR "$formatted\n";
1179        } elsif ($Destination eq "QUEUE") {
1180            # Push the message into the queue.
1181            push @Queue, "$formatted";
1182        } elsif ($Destination eq "HTML") {
1183            # Convert the message to HTML and write it to the standard output.
1184            my $escapedMessage = CGI::escapeHTML($message);
1185            print "<p>$formatted</p>\n";
1186        } elsif ($Destination eq "WARN") {
1187           # Emit the message as a warning.
1188           warn $message;
1189        } elsif ($Destination =~ m/^>>/) {
1190            # Write the trace message to an output file.
1191            (open TRACING, $Destination) || die "Tracing open for \"$Destination\" failed: $!";
1192            print TRACING "$formatted\n";
1193            close TRACING;
1194            # If the Tee flag is on, echo it to the standard output.
1195            if ($TeeFlag) {
1196                print "$formatted\n";
1197            }
1198        }
1199    }
1200    
1201    =head3 T
1202    
1203    C<< my $switch = T($category, $traceLevel); >>
1204    
1205        or
1206    
1207    C<< my $switch = T($traceLevel); >>
1208    
1209    Return TRUE if the trace level is at or above a specified value and the specified category
1210    is active, else FALSE. If no category is specified, the caller's package name is used.
1211    
1212    =over 4
1213    
1214    =item category
1215    
1216    Category to which the message belongs. If not specified, the caller's package name is
1217    used.
1218    
1219    =item traceLevel
1220    
1221    Relevant tracing level.
1222    
1223    =item RETURN
1224    
1225    TRUE if a message at the specified trace level would appear in the trace, else FALSE.
1226    
1227    =back
1228    
1229    =cut
1230    
1231    sub T {
1232        # Declare the return variable.
1233        my $retVal = 0;
1234        # Only proceed if tracing is turned on.
1235        if ($Destination ne "NONE") {
1236            # Get the parameters.
1237            my ($category, $traceLevel) = @_;
1238            if (!defined $traceLevel) {
1239                # Here we have no category, so we need to get the calling package.
1240                # The calling package is normally the first parameter. If it is
1241                # omitted, the first parameter will be the tracelevel. So, the
1242                # first thing we do is shift the so-called category into the
1243                # $traceLevel variable where it belongs.
1244                $traceLevel = $category;
1245                my ($package, $fileName, $line) = caller;
1246                # If there is no calling package, we default to "main".
1247                if (!$package) {
1248                    $category = "main";
1249                } else {
1250                    $category = $package;
1251                }
1252            }
1253            # Save the category name.
1254            $LastCategory = $category;
1255            # Convert it to lower case before we hash it.
1256            $category = lc $category;
1257            # Use the category and tracelevel to compute the result.
1258            if (ref $traceLevel) {
1259                Confess("Bad trace level.");
1260            } elsif (ref $TraceLevel) {
1261                Confess("Bad trace config.");
1262            }
1263            $retVal = ($traceLevel <= $TraceLevel && ($AllTrace || exists $Categories{$category}));
1264        }
1265        # Return the computed result.
1266        return $retVal;
1267    }
1268    
1269    =head3 ParseCommand
1270    
1271    C<< my ($options, @arguments) = Tracer::ParseCommand(\%optionTable, @inputList); >>
1272    
1273    Parse a command line consisting of a list of parameters. The initial parameters may be option
1274    specifiers of the form C<->I<option> or C<->I<option>C<=>I<value>. The options are stripped
1275    off and merged into a table of default options. The remainder of the command line is
1276    returned as a list of positional arguments. For example, consider the following invocation.
1277    
1278    C<< my ($options, @arguments) = ParseCommand({ errors => 0, logFile => 'trace.log'}, @words); >>
1279    
1280    In this case, the list @words will be treated as a command line. There are two options available,
1281    B<errors> and B<logFile>. If @words has the following format
1282    
1283    C<< -logFile=error.log apple orange rutabaga >>
1284    
1285    then at the end of the invocation, C<$options> will be
1286    
1287    C<< { errors => 0, logFile => 'error.log' } >>
1288    
1289    and C<@arguments> will contain
1290    
1291    C<< apple orange rutabaga >>
1292    
1293    The parser allows for some escape sequences. See L</UnEscape> for a description. There is no
1294    support for quote characters.
1295    
1296    =over 4
1297    
1298    =item optionTable
1299    
1300    Table of default options.
1301    
1302    =item inputList
1303    
1304    List of words on the command line.
1305    
1306    =item RETURN
1307    
1308    Returns a reference to the option table and a list of the positional arguments.
1309    
1310    =back
1311    
1312    =cut
1313    
1314    sub ParseCommand {
1315        # Get the parameters.
1316        my ($optionTable, @inputList) = @_;
1317        # Process any options in the input list.
1318        my %overrides = ();
1319        while ((@inputList > 0) && ($inputList[0] =~ /^-/)) {
1320            # Get the current option.
1321            my $arg = shift @inputList;
1322            # Pull out the option name.
1323            $arg =~ /^-([^=]*)/g;
1324            my $name = $1;
1325            # Check for an option value.
1326            if ($arg =~ /\G=(.*)$/g) {
1327                # Here we have a value for the option.
1328                $overrides{$name} = UnEscape($1);
1329            } else {
1330                # Here there is no value, so we use 1.
1331                $overrides{$name} = 1;
1332            }
1333        }
1334        # Merge the options into the defaults.
1335        GetOptions($optionTable, \%overrides);
1336        # Translate the remaining parameters.
1337        my @retVal = ();
1338        for my $inputParm (@inputList) {
1339            push @retVal, UnEscape($inputParm);
1340        }
1341        # Return the results.
1342        return ($optionTable, @retVal);
1343    }
1344    
1345    =head3 Escape
1346    
1347    C<< my $codedString = Tracer::Escape($realString); >>
1348    
1349    Escape a string for use in a command length. Tabs will be replaced by C<\t>, new-lines
1350    replaced by C<\n>, carriage returns will be deleted, and backslashes will be doubled. The
1351    result is to reverse the effect of L</UnEscape>.
1352    
1353    =over 4
1354    
1355    =item realString
1356    
1357    String to escape.
1358    
1359    =item RETURN
1360    
1361    Escaped equivalent of the real string.
1362    
1363    =back
1364    
1365    =cut
1366    
1367    sub Escape {
1368        # Get the parameter.
1369        my ($realString) = @_;
1370        # Initialize the return variable.
1371        my $retVal = "";
1372        # Loop through the parameter string, looking for sequences to escape.
1373        while (length $realString > 0) {
1374            # Look for the first sequence to escape.
1375            if ($realString =~ /^(.*?)([\n\t\r\\])/) {
1376                # Here we found it. The text preceding the sequence is in $1. The sequence
1377                # itself is in $2. First, move the clear text to the return variable.
1378                $retVal .= $1;
1379                # Strip the processed section off the real string.
1380                $realString = substr $realString, (length $2) + (length $1);
1381                # Get the matched character.
1382                my $char = $2;
1383                # If we have a CR, we are done.
1384                if ($char ne "\r") {
1385                    # It's not a CR, so encode the escape sequence.
1386                    $char =~ tr/\t\n/tn/;
1387                    $retVal .= "\\" . $char;
1388                }
1389            } else {
1390                # Here there are no more escape sequences. The rest of the string is
1391                # transferred unmodified.
1392                $retVal .= $realString;
1393                $realString = "";
1394            }
1395        }
1396        # Return the result.
1397        return $retVal;
1398    }
1399    
1400    =head3 UnEscape
1401    
1402    C<< my $realString = Tracer::UnEscape($codedString); >>
1403    
1404    Replace escape sequences with their actual equivalents. C<\t> will be replaced by
1405    a tab, C<\n> by a new-line character, and C<\\> by a backslash. C<\r> codes will
1406    be deleted.
1407    
1408    =over 4
1409    
1410    =item codedString
1411    
1412    String to un-escape.
1413    
1414    =item RETURN
1415    
1416    Returns a copy of the original string with the escape sequences converted to their actual
1417    values.
1418    
1419    =back
1420    
1421    =cut
1422    
1423    sub UnEscape {
1424        # Get the parameter.
1425        my ($codedString) = @_;
1426        # Initialize the return variable.
1427        my $retVal = "";
1428        # Only proceed if the incoming string is nonempty.
1429        if (defined $codedString) {
1430            # Loop through the parameter string, looking for escape sequences. We can't do
1431            # translating because it causes problems with the escaped slash. ("\\t" becomes
1432            # "\<tab>" no matter what we do.)
1433            while (length $codedString > 0) {
1434                # Look for the first escape sequence.
1435                if ($codedString =~ /^(.*?)\\(\\|n|t|r)/) {
1436                    # Here we found it. The text preceding the sequence is in $1. The sequence
1437                    # itself is in $2. First, move the clear text to the return variable.
1438                    $retVal .= $1;
1439                    $codedString = substr $codedString, (2 + length $1);
1440                    # Get the escape value.
1441                    my $char = $2;
1442                    # If we have a "\r", we are done.
1443                    if ($char ne 'r') {
1444                        # Here it's not an 'r', so we convert it.
1445                        $char =~ tr/\\tn/\\\t\n/;
1446                        $retVal .= $char;
1447                    }
1448                } else {
1449                    # Here there are no more escape sequences. The rest of the string is
1450                    # transferred unmodified.
1451                    $retVal .= $codedString;
1452                    $codedString = "";
1453                }
1454            }
1455        }
1456        # Return the result.
1457        return $retVal;
1458    }
1459    
1460    =head3 ParseRecord
1461    
1462    C<< my @fields = Tracer::ParseRecord($line); >>
1463    
1464    Parse a tab-delimited data line. The data line is split into field values. Embedded tab
1465    and new-line characters in the data line must be represented as C<\t> and C<\n>, respectively.
1466    These will automatically be converted.
1467    
1468    =over 4
1469    
1470    =item line
1471    
1472    Line of data containing the tab-delimited fields.
1473    
1474    =item RETURN
1475    
1476    Returns a list of the fields found in the data line.
1477    
1478    =back
1479    
1480    =cut
1481    
1482    sub ParseRecord {
1483        # Get the parameter.
1484        my ($line) = @_;
1485        # Remove the trailing new-line, if any.
1486        chomp $line;
1487        # Split the line read into pieces using the tab character.
1488        my @retVal = split /\t/, $line;
1489        # Trim and fix the escapes in each piece.
1490        for my $value (@retVal) {
1491            # Trim leading whitespace.
1492            $value =~ s/^\s+//;
1493            # Trim trailing whitespace.
1494            $value =~ s/\s+$//;
1495            # Delete the carriage returns.
1496            $value =~ s/\r//g;
1497            # Convert the escapes into their real values.
1498            $value =~ s/\\t/"\t"/ge;
1499            $value =~ s/\\n/"\n"/ge;
1500        }
1501        # Return the result.
1502        return @retVal;
1503    }
1504    
1505    =head3 Merge
1506    
1507    C<< my @mergedList = Tracer::Merge(@inputList); >>
1508    
1509    Sort a list of strings and remove duplicates.
1510    
1511    =over 4
1512    
1513    =item inputList
1514    
1515    List of scalars to sort and merge.
1516    
1517    =item RETURN
1518    
1519    Returns a list containing the same elements sorted in ascending order with duplicates
1520    removed.
1521    
1522    =back
1523    
1524    =cut
1525    
1526    sub Merge {
1527        # Get the input list in sort order.
1528        my @inputList = sort @_;
1529        # Only proceed if the list has at least two elements.
1530        if (@inputList > 1) {
1531            # Now we want to move through the list splicing out duplicates.
1532            my $i = 0;
1533            while ($i < @inputList) {
1534                # Get the current entry.
1535                my $thisEntry = $inputList[$i];
1536                # Find out how many elements duplicate the current entry.
1537                my $j = $i + 1;
1538                my $dup1 = $i + 1;
1539                while ($j < @inputList && $inputList[$j] eq $thisEntry) { $j++; };
1540                # If the number is nonzero, splice out the duplicates found.
1541                if ($j > $dup1) {
1542                    splice @inputList, $dup1, $j - $dup1;
1543                }
1544                # Now the element at position $dup1 is different from the element before it
1545                # at position $i. We push $i forward one position and start again.
1546                $i++;
1547            }
1548        }
1549        # Return the merged list.
1550        return @inputList;
1551    }
1552    
1553    =head3 Percent
1554    
1555    C<< my $percent = Tracer::Percent($number, $base); >>
1556    
1557    Returns the percent of the base represented by the given number. If the base
1558    is zero, returns zero.
1559    
1560    =over 4
1561    
1562    =item number
1563    
1564    Percent numerator.
1565    
1566    =item base
1567    
1568    Percent base.
1569    
1570    =item RETURN
1571    
1572    Returns the percentage of the base represented by the numerator.
1573    
1574    =back
1575    
1576    =cut
1577    
1578    sub Percent {
1579        # Get the parameters.
1580        my ($number, $base) = @_;
1581        # Declare the return variable.
1582        my $retVal = 0;
1583        # Compute the percent.
1584        if ($base != 0) {
1585            $retVal = $number * 100 / $base;
1586        }
1587        # Return the result.
1588        return $retVal;
1589    }
1590    
1591    =head3 GetFile
1592    
1593    C<< my @fileContents = Tracer::GetFile($fileName); >>
1594    
1595        or
1596    
1597    C<< my $fileContents = Tracer::GetFile($fileName); >>
1598    
1599    Return the entire contents of a file. In list context, line-ends are removed and
1600    each line is a list element. In scalar context, line-ends are replaced by C<\n>.
1601    
1602    =over 4
1603    
1604    =item fileName
1605    
1606    Name of the file to read.
1607    
1608    =item RETURN
1609    
1610    In a list context, returns the entire file as a list with the line terminators removed.
1611    In a scalar context, returns the entire file as a string. If an error occurs opening
1612    the file, an empty list will be returned.
1613    
1614    =back
1615    
1616    =cut
1617    
1618    sub GetFile {
1619        # Get the parameters.
1620        my ($fileName) = @_;
1621        # Declare the return variable.
1622        my @retVal = ();
1623        # Open the file for input.
1624        my $handle = Open(undef, "<$fileName");
1625        # Read the whole file into the return variable, stripping off any terminator
1626        # characters.
1627        my $lineCount = 0;
1628        while (my $line = <$handle>) {
1629            $lineCount++;
1630            $line = Strip($line);
1631            push @retVal, $line;
1632        }
1633        # Close it.
1634        close $handle;
1635        my $actualLines = @retVal;
1636        # Return the file's contents in the desired format.
1637        if (wantarray) {
1638            return @retVal;
1639        } else {
1640            return join "\n", @retVal;
1641        }
1642    }
1643    
1644    =head3 PutFile
1645    
1646    C<< Tracer::PutFile($fileName, \@lines); >>
1647    
1648    Write out a file from a list of lines of text.
1649    
1650    =over 4
1651    
1652    =item fileName
1653    
1654    Name of the output file.
1655    
1656    =item lines
1657    
1658    Reference to a list of text lines. The lines will be written to the file in order, with trailing
1659    new-line characters. Alternatively, may be a string, in which case the string will be written without
1660    modification.
1661    
1662    =back
1663    
1664    =cut
1665    
1666    sub PutFile {
1667        # Get the parameters.
1668        my ($fileName, $lines) = @_;
1669        # Open the output file.
1670        my $handle = Open(undef, ">$fileName");
1671        if (ref $lines ne 'ARRAY') {
1672            # Here we have a scalar, so we write it raw.
1673            print $handle $lines;
1674        } else {
1675            # Write the lines one at a time.
1676            for my $line (@{$lines}) {
1677                print $handle "$line\n";
1678            }
1679        }
1680        # Close the output file.
1681        close $handle;
1682    }
1683    
1684    =head3 QTrace
1685    
1686    C<< my $data = QTrace($format); >>
1687    
1688    Return the queued trace data in the specified format.
1689    
1690    =over 4
1691    
1692    =item format
1693    
1694    C<html> to format the data as an HTML list, C<text> to format it as straight text.
1695    
1696    =back
1697    
1698    =cut
1699    
1700    sub QTrace {
1701        # Get the parameter.
1702        my ($format) = @_;
1703        # Create the return variable.
1704        my $retVal = "";
1705        # Only proceed if there is an actual queue.
1706        if (@Queue) {
1707            # Process according to the format.
1708            if ($format =~ m/^HTML$/i) {
1709                # Convert the queue into an HTML list.
1710                $retVal = "<ul>\n";
1711                for my $line (@Queue) {
1712                    my $escapedLine = CGI::escapeHTML($line);
1713                    $retVal .= "<li>$escapedLine</li>\n";
1714                }
1715                $retVal .= "</ul>\n";
1716            } elsif ($format =~ m/^TEXT$/i) {
1717                # Convert the queue into a list of text lines.
1718                $retVal = join("\n", @Queue) . "\n";
1719            }
1720            # Clear the queue.
1721            @Queue = ();
1722        }
1723        # Return the formatted list.
1724        return $retVal;
1725    }
1726    
1727    =head3 Confess
1728    
1729    C<< Confess($message); >>
1730    
1731    Trace the call stack and abort the program with the specified message. When used with
1732    the OR operator and the L</Assert> method, B<Confess> can function as a debugging assert.
1733    So, for example
1734    
1735    C<< Assert($recNum >= 0) || Confess("Invalid record number $recNum."); >>
1736    
1737    Will abort the program with a stack trace if the value of C<$recNum> is negative.
1738    
1739    =over 4
1740    
1741    =item message
1742    
1743    Message to include in the trace.
1744    
1745    =back
1746    
1747    =cut
1748    
1749    sub Confess {
1750        # Get the parameters.
1751        my ($message) = @_;
1752        # Trace the call stack.
1753        Cluck($message);
1754        # Abort the program.
1755        croak(">>> $message");
1756    }
1757    
1758    =head3 Assert
1759    
1760    C<< Assert($condition1, $condition2, ... $conditionN); >>
1761    
1762    Return TRUE if all the conditions are true. This method can be used in conjunction with
1763    the OR operator and the L</Confess> method as a debugging assert.
1764    So, for example
1765    
1766    C<< Assert($recNum >= 0) || Confess("Invalid record number $recNum."); >>
1767    
1768    Will abort the program with a stack trace if the value of C<$recNum> is negative.
1769    
1770    =cut
1771    sub Assert {
1772        my $retVal = 1;
1773        LOOP: for my $condition (@_) {
1774            if (! $condition) {
1775                $retVal = 0;
1776                last LOOP;
1777            }
1778        }
1779        return $retVal;
1780    }
1781    
1782    =head3 Cluck
1783    
1784    C<< Cluck($message); >>
1785    
1786    Trace the call stack. Note that for best results, you should qualify the call with a
1787    trace condition. For example,
1788    
1789    C<< Cluck("Starting record parse.") if T(3); >>
1790    
1791    will only trace the stack if the trace level for the package is 3 or more.
1792    
1793    =over 4
1794    
1795    =item message
1796    
1797    Message to include in the trace.
1798    
1799    =back
1800    
1801    =cut
1802    
1803    sub Cluck {
1804        # Get the parameters.
1805        my ($message) = @_;
1806        # Trace what's happening.
1807        Trace("Stack trace for event: $message");
1808        my $confession = longmess($message);
1809        # Convert the confession to a series of trace messages. Note we skip any
1810        # messages relating to calls into Tracer.
1811        for my $line (split /\s*\n/, $confession) {
1812            Trace($line) if ($line !~ /Tracer\.pm/);
1813        }
1814    }
1815    
1816  sub Trace {  =head3 Min
1817    
1818    C<< my $min = Min($value1, $value2, ... $valueN); >>
1819    
1820    Return the minimum argument. The arguments are treated as numbers.
1821    
1822    =over 4
1823    
1824    =item $value1, $value2, ... $valueN
1825    
1826    List of numbers to compare.
1827    
1828    =item RETURN
1829    
1830    Returns the lowest number in the list.
1831    
1832    =back
1833    
1834    =cut
1835    
1836    sub Min {
1837        # Get the parameters. Note that we prime the return value with the first parameter.
1838        my ($retVal, @values) = @_;
1839        # Loop through the remaining parameters, looking for the lowest.
1840        for my $value (@values) {
1841            if ($value < $retVal) {
1842                $retVal = $value;
1843            }
1844        }
1845        # Return the minimum found.
1846        return $retVal;
1847    }
1848    
1849    =head3 Max
1850    
1851    C<< my $max = Max($value1, $value2, ... $valueN); >>
1852    
1853    Return the maximum argument. The arguments are treated as numbers.
1854    
1855    =over 4
1856    
1857    =item $value1, $value2, ... $valueN
1858    
1859    List of numbers to compare.
1860    
1861    =item RETURN
1862    
1863    Returns the highest number in the list.
1864    
1865    =back
1866    
1867    =cut
1868    
1869    sub Max {
1870        # Get the parameters. Note that we prime the return value with the first parameter.
1871        my ($retVal, @values) = @_;
1872        # Loop through the remaining parameters, looking for the highest.
1873        for my $value (@values) {
1874            if ($value > $retVal) {
1875                $retVal = $value;
1876            }
1877        }
1878        # Return the maximum found.
1879        return $retVal;
1880    }
1881    
1882    =head3 AddToListMap
1883    
1884    C<< Tracer::AddToListMap(\%hash, $key, $value1, $value2, ... valueN); >>
1885    
1886    Add a key-value pair to a hash of lists. If no value exists for the key, a singleton list
1887    is created for the key. Otherwise, the new value is pushed onto the list.
1888    
1889    =over 4
1890    
1891    =item hash
1892    
1893    Reference to the target hash.
1894    
1895    =item key
1896    
1897    Key for which the value is to be added.
1898    
1899    =item value1, value2, ... valueN
1900    
1901    List of values to add to the key's value list.
1902    
1903    =back
1904    
1905    =cut
1906    
1907    sub AddToListMap {
1908          # Get the parameters.          # Get the parameters.
1909          my ($message) = @_;      my ($hash, $key, @values) = @_;
1910          # Get the timestamp.      # Process according to whether or not the key already has a value.
1911          my $timeStamp = Now();      if (! exists $hash->{$key}) {
1912          # Format the message. Note we strip off any line terminators at the end.          $hash->{$key} = [@values];
1913          my $formatted = "$timeStamp <$LastCategory>: " . Strip($message);      } else {
1914          # Process according to the destination.          push @{$hash->{$key}}, @values;
1915          if ($Destination eq "TEXT") {      }
1916                  # Write the message to the standard output.  }
1917                  print "$formatted\n";  
1918          } elsif ($Destination eq "ERROR") {  =head3 DebugMode
1919                  # Write the message to the error output.  
1920                  print STDERR "$formatted\n";  C<< if (Tracer::DebugMode) { ...code... } >>
1921          } elsif ($Destination eq "QUEUE") {  
1922                  # Push the message into the queue.  Return TRUE if debug mode has been turned on, else abort.
1923                  push @Queue, "$formatted";  
1924          } elsif ($Destination eq "HTML") {  Certain CGI scripts are too dangerous to exist in the production
1925                  # Convert the message to HTML and write it to the standard output.  environment. This method provides a simple way to prevent them
1926                  my $escapedMessage = CGI::escapeHTML($message);  from working unless they are explicitly turned on by creating a password
1927                  print "<p>$formatted</p>\n";  cookie via the B<SetPassword> script.  If debugging mode
1928      } elsif ($Destination eq "WARN") {  is not turned on, an error will occur.
1929         # Emit the message as a warning.  
1930         warn $message;  =cut
1931          } elsif ($Destination =~ m/^>>/) {  
1932                  # Write the trace message to an output file.  sub DebugMode {
1933                  open TRACING, $Destination;      # Declare the return variable.
1934                  print TRACING "$formatted\n";      my $retVal = 0;
1935                  close TRACING;      # Check the debug configuration.
1936        my $password = CGI::cookie("DebugMode");
1937        my $encrypted = Digest::MD5::md5_hex($password);
1938        if ($encrypted eq "252dec43280e0c0d6a75ffcec486e61d") {
1939            $retVal = 1;
1940        } else {
1941            # Here debug mode is off, so we generate an error.
1942            Confess("Cannot use this facility without logging in.");
1943        }
1944        # Return the determination indicator.
1945        return $retVal;
1946    }
1947    
1948    =head3 Strip
1949    
1950    C<< my $string = Tracer::Strip($line); >>
1951    
1952    Strip all line terminators off a string. This is necessary when dealing with files
1953    that may have been transferred back and forth several times among different
1954    operating environments.
1955    
1956    =over 4
1957    
1958    =item line
1959    
1960    Line of text to be stripped.
1961    
1962    =item RETURN
1963    
1964    The same line of text with all the line-ending characters chopped from the end.
1965    
1966    =back
1967    
1968    =cut
1969    
1970    sub Strip {
1971        # Get a copy of the parameter string.
1972        my ($string) = @_;
1973        my $retVal = (defined $string ? $string : "");
1974        # Strip the line terminator characters.
1975        $retVal =~ s/(\r|\n)+$//g;
1976        # Return the result.
1977        return $retVal;
1978    }
1979    
1980    =head3 Pad
1981    
1982    C<< my $paddedString = Tracer::Pad($string, $len, $left, $padChar); >>
1983    
1984    Pad a string to a specified length. The pad character will be a
1985    space, and the padding will be on the right side unless specified
1986    in the third parameter.
1987    
1988    =over 4
1989    
1990    =item string
1991    
1992    String to be padded.
1993    
1994    =item len
1995    
1996    Desired length of the padded string.
1997    
1998    =item left (optional)
1999    
2000    TRUE if the string is to be left-padded; otherwise it will be padded on the right.
2001    
2002    =item padChar (optional)
2003    
2004    Character to use for padding. The default is a space.
2005    
2006    =item RETURN
2007    
2008    Returns a copy of the original string with the pad character added to the
2009    specified end so that it achieves the desired length.
2010    
2011    =back
2012    
2013    =cut
2014    
2015    sub Pad {
2016        # Get the parameters.
2017        my ($string, $len, $left, $padChar) = @_;
2018        # Compute the padding character.
2019        if (! defined $padChar) {
2020            $padChar = " ";
2021        }
2022        # Compute the number of spaces needed.
2023        my $needed = $len - length $string;
2024        # Copy the string into the return variable.
2025        my $retVal = $string;
2026        # Only proceed if padding is needed.
2027        if ($needed > 0) {
2028            # Create the pad string.
2029            my $pad = $padChar x $needed;
2030            # Affix it to the return value.
2031            if ($left) {
2032                $retVal = $pad . $retVal;
2033            } else {
2034                $retVal .= $pad;
2035            }
2036        }
2037        # Return the result.
2038        return $retVal;
2039    }
2040    
2041    =head3 EOF
2042    
2043    This is a constant that is lexically greater than any useful string.
2044    
2045    =cut
2046    
2047    sub EOF {
2048        return "\xFF\xFF\xFF\xFF\xFF";
2049    }
2050    
2051    =head3 TICK
2052    
2053    C<< my @results = TICK($commandString); >>
2054    
2055    Perform a back-tick operation on a command. If this is a Windows environment, any leading
2056    dot-slash (C<./> will be removed. So, for example, if you were doing
2057    
2058        `./protein.cgi`
2059    
2060    from inside a CGI script, it would work fine in Unix, but would issue an error message
2061    in Windows complaining that C<'.'> is not a valid command. If instead you code
2062    
2063        TICK("./protein.cgi")
2064    
2065    it will work correctly in both environments.
2066    
2067    =over 4
2068    
2069    =item commandString
2070    
2071    The command string to pass to the system.
2072    
2073    =item RETURN
2074    
2075    Returns the standard output from the specified command, as a list.
2076    
2077    =back
2078    
2079    =cut
2080    #: Return Type @;
2081    sub TICK {
2082        # Get the parameters.
2083        my ($commandString) = @_;
2084        # Chop off the dot-slash if this is Windows.
2085        if ($FIG_Config::win_mode) {
2086            $commandString =~ s!^\./!!;
2087          }          }
2088        # Activate the command and return the result.
2089        return `$commandString`;
2090  }  }
2091    
2092  =head3 T  =head3 ScriptSetup
2093    
2094  C<< my $switch = T($category, $traceLevel); >>  C<< my ($cgi, $varHash) = ScriptSetup($noTrace); >>
2095    
2096          or  Perform standard tracing and debugging setup for scripts. The value returned is
2097    the CGI object followed by a pre-built variable hash.
2098    
2099  C<< my $switch = T($traceLevel); >>  The C<Trace> form parameter is used to determine whether or not tracing is active and
2100    which trace modules (other than C<Tracer> itself) should be turned on. Specifying
2101    the C<CGI> trace module will trace parameter and environment information. Parameters are
2102    traced at level 3 and environment variables at level 4. To trace to a file instead of to
2103    the web page, set C<TF> to 1. At the end of the script, the client should call
2104    L</ScriptFinish> to output the web page.
2105    
2106  Return TRUE if the trace level is at or above a specified value and the specified category  In some situations, it is not practical to invoke tracing via form parameters. For this
2107  is active, else FALSE. If no category is specified, the caller's package name is used.  situation, you can turn on emergency tracing from the debugging control panel.
2108    Tracing will then be turned on automatically for all programs that use the L</ETracing>
2109    method, which includes every program that uses this method or L</StandardSetup>.
2110    
2111  =over 4  =over 4
2112    
2113  =item category  =item noTrace (optional)
   
 Category to which the message belongs. If not specified, the caller's package name is  
 used.  
   
 =item traceLevel  
2114    
2115  Relevant tracing level.  If specified, tracing will be suppressed. This is useful if the script wants to set up
2116    tracing manually.
2117    
2118  =item RETURN  =item RETURN
2119    
2120  TRUE if a message at the specified trace level would appear in the trace, else FALSE.  Returns a two-element list consisting of a CGI query object and a variable hash for
2121    the output page.
2122    
2123  =back  =back
2124    
2125  =cut  =cut
2126    
2127  sub T {  sub ScriptSetup {
         # Declare the return variable.  
         my $retVal = 0;  
         # Only proceed if tracing is turned on.  
         if ($Destination ne "NONE") {  
2128                  # Get the parameters.                  # Get the parameters.
2129                  my ($category, $traceLevel) = @_;      my ($noTrace) = @_;
2130                  if (!defined $traceLevel) {      # Get the CGI query object.
2131                          # Here we have no category, so we need to get the calling package.      my $cgi = CGI->new();
2132                          $traceLevel = $category;      # Set up tracing if it's not suppressed.
2133                          my ($package, $fileName, $line) = caller;      ETracing($cgi) unless $noTrace;
2134              # If there is no calling package, we default to "main".      # Create the variable hash.
2135                          if (!$package) {      my $varHash = { results => '' };
2136                  $category = "main";      # Return the query object and variable hash.
2137        return ($cgi, $varHash);
2138    }
2139    
2140    =head3 ETracing
2141    
2142    C<< ETracing($parameter); >>
2143    
2144    Set up emergency tracing. Emergency tracing is tracing that is turned
2145    on automatically for any program that calls this method. The emergency
2146    tracing parameters are stored in a a file identified by a tracing key.
2147    If this method is called with a CGI object, then the tracing key is
2148    taken from a cookie. If it is called with no parameters, then the tracing
2149    key is taken from an environment variable. If it is called with a string,
2150    the tracing key is that string.
2151    
2152    =over 4
2153    
2154    =item parameter
2155    
2156    A parameter from which the tracing key is computed. If it is a scalar,
2157    that scalar is used as the tracing key. If it is a CGI object, the
2158    tracing key is taken from the C<IP> cookie. If it is omitted, the
2159    tracing key is taken from the C<TRACING> environment variable. If it
2160    is a CGI object and emergency tracing is not on, the C<Trace> and
2161    C<TF> parameters will be used to determine the type of tracing.
2162    
2163    =back
2164    
2165    =cut
2166    
2167    sub ETracing {
2168        # Get the parameter.
2169        my ($parameter) = @_;
2170        # Check for CGI mode.
2171        my $cgi = (ref $parameter eq 'CGI' ? $parameter : undef);
2172        # Default to no tracing except errors.
2173        my ($tracing, $dest) = ("0", "WARN");
2174        # Check for emergency tracing.
2175        my $tkey = EmergencyKey($parameter);
2176        my $emergencyFile = EmergencyFileName($tkey);
2177        if (-e $emergencyFile) {
2178            # We have the file. Read in the data.
2179            my @tracing = GetFile($emergencyFile);
2180            # Pull off the time limit.
2181            my $expire = shift @tracing;
2182            # Convert it to seconds.
2183            $expire *= 3600;
2184            # Check the file data.
2185            my $stat = stat($emergencyFile);
2186            my ($now) = gettimeofday;
2187            if ($now - $stat->mtime > $expire) {
2188                # Delete the expired file.
2189                unlink $emergencyFile;
2190                          } else {                          } else {
2191                                  $category = $package;              # Emergency tracing is on. Pull off the destination and
2192                # the trace level;
2193                $dest = shift @tracing;
2194                my $level = shift @tracing;
2195                # Convert the destination to a real tracing destination.
2196                # temp directory.
2197                $dest = EmergencyTracingDest($tkey, $dest);
2198                # Insure Tracer is specified.
2199                my %moduleHash = map { $_ => 1 } @tracing;
2200                $moduleHash{Tracer} = 1;
2201                # Set the trace parameter.
2202                $tracing = join(" ", $level, sort keys %moduleHash);
2203                          }                          }
2204        } elsif (defined $cgi) {
2205            # There's no emergency tracing, but we have a CGI object, so check
2206            # for tracing from the form parameters.
2207            if ($cgi->param('Trace')) {
2208                # Here the user has requested tracing via a form.
2209                $dest = ($cgi->param('TF') ? ">$FIG_Config::temp/Trace$$.log" : "QUEUE");
2210                $tracing = $cgi->param('Trace') . " Tracer";
2211                  }                  }
         # Save the category name.  
         $LastCategory = $category;  
                 # Use the category and tracelevel to compute the result.  
                 $retVal = ($traceLevel <= $TraceLevel && exists $Categories{$category});  
2212      }      }
2213          # Return the computed result.      # Setup the tracing we've determined from all the stuff above.
2214      return $retVal;      TSetup($tracing, $dest);
2215        # If we're a web script, trace the parameter and environment data.
2216        if (defined $cgi) {
2217            TraceParms($cgi);
2218        }
2219  }  }
2220    
2221  =head3 ParseCommand  =head3 EmergencyFileName
2222    
2223  C<< my ($options, @arguments) = Tracer::ParseCommand(\%optionTable, @inputList); >>  C<< my $fileName = Tracer::EmergencyFileName($tkey); >>
2224    
2225  Parse a command line consisting of a list of parameters. The initial parameters may be option  Return the emergency tracing file name. This is the file that specifies
2226  specifiers of the form C<->I<option> or C<->I<option>C<=>I<value>. The options are stripped  the tracing information.
 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.  
2227    
2228  C<< my ($options, @arguments) = ParseCommand({ errors => 0, logFile => 'trace.log'}, @words); >>  =over 4
2229    
2230  In this case, the list @words will be treated as a command line. There are two options available,  =item tkey
 B<errors> and B<logFile>. If @words has the following format  
2231    
2232  C<< -logFile=error.log apple orange rutabaga >>  Tracing key for the current program.
2233    
2234  then at the end of the invocation, C<$options> will be  =item RETURN
2235    
2236  C<< { errors => 0, logFile => 'error.log' } >>  Returns the name of the file to contain the emergency tracing information.
2237    
2238  and C<@arguments> will contain  =back
2239    
2240  C<< apple orange rutabaga >>  =cut
2241    
2242  The parser allows for some escape sequences. See L</UnEscape> for a description. There is no  sub EmergencyFileName {
2243  support for quote characters.      # Get the parameters.
2244        my ($tkey) = @_;
2245        # Compute the emergency tracing file name.
2246        return "$FIG_Config::temp/Emergency$tkey.txt";
2247    }
2248    
2249  =over 4  =head3 EmergencyFileTarget
2250    
2251  =item optionTable  C<< my $fileName = Tracer::EmergencyFileTarget($tkey); >>
2252    
2253  Table of default options.  Return the emergency tracing target file name. This is the file that receives
2254    the tracing output for file-based tracing.
2255    
2256  =item inputList  =over 4
2257    
2258  List of words on the command line.  =item tkey
2259    
2260    Tracing key for the current program.
2261    
2262  =item RETURN  =item RETURN
2263    
2264  Returns a reference to the option table and a list of the positional arguments.  Returns the name of the file to contain the trace output.
2265    
2266  =back  =back
2267    
2268  =cut  =cut
2269    
2270  sub ParseCommand {  sub EmergencyFileTarget {
2271          # Get the parameters.          # Get the parameters.
2272          my ($optionTable, @inputList) = @_;      my ($tkey) = @_;
2273          # Process any options in the input list.      # Compute the emergency tracing file name.
2274          my %overrides = ();      return "$FIG_Config::temp/trace$tkey.log";
         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);  
                 } else {  
                         # Here there is no value, so we use 1.  
                         $overrides{$name} = 1;  
                 }  
         }  
         # Merge the options into the defaults.  
         GetOptions($optionTable, \%overrides);  
         # Translate the remaining parameters.  
         my @retVal = ();  
         for my $inputParm (@inputList) {  
                 push @retVal, UnEscape($inputParm);  
         }  
         # Return the results.  
         return ($optionTable, @retVal);  
2275  }  }
2276    
2277  =head3 Escape  =head3 EmergencyTracingDest
2278    
2279  C<< my $codedString = Tracer::Escape($realString); >>  C<< my $dest = Tracer::EmergencyTracingDest($tkey, $myDest); >>
2280    
2281  Escape a string for use in a command length. Spaces will be replaced by C<\b>,  This method converts an emergency tracing destination to a real
2282  tabs replaced by C<\t>, new-lines replaced by C<\n>, and backslashes will be  tracing destination. The main difference is that if the
2283  doubled. The effect is to exactly reverse the effect of L</UnEscape>.  destination is C<FILE> or C<APPEND>, we convert it to file
2284    output.
2285    
2286  =over 4  =over 4
2287    
2288  =item realString  =item tkey
2289    
2290  String to escape.  Tracing key for this environment.
2291    
2292    =item myDest
2293    
2294    Destination from the emergency tracing file.
2295    
2296  =item RETURN  =item RETURN
2297    
2298  Escaped equivalent of the real string.  Returns a destination that can be passed into L</TSetup>.
2299    
2300  =back  =back
2301    
2302  =cut  =cut
2303    
2304  sub Escape {  sub EmergencyTracingDest {
2305          # Get the parameter.      # Get the parameters.
2306          my ($realString) = @_;      my ($tkey, $myDest) = @_;
2307          # Initialize the return variable.      # Declare the return variable.
2308          my $retVal = "";      my $retVal;
2309          # Loop through the parameter string, looking for sequences to escape.      # Process according to the destination value.
2310          while (length $realString > 0) {      if ($myDest eq 'FILE') {
2311                  # Look for the first sequence to escape.          $retVal = ">" . EmergencyFileTarget($tkey);
2312                  if ($realString =~ /^(.*?)([ \n\t\\])/) {      } elsif ($myDest eq 'APPEND') {
2313                          # Here we found it. The text preceding the sequence is in $1. The sequence          $retVal = ">>" . EmergencyFileTarget($tkey);
                         # itself is in $2. First, move the clear text to the return variable.  
                         $retVal .= $1;  
                         $realString = substr $realString, (length $2 + length $1);  
                         # Encode the escape sequence.  
                         my $char = $2;  
                         $char =~ tr/ \t\n/btn/;  
                         $retVal .= "\\" . $char;  
2314                  } else {                  } else {
2315                          # Here there are no more escape sequences. The rest of the string is          $retVal = $myDest;
                         # transferred unmodified.  
                         $retVal .= $realString;  
                         $realString = "";  
                 }  
2316          }          }
2317          # Return the result.          # Return the result.
2318          return $retVal;          return $retVal;
2319  }  }
2320    
2321  =head3 UnEscape  =head3 Emergency
2322    
2323  C<< my $realString = Tracer::UnEscape($codedString); >>  C<< Emergency($key, $hours, $dest, $level, @modules); >>
2324    
2325  Replace escape sequences with their actual equivalents. C<\b> will be replaced by a space,  Turn on emergency tracing. This method can only be invoked over the web and is
2326  C<\t> by a tab, C<\n> by a new-line character, and C<\\> by a back-slash.  should not be called if debug mode is off. The caller specifies the duration of the
2327    emergency in hours, the desired tracing destination, the trace level,
2328    and a list of the trace modules to activate. For the length of the duration, when a
2329    program in an environment with the specified tracing key active invokes a Sprout
2330    CGI script, tracing will be turned on automatically. See L</TSetup> for more
2331    about tracing setup and L</ETracing> for more about emergency tracing.
2332    
2333  =over 4  =over 4
2334    
2335  =item codedString  =item tkey
2336    
2337  String to un-escape.  The tracing key. This is used to identify the control file and the trace file.
2338    
2339  =item RETURN  =item hours
2340    
2341  Returns a copy of the original string with the escape sequences converted to their actual  Number of hours to keep emergency tracing alive.
2342  values.  
2343    =item dest
2344    
2345    Tracing destination. If no path information is specified for a file
2346    destination, it is put in the FIG temporary directory.
2347    
2348    =item level
2349    
2350    Tracing level. A higher level means more trace messages.
2351    
2352    =item modules
2353    
2354    A list of the tracing modules to activate.
2355    
2356  =back  =back
2357    
2358  =cut  =cut
2359    
2360  sub UnEscape {  sub Emergency {
2361          # Get the parameter.      # Get the parameters.
2362          my ($codedString) = @_;      my ($tkey, $hours, $dest, $level, @modules) = @_;
2363          # Initialize the return variable.      # Create the emergency file.
2364          my $retVal = "";      my $specFile = EmergencyFileName($tkey);
2365          # Only proceed if the incoming string is nonempty.      my $outHandle = Open(undef, ">$specFile");
2366          if (defined $codedString) {      print $outHandle join("\n", $hours, $dest, $level, @modules, "");
                 # Loop through the parameter string, looking for escape sequences. We can't do  
                 # translating because it causes problems with the escaped slash. ("\\b" becomes  
                 # "\ " no matter what we do.)  
                 while (length $codedString > 0) {  
                         # Look for the first escape sequence.  
                         if ($codedString =~ /^(.*?)\\(\\|b|n|t)/) {  
                                 # Here we found it. The text preceding the sequence is in $1. The sequence  
                                 # itself is in $2. First, move the clear text to the return variable.  
                                 $retVal .= $1;  
                                 $codedString = substr $codedString, (2 + length $1);  
                                 # Decode the escape sequence.  
                                 my $char = $2;  
                                 $char =~ tr/\\btn/\\ \t\n/;  
                                 $retVal .= $char;  
                         } else {  
                                 # Here there are no more escape sequences. The rest of the string is  
                                 # transferred unmodified.  
                                 $retVal .= $codedString;  
                                 $codedString = "";  
                         }  
                 }  
         }  
         # Return the result.  
         return $retVal;  
2367  }  }
2368    
2369  =head3 ParseRecord  =head3 EmergencyKey
2370    
2371  C<< my @fields = Tracer::ParseRecord($line); >>  C<< my $tkey = EmergencyKey($parameter); >>
2372    
2373  Parse a tab-delimited data line. The data line is split into field values. Embedded tab  Return the Key to be used for emergency tracing. This could be an IP address,
2374  and new-line characters in the data line must be represented as C<\t> and C<\n>, respectively.   a session ID, or a user name, depending on the environment.
 These will automatically be converted.  
2375    
2376  =over 4  =over 4
2377    
2378  =item line  =item parameter
2379    
2380  Line of data containing the tab-delimited fields.  Parameter defining the method for finding the tracing key. If it is a scalar,
2381    then it is presumed to be the tracing key itself. If it is a CGI object, then
2382    the tracing key is taken from the C<IP> cookie. Otherwise, the tracing key is
2383    taken from the C<TRACING> environment variable.
2384    
2385  =item RETURN  =item RETURN
2386    
2387  Returns a list of the fields found in the data line.  Returns the key to be used for labels in emergency tracing.
2388    
2389  =back  =back
2390    
2391  =cut  =cut
2392    
2393  sub ParseRecord {  sub EmergencyKey {
2394          # Get the parameter.      # Get the parameters.
2395          my ($line) = @_;      my ($parameter) = @_;
2396          # Remove the trailing new-line, if any.      # Declare the return variable.
2397          chomp $line;      my $retVal;
2398          # Split the line read into pieces using the tab character.      # Determine the parameter type.
2399          my @retVal = split /\t/, $line;      if (! defined $parameter) {
2400          # Trim and fix the escapes in each piece.          # Here we're supposed to check the environment.
2401          for my $value (@retVal) {          $retVal = $ENV{TRACING};
2402                  # Trim leading whitespace.      } else {
2403                  $value =~ s/^\s+//;          my $ptype = ref $parameter;
2404                  # Trim trailing whitespace.          if ($ptype eq 'CGI') {
2405                  $value =~ s/\s+$//;              # Here we were invoked from a web page. Look for a cookie.
2406                  # Delete the carriage returns.              $retVal = $parameter->cookie('IP');
2407                  $value =~ s/\r//g;          } elsif (! $ptype) {
2408                  # Convert the escapes into their real values.              # Here the key was passed in.
2409                  $value =~ s/\\t/"\t"/ge;              $retVal = $parameter;
2410                  $value =~ s/\\n/"\n"/ge;          }
2411        }
2412        # If no luck finding a key, use the PID.
2413        if (! defined $retVal) {
2414            $retVal = $$;
2415          }          }
2416          # Return the result.          # Return the result.
2417          return @retVal;      return $retVal;
2418  }  }
2419    
 =head3 Merge  
   
 C<< my @mergedList = Tracer::Merge(@inputList); >>  
2420    
2421  Sort a list of strings and remove duplicates.  =head3 TraceParms
2422    
2423  =over 4  C<< Tracer::TraceParms($cgi); >>
2424    
2425  =item inputList  Trace the CGI parameters at trace level CGI => 3 and the environment variables
2426    at level CGI => 4.
2427    
2428  List of scalars to sort and merge.  =over 4
2429    
2430  =item RETURN  =item cgi
2431    
2432  Returns a list containing the same elements sorted in ascending order with duplicates  CGI query object containing the parameters to trace.
 removed.  
2433    
2434  =back  =back
2435    
2436  =cut  =cut
2437    
2438  sub Merge {  sub TraceParms {
2439          # Get the input list in sort order.      # Get the parameters.
2440          my @inputList = sort @_;      my ($cgi) = @_;
2441          # Only proceed if the list has at least two elements.      if (T(CGI => 3)) {
2442          if (@inputList > 1) {          # Here we want to trace the parameter data.
2443                  # Now we want to move through the list splicing out duplicates.          my @names = $cgi->param;
2444                  my $i = 0;          for my $parmName (sort @names) {
2445                  while ($i < @inputList) {              # Note we skip the Trace parameters, which are for our use only.
2446                          # Get the current entry.              if ($parmName ne 'Trace' && $parmName ne 'TF') {
2447                          my $thisEntry = $inputList[$i];                  my @values = $cgi->param($parmName);
2448                          # Find out how many elements duplicate the current entry.                  Trace("CGI: $parmName = " . join(", ", @values));
                         my $j = $i + 1;  
                         my $dup1 = $i + 1;  
                         while ($j < @inputList && $inputList[$j] eq $thisEntry) { $j++; };  
                         # If the number is nonzero, splice out the duplicates found.  
                         if ($j > $dup1) {  
                                 splice @inputList, $dup1, $j - $dup1;  
2449                          }                          }
2450                          # Now the element at position $dup1 is different from the element before it          }
2451                          # at position $i. We push $i forward one position and start again.          # Display the request method.
2452                          $i++;          my $method = $cgi->request_method();
2453            Trace("Method: $method");
2454        }
2455        if (T(CGI => 4)) {
2456            # Here we want the environment data too.
2457            for my $envName (sort keys %ENV) {
2458                Trace("ENV: $envName = $ENV{$envName}");
2459                  }                  }
2460          }          }
         # Return the merged list.  
         return @inputList;  
2461  }  }
2462    
2463  =head3 GetFile  =head3 ScriptFinish
2464    
2465  C<< my @fileContents = Tracer::GetFile($fileName); >>  C<< ScriptFinish($webData, $varHash); >>
2466    
2467    Output a web page at the end of a script. Either the string to be output or the
2468    name of a template file can be specified. If the second parameter is omitted,
2469    it is assumed we have a string to be output; otherwise, it is assumed we have the
2470    name of a template file. The template should have the variable C<DebugData>
2471    specified in any form that invokes a standard script. If debugging mode is turned
2472    on, a form field will be put in that allows the user to enter tracing data.
2473    Trace messages will be placed immediately before the terminal C<BODY> tag in
2474    the output, formatted as a list.
2475    
2476    A typical standard script would loook like the following.
2477    
2478        BEGIN {
2479            # Print the HTML header.
2480            print "CONTENT-TYPE: text/html\n\n";
2481        }
2482        use Tracer;
2483        use CGI;
2484        use FIG;
2485        # ... more uses ...
2486    
2487        my ($cgi, $varHash) = ScriptSetup();
2488        eval {
2489            # ... get data from $cgi, put it in $varHash ...
2490        };
2491        if ($@) {
2492            Trace("Script Error: $@") if T(0);
2493        }
2494        ScriptFinish("Html/MyTemplate.html", $varHash);
2495    
2496  Return the entire contents of a file.  The idea here is that even if the script fails, you'll see trace messages and
2497    useful output.
2498    
2499  =over 4  =over 4
2500    
2501  =item fileName  =item webData
2502    
2503  Name of the file to read.  A string containing either the full web page to be written to the output or the
2504    name of a template file from which the page is to be constructed. If the name
2505    of a template file is specified, then the second parameter must be present;
2506    otherwise, it must be absent.
2507    
2508  =item RETURN  =item varHash (optional)
2509    
2510  In a list context, returns the entire file as a list with the line terminators removed.  If specified, then a reference to a hash mapping variable names for a template
2511  In a scalar context, returns the entire file as a string.  to their values. The template file will be read into memory, and variable markers
2512    will be replaced by data in this hash reference.
2513    
2514  =back  =back
2515    
2516  =cut  =cut
2517    
2518  sub GetFile {  sub ScriptFinish {
2519          # Get the parameters.          # Get the parameters.
2520          my ($fileName) = @_;      my ($webData, $varHash) = @_;
2521          # Declare the return variable.      # Check for a template file situation.
2522          my @retVal = ();      my $outputString;
2523          # Open the file for input.      if (defined $varHash) {
2524          my $ok = open INPUTFILE, "<$fileName";          # Here we have a template file. We need to determine the template type.
2525          if (!$ok) {          my $template;
2526                  # If we had an error, trace it. We will automatically return a null value.          if ($FIG_Config::template_url && $webData =~ /\.php$/) {
2527                  Trace("Could not open \"$fileName\" for input.") if T(0);              $template = "$FIG_Config::template_url/$webData";
2528          } else {          } else {
2529                  # Read the whole file into the return variable, stripping off any terminator              $template = "<<$webData";
         # characters.  
         my $lineCount = 0;  
                 while (my $line = <INPUTFILE>) {  
             $lineCount++;  
             $line = Strip($line);  
                         push @retVal, $line;  
2530                  }                  }
2531                  # Close it.          $outputString = PageBuilder::Build($template, $varHash, "Html");
2532                  close INPUTFILE;      } else {
2533          my $actualLines = @retVal;          # Here the user gave us a raw string.
2534          Trace("$lineCount lines read from $fileName. $actualLines processed.") if T(3);          $outputString = $webData;
2535          }          }
2536          # Return the file's contents in the desired format.      # Check for trace messages.
2537      if (wantarray) {      if ($Destination ne "NONE" && $TraceLevel > 0) {
2538              return @retVal;          # We have trace messages, so we want to put them at the end of the body. This
2539            # is either at the end of the whole string or at the beginning of the BODY
2540            # end-tag.
2541            my $pos = length $outputString;
2542            if ($outputString =~ m#</body>#gi) {
2543                $pos = (pos $outputString) - 7;
2544            }
2545            # If the trace messages were queued, we unroll them. Otherwise, we display the
2546            # destination.
2547            my $traceHtml;
2548            if ($Destination eq "QUEUE") {
2549                $traceHtml = QTrace('Html');
2550            } elsif ($Destination =~ /^>>(.+)$/) {
2551                # Here the tracing output it to a file. We code it as a hyperlink so the user
2552                # can copy the file name into the clipboard easily.
2553                my $actualDest = $1;
2554                $traceHtml = "<p>Tracing output to $actualDest.</p>\n";
2555      } else {      } else {
2556          return join "\n", @retVal;              # Here we have one of the special destinations.
2557                $traceHtml = "<P>Tracing output type is $Destination.</p>\n";
2558            }
2559            substr $outputString, $pos, 0, $traceHtml;
2560      }      }
2561        # Write the output string.
2562        print $outputString;
2563  }  }
2564    
2565  =head3 QTrace  =head3 Insure
2566    
2567  C<< my $data = QTrace($format); >>  C<< Insure($dirName); >>
2568    
2569  Return the queued trace data in the specified format.  Insure a directory is present.
2570    
2571  =over 4  =over 4
2572    
2573  =item format  =item dirName
2574    
2575  C<html> to format the data as an HTML list, C<text> to format it as straight text.  Name of the directory to check. If it does not exist, it will be created.
2576    
2577  =back  =back
2578    
2579  =cut  =cut
2580    
2581  sub QTrace {  sub Insure {
2582          # Get the parameter.      my ($dirName) = @_;
2583          my ($format) = @_;      if (! -d $dirName) {
2584          # Create the return variable.          Trace("Creating $dirName directory.") if T(2);
2585          my $retVal = "";          eval { mkpath $dirName; };
2586          # Process according to the format.          if ($@) {
2587          if ($format =~ m/^HTML$/i) {              Confess("Error creating $dirName: $@");
                 # Convert the queue into an HTML list.  
                 $retVal = "<ul>\n";  
                 for my $line (@Queue) {  
                         my $escapedLine = CGI::escapeHTML($line);  
                         $retVal .= "<li>$escapedLine</li>\n";  
2588                  }                  }
                 $retVal .= "</ul>\n";  
         } elsif ($format =~ m/^TEXT$/i) {  
                 # Convert the queue into a list of text lines.  
                 $retVal = join("\n", @Queue) . "\n";  
2589          }          }
         # Clear the queue.  
         @Queue = ();  
         # Return the formatted list.  
         return $retVal;  
2590  }  }
2591    
2592  =head3 Confess  =head3 ChDir
   
 C<< Confess($message); >>  
   
 Trace the call stack and abort the program with the specified message. The stack  
 trace will only appear if the trace level for this package is 1 or more. When used with  
 the OR operator and the L</Assert> method, B<Confess> can function as a debugging assert.  
 So, for example  
2593    
2594  C<< Assert($recNum >= 0) || Confess("Invalid record number $recNum."); >>  C<< ChDir($dirName); >>
2595    
2596  Will abort the program with a stack trace if the value of C<$recNum> is negative.  Change to the specified directory.
2597    
2598  =over 4  =over 4
2599    
2600  =item message  =item dirName
2601    
2602  Message to include in the trace.  Name of the directory to which we want to change.
2603    
2604  =back  =back
2605    
2606  =cut  =cut
2607    
2608  sub Confess {  sub ChDir {
2609          # Get the parameters.      my ($dirName) = @_;
2610          my ($message) = @_;      if (! -d $dirName) {
2611          # Trace the call stack.          Confess("Cannot change to directory $dirName: no such directory.");
2612          Cluck($message) if T(1);      } else {
2613          # Abort the program.          Trace("Changing to directory $dirName.") if T(4);
2614          croak(">>> $message");          my $okFlag = chdir $dirName;
2615            if (! $okFlag) {
2616                Confess("Error switching to directory $dirName.");
2617            }
2618        }
2619  }  }
2620    
2621  =head3 Assert  =head3 SendSMS
   
 C<< Assert($condition1, $condition2, ... $conditionN); >>  
2622    
2623  Return TRUE if all the conditions are true. This method can be used in conjunction with  C<< my $msgID = Tracer::SendSMS($phoneNumber, $msg); >>
 the OR operator and the L</Confess> method, B<Assert> can function as a debugging assert.  
 So, for example  
2624    
2625  C<< Assert($recNum >= 0) || Confess("Invalid record number $recNum."); >>  Send a text message to a phone number using Clickatell. The FIG_Config file must contain the
2626    user name, password, and API ID for the relevant account in the hash reference variable
2627    I<$FIG_Config::phone>, using the keys C<user>, C<password>, and C<api_id>. For
2628    example, if the user name is C<BruceTheHumanPet>, the password is C<silly>, and the API ID
2629    is C<2561022>, then the FIG_Config file must contain
2630    
2631  Will abort the program with a stack trace if the value of C<$recNum> is negative.      $phone =  { user => 'BruceTheHumanPet',
2632                    password => 'silly',
2633                    api_id => '2561022' };
2634    
2635  =cut  The original purpose of this method was to insure Bruce would be notified immediately when the
2636  sub Assert {  Sprout Load terminates. Care should be taken if you do not wish Bruce to be notified immediately
2637      my $retVal = 1;  when you call this method.
     LOOP: for my $condition (@_) {  
         if (! $condition) {  
             $retVal = 0;  
             last LOOP;  
         }  
     }  
     return $retVal;  
 }  
2638    
2639  =head3 Cluck  The message ID will be returned if successful, and C<undef> if an error occurs.
2640    
2641  C<< Cluck($message); >>  =over 4
2642    
2643  Trace the call stack. Note that for best results, you should qualify the call with a  =item phoneNumber
 trace condition. For example,  
2644    
2645  C<< Cluck("Starting record parse.") if T(3); >>  Phone number to receive the message, in international format. A United States phone number
2646    would be prefixed by "1". A British phone number would be prefixed by "44".
2647    
2648  will only trace the stack if the trace level for the package is 3 or more.  =item msg
2649    
2650  =over 4  Message to send to the specified phone.
2651    
2652  =item message  =item RETURN
2653    
2654  Message to include in the trace.  Returns the message ID if successful, and C<undef> if the message could not be sent.
2655    
2656  =back  =back
2657    
2658  =cut  =cut
2659    
2660  sub Cluck {  sub SendSMS {
2661          # Get the parameters.          # Get the parameters.
2662          my ($message) = @_;      my ($phoneNumber, $msg) = @_;
2663      # Trace what's happening.      # Declare the return variable. If we do not change it, C<undef> will be returned.
2664      Trace("Stack trace for event: $message");      my $retVal;
2665          my $confession = longmess($message);      # Only proceed if we have phone support.
2666          # Convert the confession to a series of trace messages. Note we skip any      if (! defined $FIG_Config::phone) {
2667      # messages relating to calls into Tracer.          Trace("Phone support not present in FIG_Config.") if T(1);
2668          for my $line (split /\s*\n/, $confession) {      } else {
2669                  Trace($line) if ($line !~ /Tracer\.pm/);          # Get the phone data.
2670            my $parms = $FIG_Config::phone;
2671            # Get the Clickatell URL.
2672            my $url = "http://api.clickatell.com/http/";
2673            # Create the user agent.
2674            my $ua = LWP::UserAgent->new;
2675            # Request a Clickatell session.
2676            my $resp = $ua->post("$url/sendmsg", { user => $parms->{user},
2677                                         password => $parms->{password},
2678                                         api_id => $parms->{api_id},
2679                                         to => $phoneNumber,
2680                                         text => $msg});
2681            # Check for an error.
2682            if (! $resp->is_success) {
2683                Trace("Alert failed.") if T(1);
2684            } else {
2685                # Get the message ID.
2686                my $rstring = $resp->content;
2687                if ($rstring =~ /^ID:\s+(.*)$/) {
2688                    $retVal = $1;
2689                } else {
2690                    Trace("Phone attempt failed with $rstring") if T(1);
2691                }
2692            }
2693          }          }
2694        # Return the result.
2695        return $retVal;
2696  }  }
2697    
2698  =head3 Min  =head3 CommaFormat
2699    
2700  C<< my $min = Min($value1, $value2, ... $valueN); >>  C<< my $formatted = Tracer::CommaFormat($number); >>
2701    
2702  Return the minimum argument. The arguments are treated as numbers.  Insert commas into a number.
2703    
2704  =over 4  =over 4
2705    
2706  =item $value1, $value2, ... $valueN  =item number
2707    
2708  List of numbers to compare.  A sequence of digits.
2709    
2710  =item RETURN  =item RETURN
2711    
2712  Returns the lowest number in the list.  Returns the same digits with commas strategically inserted.
2713    
2714  =back  =back
2715    
2716  =cut  =cut
2717    
2718  sub Min {  sub CommaFormat {
2719          # Get the parameters. Note that we prime the return value with the first parameter.      # Get the parameters.
2720          my ($retVal, @values) = @_;      my ($number) = @_;
2721          # Loop through the remaining parameters, looking for the lowest.      # Pad the length up to a multiple of three.
2722          for my $value (@values) {      my $padded = "$number";
2723                  if ($value < $retVal) {      $padded = " " . $padded while length($padded) % 3 != 0;
2724                          $retVal = $value;      # This is a fancy PERL trick. The parentheses in the SPLIT pattern
2725                  }      # cause the delimiters to be included in the output stream. The
2726          }      # GREP removes the empty strings in between the delimiters.
2727          # Return the minimum found.      my $retVal = join(",", grep { $_ ne '' } split(/(...)/, $padded));
2728        # Clean out the spaces.
2729        $retVal =~ s/ //g;
2730        # Return the result.
2731          return $retVal;          return $retVal;
2732  }  }
2733    =head3 SetPermissions
2734    
2735  =head3 Max  C<< Tracer::SetPermissions($dirName, $group, $mask, %otherMasks); >>
2736    
2737  C<< my $max = Max($value1, $value2, ... $valueN); >>  Set the permissions for a directory and all the files and folders inside it.
2738    In addition, the group ownership will be changed to the specified value.
2739    
2740  Return the maximum argument. The arguments are treated as numbers.  This method is more vulnerable than most to permission and compatability
2741    problems, so it does internal error recovery.
2742    
2743  =over 4  =over 4
2744    
2745  =item $value1, $value2, ... $valueN  =item dirName
2746    
2747  List of numbers to compare.  Name of the directory to process.
2748    
2749  =item RETURN  =item group
2750    
2751  Returns the highest number in the list.  Name of the group to be assigned.
2752    
2753    =item mask
2754    
2755    Permission mask. Bits that are C<1> in this mask will be ORed into the
2756    permission bits of any file or directory that does not already have them
2757    set to 1.
2758    
2759    =item otherMasks
2760    
2761    Map of search patterns to permission masks. If a directory name matches
2762    one of the patterns, that directory and all its members and subdirectories
2763    will be assigned the new pattern. For example, the following would
2764    assign 01664 to most files, but would use 01777 for directories named C<tmp>.
2765    
2766        Tracer::SetPermissions($dirName, 'fig', 01664, '^tmp$' => 01777);
2767    
2768    The list is ordered, so the following would use 0777 for C<tmp1> and
2769    0666 for C<tmp>, C<tmp2>, or C<tmp3>.
2770    
2771        Tracer::SetPermissions($dirName, 'fig', 01664, '^tmp1' => 0777,
2772                                                       '^tmp' => 0666);
2773    
2774    Note that the pattern matches are all case-insensitive, and only directory
2775    names are matched, not file names.
2776    
2777  =back  =back
2778    
2779  =cut  =cut
2780    
2781  sub Max {  sub SetPermissions {
2782          # Get the parameters. Note that we prime the return value with the first parameter.      # Get the parameters.
2783          my ($retVal, @values) = @_;      my ($dirName, $group, $mask, @otherMasks) = @_;
2784          # Loop through the remaining parameters, looking for the highest.      # Set up for error recovery.
2785          for my $value (@values) {      eval {
2786                  if ($value > $retVal) {          # Switch to the specified directory.
2787                          $retVal = $value;          ChDir($dirName);
2788            # Get the group ID.
2789            my $gid = getgrnam($group);
2790            # Get the mask for tracing.
2791            my $traceMask = sprintf("%04o", $mask) . "($mask)";
2792            Trace("Fixing permissions for directory $dirName using group $group($gid) and mask $traceMask.") if T(2);
2793            my $fixCount = 0;
2794            my $lookCount = 0;
2795            # @dirs will be a stack of directories to be processed.
2796            my @dirs = (getcwd());
2797            while (scalar(@dirs) > 0) {
2798                # Get the current directory.
2799                my $dir = pop @dirs;
2800                # Check for a match to one of the specified directory names. To do
2801                # that, we need to pull the individual part of the name off of the
2802                # whole path.
2803                my $simpleName = $dir;
2804                if ($dir =~ m!/([^/]+)$!) {
2805                    $simpleName = $1;
2806                }
2807                Trace("Simple directory name for $dir is $simpleName.") if T(4);
2808                # Search for a match.
2809                my $match = 0;
2810                my $i;
2811                for ($i = 0; $i < $#otherMasks && ! $match; $i += 2) {
2812                    my $pattern = $otherMasks[$i];
2813                    if ($simpleName =~ /$pattern/i) {
2814                        $match = 1;
2815                    }
2816                }
2817                # Check for a match. Note we use $i-1 because the loop added 2
2818                # before terminating due to the match.
2819                if ($match && $otherMasks[$i-1] != $mask) {
2820                    # This directory matches one of the incoming patterns, and it's
2821                    # a different mask, so we process it recursively with that mask.
2822                    SetPermissions($dir, $group, $otherMasks[$i-1], @otherMasks);
2823                } else {
2824                    # Here we can process normally. Get all of the non-hidden members.
2825                    my @submems = OpenDir($dir, 1);
2826                    for my $submem (@submems) {
2827                        # Get the full name.
2828                        my $thisMem = "$dir/$submem";
2829                        Trace("Checking member $thisMem.") if T(4);
2830                        $lookCount++;
2831                        if ($lookCount % 1000 == 0) {
2832                            Trace("$lookCount members examined. Current is $thisMem. Mask is $traceMask") if T(3);
2833                        }
2834                        # Fix the group.
2835                        chown -1, $gid, $thisMem;
2836                        # Insure this member is not a symlink.
2837                        if (! -l $thisMem) {
2838                            # Get its info.
2839                            my $fileInfo = stat $thisMem;
2840                            # Only proceed if we got the info. Otherwise, it's a hard link
2841                            # and we want to skip it anyway.
2842                            if ($fileInfo) {
2843                                my $fileMode = $fileInfo->mode;
2844                                if (($fileMode & $mask) != $mask) {
2845                                    # Fix this member.
2846                                    $fileMode |= $mask;
2847                                    chmod $fileMode, $thisMem;
2848                                    $fixCount++;
2849                                }
2850                                # If it's a subdirectory, stack it.
2851                                if (-d $thisMem) {
2852                                    push @dirs, $thisMem;
2853                  }                  }
2854          }          }
2855          # Return the maximum found.                      }
2856          return $retVal;                  }
2857                }
2858            }
2859            Trace("$lookCount files and directories processed, $fixCount fixed.") if T(2);
2860        };
2861        # Check for an error.
2862        if ($@) {
2863            Confess("SetPermissions error: $@");
2864        }
2865  }  }
2866    
2867  =head3 AddToListMap  =head3 CompareLists
2868    
2869  C<< Tracer::AddToListMap(\%hash, $key, $value); >>  C<< my ($inserted, $deleted) = Tracer::CompareLists(\@newList, \@oldList, $keyIndex); >>
2870    
2871  Add a key-value pair to a hash of lists. If no value exists for the key, a singleton list  Compare two lists of tuples, and return a hash analyzing the differences. The lists
2872  is created for the key. Otherwise, the new value is pushed onto the list.  are presumed to be sorted alphabetically by the value in the $keyIndex column.
2873    The return value contains a list of items that are only in the new list
2874    (inserted) and only in the old list (deleted).
2875    
2876  =over 4  =over 4
2877    
2878  =item hash  =item newList
2879    
2880  Reference to the target hash.  Reference to a list of new tuples.
2881    
2882  =item key  =item oldList
2883    
2884  Key for which the value is to be added.  Reference to a list of old tuples.
2885    
2886  =item value  =item keyIndex (optional)
2887    
2888  Value to add to the key's value list.  Index into each tuple of its key field. The default is 0.
2889    
2890    =item RETURN
2891    
2892    Returns a 2-tuple consisting of a reference to the list of items that are only in the new
2893    list (inserted) followed by a reference to the list of items that are only in the old
2894    list (deleted).
2895    
2896  =back  =back
2897    
2898  =cut  =cut
2899    
2900  sub AddToListMap {  sub CompareLists {
2901      # Get the parameters.      # Get the parameters.
2902      my ($hash, $key, $value) = @_;      my ($newList, $oldList, $keyIndex) = @_;
2903      # Process according to whether or not the key already has a value.      if (! defined $keyIndex) {
2904      if (! exists $hash->{$key}) {          $keyIndex = 0;
2905          $hash->{$key} = [$value];      }
2906        # Declare the return variables.
2907        my ($inserted, $deleted) = ([], []);
2908        # Loop through the two lists simultaneously.
2909        my ($newI, $oldI) = (0, 0);
2910        my ($newN, $oldN) = (scalar @{$newList}, scalar @{$oldList});
2911        while ($newI < $newN || $oldI < $oldN) {
2912            # Get the current object in each list. Note that if one
2913            # of the lists is past the end, we'll get undef.
2914            my $newItem = $newList->[$newI];
2915            my $oldItem = $oldList->[$oldI];
2916            if (! defined($newItem) || defined($oldItem) && $newItem->[$keyIndex] gt $oldItem->[$keyIndex]) {
2917                # The old item is not in the new list, so mark it deleted.
2918                push @{$deleted}, $oldItem;
2919                $oldI++;
2920            } elsif (! defined($oldItem) || $oldItem->[$keyIndex] gt $newItem->[$keyIndex]) {
2921                # The new item is not in the old list, so mark it inserted.
2922                push @{$inserted}, $newItem;
2923                $newI++;
2924      } else {      } else {
2925          push @{$hash->{$key}}, $value;              # The item is in both lists, so push forward.
2926                $oldI++;
2927                $newI++;
2928      }      }
2929  }  }
2930        # Return the result.
2931        return ($inserted, $deleted);
2932    }
2933    
2934  =head3 DebugMode  =head3 GetLine
2935    
2936  C<< if (Tracer::DebugMode) { ...code... } >>  C<< my @data = Tracer::GetLine($handle); >>
2937    
2938  Return TRUE if debug mode has been turned on in FIG_Config, else output  Read a line of data from a tab-delimited file.
 an error page and return FALSE.  
2939    
2940  Certain CGI scripts are too dangerous to exist in the production  =over 4
2941  environment. This method provides a simple way to prevent them  
2942  from working unless they are explicitly turned on in the configuration  =item handle
2943  file by setting C<$FIG_Config::debug_mode> to 1. If debugging mode  
2944  is not turned on, an error web page will be output.  Open file handle from which to read.
2945    
2946    =item RETURN
2947    
2948    Returns a list of the fields in the record read. The fields are presumed to be
2949    tab-delimited. If we are at the end of the file, then an empty list will be
2950    returned. If an empty line is read, a single list item consisting of a null
2951    string will be returned.
2952    
2953    =back
2954    
2955  =cut  =cut
2956    
2957  sub DebugMode {  sub GetLine {
2958        # Get the parameters.
2959        my ($handle) = @_;
2960          # Declare the return variable.          # Declare the return variable.
2961          my $retVal;      my @retVal = ();
2962          # Check the debug configuration.      # Read from the file.
2963          if ($FIG_Config::debug_mode) {      my $line = <$handle>;
2964                  $retVal = 1;      # Only proceed if we found something.
2965        if (defined $line) {
2966            # Remove the new-line.
2967            chomp $line;
2968            # If the line is empty, return a single empty string; otherwise, parse
2969            # it into fields.
2970            if ($line eq "") {
2971                push @retVal, "";
2972          } else {          } else {
2973                  # Here debug mode is off, so we generate an error page.              push @retVal, split /\t/,$line;
         my $pageString = PageBuilder::Build("<Html/ErrorPage.html", {}, "Html");  
                 print $pageString;  
2974          }          }
2975          # Return the determination indicator.      }
2976          return $retVal;      # Return the result.
2977        return @retVal;
2978  }  }
2979    
2980  =head3 Strip  =head3 PutLine
2981    
2982  C<< my $string = Tracer::Strip($line); >>  C<< Tracer::PutLine($handle, \@fields); >>
2983    
2984  Strip all line terminators off a string. This is necessary when dealing with files  Write a line of data to a tab-delimited file. The specified field values will be
2985  that may have been transferred back and forth several times among different  output in tab-separated form, with a trailing new-line.
 operating environments.  
2986    
2987  =over 4  =over 4
2988    
2989  =item line  =item handle
2990    
2991  Line of text to be stripped.  Output file handle.
2992    
2993  =item RETURN  =item fields
2994    
2995  The same line of text with all the line-ending characters chopped from the end.  List of field values.
2996    
2997  =back  =back
2998    
2999  =cut  =cut
3000    
3001  sub Strip {  sub PutLine {
3002          # Get a copy of the parameter string.      # Get the parameters.
3003          my ($string) = @_;      my ($handle, $fields) = @_;
3004          my $retVal = $string;      # Write the data.
3005      # Strip the line terminator characters.      print $handle join("\t", @{$fields}) . "\n";
     $retVal =~ s/(\r|\n)+$//g;  
         # Return the result.  
         return $retVal;  
3006  }  }
3007    
3008  =head3 Pad  =head3 GenerateURL
3009    
3010  C<< my $paddedString = Tracer::Pad($string, $len, $left, $padChar); >>  C<< my $queryUrl = Tracer::GenerateURL($page, %parameters); >>
3011    
3012  Pad a string to a specified length. The pad character will be a  Generate a GET-style URL for the specified page with the specified parameter
3013  space, and the padding will be on the right side unless specified  names and values. The values will be URL-escaped automatically. So, for
3014  in the third parameter.  example
3015    
3016  =over 4      Tracer::GenerateURL("form.cgi", type => 1, string => "\"high pass\" or highway")
3017    
3018  =item string  would return
3019    
3020  String to be padded.      form.cgi?type=1&string=%22high%20pass%22%20or%20highway
3021    
3022  =item len  =over 4
3023    
3024  Desired length of the padded string.  =item page
3025    
3026  =item left (optional)  Page URL.
3027    
3028  TRUE if the string is to be left-padded; otherwise it will be padded on the right.  =item parameters
3029    
3030  =item padChar (optional)  Hash mapping parameter names to parameter values.
3031    
3032  =item RETURN  =item RETURN
3033    
3034  Returns a copy of the original string with the spaces added to the specified end so  Returns a GET-style URL that goes to the specified page and passes in the
3035  that it achieves the desired length.  specified parameters and values.
3036    
3037  =back  =back
3038    
3039  =cut  =cut
3040    
3041  sub Pad {  sub GenerateURL {
3042          # Get the parameters.          # Get the parameters.
3043          my ($string, $len, $left, $padChar) = @_;      my ($page, %parameters) = @_;
3044          # Compute the padding character.      # Prime the return variable with the page URL.
3045          if (! defined $padChar) {      my $retVal = $page;
3046                  $padChar = " ";      # Loop through the parameters, creating parameter elements in a list.
3047          }      my @parmList = map { "$_=" . uri_escape($parameters{$_}) } keys %parameters;
3048          # Compute the number of spaces needed.      # If the list is nonempty, tack it on.
3049          my $needed = $len - length $string;      if (@parmList) {
3050          # Copy the string into the return variable.          $retVal .= "?" . join("&", @parmList);
         my $retVal = $string;  
         # Only proceed if padding is needed.  
         if ($needed > 0) {  
                 # Create the pad string.  
                 my $pad = $padChar x $needed;  
                 # Affix it to the return value.  
                 if ($left) {  
                         $retVal = $pad . $retVal;  
                 } else {  
                         $retVal .= $pad;  
                 }  
3051          }          }
3052          # Return the result.          # Return the result.
3053          return $retVal;          return $retVal;

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