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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. Note we need to convert the day, month,
963            # and year to a different base. Years count from 1900, and
964            # the internal month value is relocated to January = 0.
965            $retVal = timelocal($6, $5, $4, $2, $1 - 1, $3 - 1900);
966        }
967        # Return the result.
968        return $retVal;
969    }
970    
971    =head3 LogErrors
972    
973    C<< Tracer::LogErrors($fileName); >>
974    
975    Route the standard error output to a log file.
976    
977    =over 4
978    
979    =item fileName
980    
981    Name of the file to receive the error output.
982    
983    =back
984    
985    =cut
986    
987    sub LogErrors {
988        # Get the file name.
989        my ($fileName) = @_;
990        # Open the file as the standard error output.
991        open STDERR, '>', $fileName;
992    }
993    
994    =head3 ReadOptions
995    
996    C<< my %options = Tracer::ReadOptions($fileName); >>
997    
998    Read a set of options from a file. Each option is encoded in a line of text that has the
999    format
1000    
1001    I<optionName>C<=>I<optionValue>C<; >I<comment>
1002    
1003    The option name must consist entirely of letters, digits, and the punctuation characters
1004    C<.> and C<_>, and is case sensitive. Blank lines and lines in which the first nonblank
1005    character is a semi-colon will be ignored. The return hash will map each option name to
1006    the corresponding option value.
1007    
1008    =over 4
1009    
1010    =item fileName
1011    
1012    Name of the file containing the option data.
1013    
1014    =item RETURN
1015    
1016    Returns a hash mapping the option names specified in the file to their corresponding option
1017    value.
1018    
1019    =back
1020    
1021    =cut
1022    
1023    sub ReadOptions {
1024        # Get the parameters.
1025        my ($fileName) = @_;
1026        # Open the file.
1027        (open CONFIGFILE, "<$fileName") || Confess("Could not open option file $fileName.");
1028        # Count the number of records read.
1029        my ($records, $comments) = 0;
1030        # Create the return hash.
1031        my %retVal = ();
1032        # Loop through the file, accumulating key-value pairs.
1033        while (my $line = <CONFIGFILE>) {
1034            # Denote we've read a line.
1035            $records++;
1036            # Determine the line type.
1037            if ($line =~ /^\s*[\n\r]/) {
1038                # A blank line is a comment.
1039                $comments++;
1040            } elsif ($line =~ /^\s*([A-Za-z0-9_\.]+)=([^;]*);/) {
1041                # Here we have an option assignment.
1042                retVal{$1} = $2;
1043            } elsif ($line =~ /^\s*;/) {
1044                # Here we have a text comment.
1045                $comments++;
1046            } else {
1047                # Here we have an invalid line.
1048                Trace("Invalid option statement in record $records.") if T(0);
1049            }
1050        }
1051        # Return the hash created.
1052        return %retVal;
1053    }
1054    
1055    =head3 GetOptions
1056    
1057    C<< Tracer::GetOptions(\%defaults, \%options); >>
1058    
1059    Merge a specified set of options into a table of defaults. This method takes two hash references
1060    as input and uses the data from the second to update the first. If the second does not exist,
1061    there will be no effect. An error will be thrown if one of the entries in the second hash does not
1062    exist in the first.
1063    
1064    Consider the following example.
1065    
1066    C<< my $optionTable = GetOptions({ dbType => 'mySQL', trace => 0 }, $options); >>
1067    
1068    In this example, the variable B<$options> is expected to contain at most two options-- B<dbType> and
1069    B<trace>. The default database type is C<mySQL> and the default trace level is C<0>. If the value of
1070    B<$options> is C<< {dbType => 'Oracle'} >>, then the database type will be changed to C<Oracle> and
1071    the trace level will remain at 0. If B<$options> is undefined, then the database type and trace level
1072    will remain C<mySQL> and C<0>. If, on the other hand, B<$options> is defined as
1073    
1074    C<< {databaseType => 'Oracle'} >>
1075    
1076    an error will occur because the B<databaseType> option does not exist.
1077    
1078    =over 4
1079    
1080    =item defaults
1081    
1082    Table of default option values.
1083    
1084    =item options
1085    
1086    Table of overrides, if any.
1087    
1088    =item RETURN
1089    
1090    Returns a reference to the default table passed in as the first parameter.
1091    
1092    =back
1093    
1094    =cut
1095    
1096    sub GetOptions {
1097        # Get the parameters.
1098        my ($defaults, $options) = @_;
1099        # Check for overrides.
1100        if ($options) {
1101            # Loop through the overrides.
1102            while (my ($option, $setting) = each %{$options}) {
1103                # Insure this override exists.
1104                if (!exists $defaults->{$option}) {
1105                    croak "Unrecognized option $option encountered.";
1106                } else {
1107                    # Apply the override.
1108                    $defaults->{$option} = $setting;
1109                }
1110            }
1111        }
1112        # Return the merged table.
1113        return $defaults;
1114    }
1115    
1116    =head3 MergeOptions
1117    
1118    C<< Tracer::MergeOptions(\%table, \%defaults); >>
1119    
1120    Merge default values into a hash table. This method looks at the key-value pairs in the
1121    second (default) hash, and if a matching key is not found in the first hash, the default
1122    pair is copied in. The process is similar to L</GetOptions>, but there is no error-
1123    checking and no return value.
1124    
1125    =over 4
1126    
1127    =item table
1128    
1129    Hash table to be updated with the default values.
1130    
1131    =item defaults
1132    
1133    Default values to be merged into the first hash table if they are not already present.
1134    
1135    =back
1136    
1137    =cut
1138    
1139    sub MergeOptions {
1140        # Get the parameters.
1141        my ($table, $defaults) = @_;
1142        # Loop through the defaults.
1143        while (my ($key, $value) = each %{$defaults}) {
1144            if (!exists $table->{$key}) {
1145                $table->{$key} = $value;
1146            }
1147        }
1148    }
1149    
1150    =head3 Trace
1151    
1152    C<< Trace($message); >>
1153    
1154    Write a trace message to the target location specified in L</TSetup>. If there has not been
1155    any prior call to B<TSetup>.
1156    
1157    =over 4
1158    
1159    =item message
1160    
1161    Message to write.
1162    
1163    =back
1164    
1165    =cut
1166    
1167    sub Trace {
1168        # Get the parameters.
1169        my ($message) = @_;
1170        # Get the timestamp.
1171        my $timeStamp = Now();
1172        # Format the message. Note we strip off any line terminators at the end.
1173        my $formatted = "[$timeStamp] <$LastCategory>: " . Strip($message);
1174        # Process according to the destination.
1175        if ($Destination eq "TEXT") {
1176            # Write the message to the standard output.
1177            print "$formatted\n";
1178        } elsif ($Destination eq "ERROR") {
1179            # Write the message to the error output.
1180            print STDERR "$formatted\n";
1181        } elsif ($Destination eq "QUEUE") {
1182            # Push the message into the queue.
1183            push @Queue, "$formatted";
1184        } elsif ($Destination eq "HTML") {
1185            # Convert the message to HTML and write it to the standard output.
1186            my $escapedMessage = CGI::escapeHTML($message);
1187            print "<p>$formatted</p>\n";
1188        } elsif ($Destination eq "WARN") {
1189           # Emit the message as a warning.
1190           warn $message;
1191        } elsif ($Destination =~ m/^>>/) {
1192            # Write the trace message to an output file.
1193            (open TRACING, $Destination) || die "Tracing open for \"$Destination\" failed: $!";
1194            print TRACING "$formatted\n";
1195            close TRACING;
1196            # If the Tee flag is on, echo it to the standard output.
1197            if ($TeeFlag) {
1198                print "$formatted\n";
1199            }
1200        }
1201    }
1202    
1203    =head3 T
1204    
1205    C<< my $switch = T($category, $traceLevel); >>
1206    
1207        or
1208    
1209    C<< my $switch = T($traceLevel); >>
1210    
1211    Return TRUE if the trace level is at or above a specified value and the specified category
1212    is active, else FALSE. If no category is specified, the caller's package name is used.
1213    
1214    =over 4
1215    
1216    =item category
1217    
1218    Category to which the message belongs. If not specified, the caller's package name is
1219    used.
1220    
1221    =item traceLevel
1222    
1223    Relevant tracing level.
1224    
1225    =item RETURN
1226    
1227    TRUE if a message at the specified trace level would appear in the trace, else FALSE.
1228    
1229    =back
1230    
1231    =cut
1232    
1233    sub T {
1234        # Declare the return variable.
1235        my $retVal = 0;
1236        # Only proceed if tracing is turned on.
1237        if ($Destination ne "NONE") {
1238            # Get the parameters.
1239            my ($category, $traceLevel) = @_;
1240            if (!defined $traceLevel) {
1241                # Here we have no category, so we need to get the calling package.
1242                # The calling package is normally the first parameter. If it is
1243                # omitted, the first parameter will be the tracelevel. So, the
1244                # first thing we do is shift the so-called category into the
1245                # $traceLevel variable where it belongs.
1246                $traceLevel = $category;
1247                my ($package, $fileName, $line) = caller;
1248                # If there is no calling package, we default to "main".
1249                if (!$package) {
1250                    $category = "main";
1251                } else {
1252                    $category = $package;
1253                }
1254            }
1255            # Save the category name.
1256            $LastCategory = $category;
1257            # Convert it to lower case before we hash it.
1258            $category = lc $category;
1259            # Use the category and tracelevel to compute the result.
1260            if (ref $traceLevel) {
1261                Confess("Bad trace level.");
1262            } elsif (ref $TraceLevel) {
1263                Confess("Bad trace config.");
1264            }
1265            $retVal = ($traceLevel <= $TraceLevel && ($AllTrace || exists $Categories{$category}));
1266        }
1267        # Return the computed result.
1268        return $retVal;
1269    }
1270    
1271    =head3 ParseCommand
1272    
1273    C<< my ($options, @arguments) = Tracer::ParseCommand(\%optionTable, @inputList); >>
1274    
1275    Parse a command line consisting of a list of parameters. The initial parameters may be option
1276    specifiers of the form C<->I<option> or C<->I<option>C<=>I<value>. The options are stripped
1277    off and merged into a table of default options. The remainder of the command line is
1278    returned as a list of positional arguments. For example, consider the following invocation.
1279    
1280    C<< my ($options, @arguments) = ParseCommand({ errors => 0, logFile => 'trace.log'}, @words); >>
1281    
1282    In this case, the list @words will be treated as a command line. There are two options available,
1283    B<errors> and B<logFile>. If @words has the following format
1284    
1285    C<< -logFile=error.log apple orange rutabaga >>
1286    
1287    then at the end of the invocation, C<$options> will be
1288    
1289    C<< { errors => 0, logFile => 'error.log' } >>
1290    
1291    and C<@arguments> will contain
1292    
1293    C<< apple orange rutabaga >>
1294    
1295    The parser allows for some escape sequences. See L</UnEscape> for a description. There is no
1296    support for quote characters.
1297    
1298    =over 4
1299    
1300    =item optionTable
1301    
1302    Table of default options.
1303    
1304    =item inputList
1305    
1306    List of words on the command line.
1307    
1308    =item RETURN
1309    
1310    Returns a reference to the option table and a list of the positional arguments.
1311    
1312    =back
1313    
1314    =cut
1315    
1316    sub ParseCommand {
1317        # Get the parameters.
1318        my ($optionTable, @inputList) = @_;
1319        # Process any options in the input list.
1320        my %overrides = ();
1321        while ((@inputList > 0) && ($inputList[0] =~ /^-/)) {
1322            # Get the current option.
1323            my $arg = shift @inputList;
1324            # Pull out the option name.
1325            $arg =~ /^-([^=]*)/g;
1326            my $name = $1;
1327            # Check for an option value.
1328            if ($arg =~ /\G=(.*)$/g) {
1329                # Here we have a value for the option.
1330                $overrides{$name} = UnEscape($1);
1331            } else {
1332                # Here there is no value, so we use 1.
1333                $overrides{$name} = 1;
1334            }
1335        }
1336        # Merge the options into the defaults.
1337        GetOptions($optionTable, \%overrides);
1338        # Translate the remaining parameters.
1339        my @retVal = ();
1340        for my $inputParm (@inputList) {
1341            push @retVal, UnEscape($inputParm);
1342        }
1343        # Return the results.
1344        return ($optionTable, @retVal);
1345    }
1346    
1347    =head3 Escape
1348    
1349    C<< my $codedString = Tracer::Escape($realString); >>
1350    
1351    Escape a string for use in a command length. Tabs will be replaced by C<\t>, new-lines
1352    replaced by C<\n>, carriage returns will be deleted, and backslashes will be doubled. The
1353    result is to reverse the effect of L</UnEscape>.
1354    
1355    =over 4
1356    
1357    =item realString
1358    
1359    String to escape.
1360    
1361    =item RETURN
1362    
1363    Escaped equivalent of the real string.
1364    
1365    =back
1366    
1367    =cut
1368    
1369    sub Escape {
1370        # Get the parameter.
1371        my ($realString) = @_;
1372        # Initialize the return variable.
1373        my $retVal = "";
1374        # Loop through the parameter string, looking for sequences to escape.
1375        while (length $realString > 0) {
1376            # Look for the first sequence to escape.
1377            if ($realString =~ /^(.*?)([\n\t\r\\])/) {
1378                # Here we found it. The text preceding the sequence is in $1. The sequence
1379                # itself is in $2. First, move the clear text to the return variable.
1380                $retVal .= $1;
1381                # Strip the processed section off the real string.
1382                $realString = substr $realString, (length $2) + (length $1);
1383                # Get the matched character.
1384                my $char = $2;
1385                # If we have a CR, we are done.
1386                if ($char ne "\r") {
1387                    # It's not a CR, so encode the escape sequence.
1388                    $char =~ tr/\t\n/tn/;
1389                    $retVal .= "\\" . $char;
1390                }
1391            } else {
1392                # Here there are no more escape sequences. The rest of the string is
1393                # transferred unmodified.
1394                $retVal .= $realString;
1395                $realString = "";
1396            }
1397        }
1398        # Return the result.
1399        return $retVal;
1400    }
1401    
1402    =head3 UnEscape
1403    
1404    C<< my $realString = Tracer::UnEscape($codedString); >>
1405    
1406    Replace escape sequences with their actual equivalents. C<\t> will be replaced by
1407    a tab, C<\n> by a new-line character, and C<\\> by a backslash. C<\r> codes will
1408    be deleted.
1409    
1410    =over 4
1411    
1412    =item codedString
1413    
1414    String to un-escape.
1415    
1416    =item RETURN
1417    
1418    Returns a copy of the original string with the escape sequences converted to their actual
1419    values.
1420    
1421    =back
1422    
1423    =cut
1424    
1425    sub UnEscape {
1426        # Get the parameter.
1427        my ($codedString) = @_;
1428        # Initialize the return variable.
1429        my $retVal = "";
1430        # Only proceed if the incoming string is nonempty.
1431        if (defined $codedString) {
1432            # Loop through the parameter string, looking for escape sequences. We can't do
1433            # translating because it causes problems with the escaped slash. ("\\t" becomes
1434            # "\<tab>" no matter what we do.)
1435            while (length $codedString > 0) {
1436                # Look for the first escape sequence.
1437                if ($codedString =~ /^(.*?)\\(\\|n|t|r)/) {
1438                    # Here we found it. The text preceding the sequence is in $1. The sequence
1439                    # itself is in $2. First, move the clear text to the return variable.
1440                    $retVal .= $1;
1441                    $codedString = substr $codedString, (2 + length $1);
1442                    # Get the escape value.
1443                    my $char = $2;
1444                    # If we have a "\r", we are done.
1445                    if ($char ne 'r') {
1446                        # Here it's not an 'r', so we convert it.
1447                        $char =~ tr/\\tn/\\\t\n/;
1448                        $retVal .= $char;
1449                    }
1450                } else {
1451                    # Here there are no more escape sequences. The rest of the string is
1452                    # transferred unmodified.
1453                    $retVal .= $codedString;
1454                    $codedString = "";
1455                }
1456            }
1457        }
1458        # Return the result.
1459        return $retVal;
1460    }
1461    
1462    =head3 ParseRecord
1463    
1464    C<< my @fields = Tracer::ParseRecord($line); >>
1465    
1466    Parse a tab-delimited data line. The data line is split into field values. Embedded tab
1467    and new-line characters in the data line must be represented as C<\t> and C<\n>, respectively.
1468    These will automatically be converted.
1469    
1470    =over 4
1471    
1472    =item line
1473    
1474    Line of data containing the tab-delimited fields.
1475    
1476    =item RETURN
1477    
1478    Returns a list of the fields found in the data line.
1479    
1480    =back
1481    
1482    =cut
1483    
1484    sub ParseRecord {
1485        # Get the parameter.
1486        my ($line) = @_;
1487        # Remove the trailing new-line, if any.
1488        chomp $line;
1489        # Split the line read into pieces using the tab character.
1490        my @retVal = split /\t/, $line;
1491        # Trim and fix the escapes in each piece.
1492        for my $value (@retVal) {
1493            # Trim leading whitespace.
1494            $value =~ s/^\s+//;
1495            # Trim trailing whitespace.
1496            $value =~ s/\s+$//;
1497            # Delete the carriage returns.
1498            $value =~ s/\r//g;
1499            # Convert the escapes into their real values.
1500            $value =~ s/\\t/"\t"/ge;
1501            $value =~ s/\\n/"\n"/ge;
1502        }
1503        # Return the result.
1504        return @retVal;
1505    }
1506    
1507    =head3 Merge
1508    
1509    C<< my @mergedList = Tracer::Merge(@inputList); >>
1510    
1511    Sort a list of strings and remove duplicates.
1512    
1513    =over 4
1514    
1515    =item inputList
1516    
1517    List of scalars to sort and merge.
1518    
1519    =item RETURN
1520    
1521    Returns a list containing the same elements sorted in ascending order with duplicates
1522    removed.
1523    
1524    =back
1525    
1526    =cut
1527    
1528    sub Merge {
1529        # Get the input list in sort order.
1530        my @inputList = sort @_;
1531        # Only proceed if the list has at least two elements.
1532        if (@inputList > 1) {
1533            # Now we want to move through the list splicing out duplicates.
1534            my $i = 0;
1535            while ($i < @inputList) {
1536                # Get the current entry.
1537                my $thisEntry = $inputList[$i];
1538                # Find out how many elements duplicate the current entry.
1539                my $j = $i + 1;
1540                my $dup1 = $i + 1;
1541                while ($j < @inputList && $inputList[$j] eq $thisEntry) { $j++; };
1542                # If the number is nonzero, splice out the duplicates found.
1543                if ($j > $dup1) {
1544                    splice @inputList, $dup1, $j - $dup1;
1545                }
1546                # Now the element at position $dup1 is different from the element before it
1547                # at position $i. We push $i forward one position and start again.
1548                $i++;
1549            }
1550        }
1551        # Return the merged list.
1552        return @inputList;
1553    }
1554    
1555    =head3 Percent
1556    
1557    C<< my $percent = Tracer::Percent($number, $base); >>
1558    
1559    Returns the percent of the base represented by the given number. If the base
1560    is zero, returns zero.
1561    
1562    =over 4
1563    
1564    =item number
1565    
1566    Percent numerator.
1567    
1568    =item base
1569    
1570    Percent base.
1571    
1572    =item RETURN
1573    
1574    Returns the percentage of the base represented by the numerator.
1575    
1576    =back
1577    
1578    =cut
1579    
1580    sub Percent {
1581        # Get the parameters.
1582        my ($number, $base) = @_;
1583        # Declare the return variable.
1584        my $retVal = 0;
1585        # Compute the percent.
1586        if ($base != 0) {
1587            $retVal = $number * 100 / $base;
1588        }
1589        # Return the result.
1590        return $retVal;
1591    }
1592    
1593    =head3 GetFile
1594    
1595    C<< my @fileContents = Tracer::GetFile($fileName); >>
1596    
1597        or
1598    
1599    C<< my $fileContents = Tracer::GetFile($fileName); >>
1600    
1601    Return the entire contents of a file. In list context, line-ends are removed and
1602    each line is a list element. In scalar context, line-ends are replaced by C<\n>.
1603    
1604    =over 4
1605    
1606    =item fileName
1607    
1608    Name of the file to read.
1609    
1610    =item RETURN
1611    
1612    In a list context, returns the entire file as a list with the line terminators removed.
1613    In a scalar context, returns the entire file as a string. If an error occurs opening
1614    the file, an empty list will be returned.
1615    
1616    =back
1617    
1618    =cut
1619    
1620    sub GetFile {
1621        # Get the parameters.
1622        my ($fileName) = @_;
1623        # Declare the return variable.
1624        my @retVal = ();
1625        # Open the file for input.
1626        my $handle = Open(undef, "<$fileName");
1627        # Read the whole file into the return variable, stripping off any terminator
1628        # characters.
1629        my $lineCount = 0;
1630        while (my $line = <$handle>) {
1631            $lineCount++;
1632            $line = Strip($line);
1633            push @retVal, $line;
1634        }
1635        # Close it.
1636        close $handle;
1637        my $actualLines = @retVal;
1638        Trace("$actualLines lines read from file $fileName.") if T(File => 2);
1639        # Return the file's contents in the desired format.
1640        if (wantarray) {
1641            return @retVal;
1642        } else {
1643            return join "\n", @retVal;
1644        }
1645    }
1646    
1647    =head3 PutFile
1648    
1649    C<< Tracer::PutFile($fileName, \@lines); >>
1650    
1651    Write out a file from a list of lines of text.
1652    
1653    =over 4
1654    
1655    =item fileName
1656    
1657    Name of the output file.
1658    
1659    =item lines
1660    
1661    Reference to a list of text lines. The lines will be written to the file in order, with trailing
1662    new-line characters. Alternatively, may be a string, in which case the string will be written without
1663    modification.
1664    
1665    =back
1666    
1667    =cut
1668    
1669    sub PutFile {
1670        # Get the parameters.
1671        my ($fileName, $lines) = @_;
1672        # Open the output file.
1673        my $handle = Open(undef, ">$fileName");
1674        # Count the lines written.
1675        if (ref $lines ne 'ARRAY') {
1676            # Here we have a scalar, so we write it raw.
1677            print $handle $lines;
1678            Trace("Scalar put to file $fileName.") if T(File => 3);
1679        } else {
1680            # Write the lines one at a time.
1681            my $count = 0;
1682            for my $line (@{$lines}) {
1683                print $handle "$line\n";
1684                $count++;
1685            }
1686            Trace("$count lines put to file $fileName.") if T(File => 3);
1687        }
1688        # Close the output file.
1689        close $handle;
1690    }
1691    
1692    =head3 QTrace
1693    
1694    C<< my $data = QTrace($format); >>
1695    
1696    Return the queued trace data in the specified format.
1697    
1698    =over 4
1699    
1700    =item format
1701    
1702    C<html> to format the data as an HTML list, C<text> to format it as straight text.
1703    
1704    =back
1705    
1706    =cut
1707    
1708    sub QTrace {
1709        # Get the parameter.
1710        my ($format) = @_;
1711        # Create the return variable.
1712        my $retVal = "";
1713        # Only proceed if there is an actual queue.
1714        if (@Queue) {
1715            # Process according to the format.
1716            if ($format =~ m/^HTML$/i) {
1717                # Convert the queue into an HTML list.
1718                $retVal = "<ul>\n";
1719                for my $line (@Queue) {
1720                    my $escapedLine = CGI::escapeHTML($line);
1721                    $retVal .= "<li>$escapedLine</li>\n";
1722                }
1723                $retVal .= "</ul>\n";
1724            } elsif ($format =~ m/^TEXT$/i) {
1725                # Convert the queue into a list of text lines.
1726                $retVal = join("\n", @Queue) . "\n";
1727            }
1728            # Clear the queue.
1729            @Queue = ();
1730        }
1731        # Return the formatted list.
1732        return $retVal;
1733    }
1734    
1735    =head3 Confess
1736    
1737    C<< Confess($message); >>
1738    
1739    Trace the call stack and abort the program with the specified message. When used with
1740    the OR operator and the L</Assert> method, B<Confess> can function as a debugging assert.
1741    So, for example
1742    
1743    C<< Assert($recNum >= 0) || Confess("Invalid record number $recNum."); >>
1744    
1745    Will abort the program with a stack trace if the value of C<$recNum> is negative.
1746    
1747    =over 4
1748    
1749    =item message
1750    
1751    Message to include in the trace.
1752    
1753    =back
1754    
1755    =cut
1756    
1757    sub Confess {
1758        # Get the parameters.
1759        my ($message) = @_;
1760        # Trace the call stack.
1761        Cluck($message);
1762        # Abort the program.
1763        croak(">>> $message");
1764    }
1765    
1766    =head3 Assert
1767    
1768    C<< Assert($condition1, $condition2, ... $conditionN); >>
1769    
1770    Return TRUE if all the conditions are true. This method can be used in conjunction with
1771    the OR operator and the L</Confess> method as a debugging assert.
1772    So, for example
1773    
1774    C<< Assert($recNum >= 0) || Confess("Invalid record number $recNum."); >>
1775    
1776    Will abort the program with a stack trace if the value of C<$recNum> is negative.
1777    
1778    =cut
1779    sub Assert {
1780        my $retVal = 1;
1781        LOOP: for my $condition (@_) {
1782            if (! $condition) {
1783                $retVal = 0;
1784                last LOOP;
1785            }
1786        }
1787        return $retVal;
1788    }
1789    
1790    =head3 Cluck
1791    
1792    C<< Cluck($message); >>
1793    
1794    Trace the call stack. Note that for best results, you should qualify the call with a
1795    trace condition. For example,
1796    
1797    C<< Cluck("Starting record parse.") if T(3); >>
1798    
1799    will only trace the stack if the trace level for the package is 3 or more.
1800    
1801    =over 4
1802    
1803    =item message
1804    
1805    Message to include in the trace.
1806    
1807    =back
1808    
1809    =cut
1810    
1811    sub Cluck {
1812        # Get the parameters.
1813        my ($message) = @_;
1814        # Trace what's happening.
1815        Trace("Stack trace for event: $message");
1816        my $confession = longmess($message);
1817        # Convert the confession to a series of trace messages. Note we skip any
1818        # messages relating to calls into Tracer.
1819        for my $line (split /\s*\n/, $confession) {
1820            Trace($line) if ($line !~ /Tracer\.pm/);
1821        }
1822    }
1823    
1824  sub Trace {  =head3 Min
1825    
1826    C<< my $min = Min($value1, $value2, ... $valueN); >>
1827    
1828    Return the minimum argument. The arguments are treated as numbers.
1829    
1830    =over 4
1831    
1832    =item $value1, $value2, ... $valueN
1833    
1834    List of numbers to compare.
1835    
1836    =item RETURN
1837    
1838    Returns the lowest number in the list.
1839    
1840    =back
1841    
1842    =cut
1843    
1844    sub Min {
1845        # Get the parameters. Note that we prime the return value with the first parameter.
1846        my ($retVal, @values) = @_;
1847        # Loop through the remaining parameters, looking for the lowest.
1848        for my $value (@values) {
1849            if ($value < $retVal) {
1850                $retVal = $value;
1851            }
1852        }
1853        # Return the minimum found.
1854        return $retVal;
1855    }
1856    
1857    =head3 Max
1858    
1859    C<< my $max = Max($value1, $value2, ... $valueN); >>
1860    
1861    Return the maximum argument. The arguments are treated as numbers.
1862    
1863    =over 4
1864    
1865    =item $value1, $value2, ... $valueN
1866    
1867    List of numbers to compare.
1868    
1869    =item RETURN
1870    
1871    Returns the highest number in the list.
1872    
1873    =back
1874    
1875    =cut
1876    
1877    sub Max {
1878        # Get the parameters. Note that we prime the return value with the first parameter.
1879        my ($retVal, @values) = @_;
1880        # Loop through the remaining parameters, looking for the highest.
1881        for my $value (@values) {
1882            if ($value > $retVal) {
1883                $retVal = $value;
1884            }
1885        }
1886        # Return the maximum found.
1887        return $retVal;
1888    }
1889    
1890    =head3 AddToListMap
1891    
1892    C<< Tracer::AddToListMap(\%hash, $key, $value1, $value2, ... valueN); >>
1893    
1894    Add a key-value pair to a hash of lists. If no value exists for the key, a singleton list
1895    is created for the key. Otherwise, the new value is pushed onto the list.
1896    
1897    =over 4
1898    
1899    =item hash
1900    
1901    Reference to the target hash.
1902    
1903    =item key
1904    
1905    Key for which the value is to be added.
1906    
1907    =item value1, value2, ... valueN
1908    
1909    List of values to add to the key's value list.
1910    
1911    =back
1912    
1913    =cut
1914    
1915    sub AddToListMap {
1916          # Get the parameters.          # Get the parameters.
1917          my ($message) = @_;      my ($hash, $key, @values) = @_;
1918          # Get the timestamp.      # Process according to whether or not the key already has a value.
1919          my $timeStamp = Now();      if (! exists $hash->{$key}) {
1920          # Format the message. Note we strip off any line terminators at the end.          $hash->{$key} = [@values];
1921          my $formatted = "$timeStamp <$LastCategory>: " . Strip($message);      } else {
1922          # Process according to the destination.          push @{$hash->{$key}}, @values;
1923          if ($Destination eq "TEXT") {      }
1924                  # Write the message to the standard output.  }
1925                  print "$formatted\n";  
1926          } elsif ($Destination eq "ERROR") {  =head3 DebugMode
1927                  # Write the message to the error output.  
1928                  print STDERR "$formatted\n";  C<< if (Tracer::DebugMode) { ...code... } >>
1929          } elsif ($Destination eq "QUEUE") {  
1930                  # Push the message into the queue.  Return TRUE if debug mode has been turned on, else abort.
1931                  push @Queue, "$formatted";  
1932          } elsif ($Destination eq "HTML") {  Certain CGI scripts are too dangerous to exist in the production
1933                  # Convert the message to HTML and write it to the standard output.  environment. This method provides a simple way to prevent them
1934                  my $escapedMessage = CGI::escapeHTML($message);  from working unless they are explicitly turned on by creating a password
1935                  print "<p>$formatted</p>\n";  cookie via the B<SetPassword> script.  If debugging mode
1936      } elsif ($Destination eq "WARN") {  is not turned on, an error will occur.
1937         # Emit the message as a warning.  
1938         warn $message;  =cut
1939          } elsif ($Destination =~ m/^>>/) {  
1940                  # Write the trace message to an output file.  sub DebugMode {
1941                  open TRACING, $Destination;      # Declare the return variable.
1942                  print TRACING "$formatted\n";      my $retVal = 0;
1943                  close TRACING;      # Check the debug configuration.
1944        my $password = CGI::cookie("DebugMode");
1945        my $encrypted = Digest::MD5::md5_hex($password);
1946        if ($encrypted eq "252dec43280e0c0d6a75ffcec486e61d") {
1947            $retVal = 1;
1948        } else {
1949            # Here debug mode is off, so we generate an error.
1950            Confess("Cannot use this facility without logging in.");
1951        }
1952        # Return the determination indicator.
1953        return $retVal;
1954    }
1955    
1956    =head3 Strip
1957    
1958    C<< my $string = Tracer::Strip($line); >>
1959    
1960    Strip all line terminators off a string. This is necessary when dealing with files
1961    that may have been transferred back and forth several times among different
1962    operating environments.
1963    
1964    =over 4
1965    
1966    =item line
1967    
1968    Line of text to be stripped.
1969    
1970    =item RETURN
1971    
1972    The same line of text with all the line-ending characters chopped from the end.
1973    
1974    =back
1975    
1976    =cut
1977    
1978    sub Strip {
1979        # Get a copy of the parameter string.
1980        my ($string) = @_;
1981        my $retVal = (defined $string ? $string : "");
1982        # Strip the line terminator characters.
1983        $retVal =~ s/(\r|\n)+$//g;
1984        # Return the result.
1985        return $retVal;
1986    }
1987    
1988    =head3 Pad
1989    
1990    C<< my $paddedString = Tracer::Pad($string, $len, $left, $padChar); >>
1991    
1992    Pad a string to a specified length. The pad character will be a
1993    space, and the padding will be on the right side unless specified
1994    in the third parameter.
1995    
1996    =over 4
1997    
1998    =item string
1999    
2000    String to be padded.
2001    
2002    =item len
2003    
2004    Desired length of the padded string.
2005    
2006    =item left (optional)
2007    
2008    TRUE if the string is to be left-padded; otherwise it will be padded on the right.
2009    
2010    =item padChar (optional)
2011    
2012    Character to use for padding. The default is a space.
2013    
2014    =item RETURN
2015    
2016    Returns a copy of the original string with the pad character added to the
2017    specified end so that it achieves the desired length.
2018    
2019    =back
2020    
2021    =cut
2022    
2023    sub Pad {
2024        # Get the parameters.
2025        my ($string, $len, $left, $padChar) = @_;
2026        # Compute the padding character.
2027        if (! defined $padChar) {
2028            $padChar = " ";
2029        }
2030        # Compute the number of spaces needed.
2031        my $needed = $len - length $string;
2032        # Copy the string into the return variable.
2033        my $retVal = $string;
2034        # Only proceed if padding is needed.
2035        if ($needed > 0) {
2036            # Create the pad string.
2037            my $pad = $padChar x $needed;
2038            # Affix it to the return value.
2039            if ($left) {
2040                $retVal = $pad . $retVal;
2041            } else {
2042                $retVal .= $pad;
2043            }
2044        }
2045        # Return the result.
2046        return $retVal;
2047    }
2048    
2049    =head3 EOF
2050    
2051    This is a constant that is lexically greater than any useful string.
2052    
2053    =cut
2054    
2055    sub EOF {
2056        return "\xFF\xFF\xFF\xFF\xFF";
2057    }
2058    
2059    =head3 TICK
2060    
2061    C<< my @results = TICK($commandString); >>
2062    
2063    Perform a back-tick operation on a command. If this is a Windows environment, any leading
2064    dot-slash (C<./> will be removed. So, for example, if you were doing
2065    
2066        `./protein.cgi`
2067    
2068    from inside a CGI script, it would work fine in Unix, but would issue an error message
2069    in Windows complaining that C<'.'> is not a valid command. If instead you code
2070    
2071        TICK("./protein.cgi")
2072    
2073    it will work correctly in both environments.
2074    
2075    =over 4
2076    
2077    =item commandString
2078    
2079    The command string to pass to the system.
2080    
2081    =item RETURN
2082    
2083    Returns the standard output from the specified command, as a list.
2084    
2085    =back
2086    
2087    =cut
2088    #: Return Type @;
2089    sub TICK {
2090        # Get the parameters.
2091        my ($commandString) = @_;
2092        # Chop off the dot-slash if this is Windows.
2093        if ($FIG_Config::win_mode) {
2094            $commandString =~ s!^\./!!;
2095          }          }
2096        # Activate the command and return the result.
2097        return `$commandString`;
2098  }  }
2099    
2100  =head3 T  =head3 ScriptSetup
2101    
2102  C<< my $switch = T($category, $traceLevel); >>  C<< my ($cgi, $varHash) = ScriptSetup($noTrace); >>
2103    
2104          or  Perform standard tracing and debugging setup for scripts. The value returned is
2105    the CGI object followed by a pre-built variable hash.
2106    
2107  C<< my $switch = T($traceLevel); >>  The C<Trace> form parameter is used to determine whether or not tracing is active and
2108    which trace modules (other than C<Tracer> itself) should be turned on. Specifying
2109    the C<CGI> trace module will trace parameter and environment information. Parameters are
2110    traced at level 3 and environment variables at level 4. To trace to a file instead of to
2111    the web page, set C<TF> to 1. At the end of the script, the client should call
2112    L</ScriptFinish> to output the web page.
2113    
2114  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
2115  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.
2116    Tracing will then be turned on automatically for all programs that use the L</ETracing>
2117    method, which includes every program that uses this method or L</StandardSetup>.
2118    
2119  =over 4  =over 4
2120    
2121  =item category  =item noTrace (optional)
   
 Category to which the message belongs. If not specified, the caller's package name is  
 used.  
   
 =item traceLevel  
2122    
2123  Relevant tracing level.  If specified, tracing will be suppressed. This is useful if the script wants to set up
2124    tracing manually.
2125    
2126  =item RETURN  =item RETURN
2127    
2128  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
2129    the output page.
2130    
2131  =back  =back
2132    
2133  =cut  =cut
2134    
2135  sub T {  sub ScriptSetup {
         # Declare the return variable.  
         my $retVal = 0;  
         # Only proceed if tracing is turned on.  
         if ($Destination ne "NONE") {  
2136                  # Get the parameters.                  # Get the parameters.
2137                  my ($category, $traceLevel) = @_;      my ($noTrace) = @_;
2138                  if (!defined $traceLevel) {      # Get the CGI query object.
2139                          # Here we have no category, so we need to get the calling package.      my $cgi = CGI->new();
2140                          $traceLevel = $category;      # Set up tracing if it's not suppressed.
2141                          my ($package, $fileName, $line) = caller;      ETracing($cgi) unless $noTrace;
2142              # If there is no calling package, we default to "main".      # Create the variable hash.
2143                          if (!$package) {      my $varHash = { results => '' };
2144                  $category = "main";      # Return the query object and variable hash.
2145        return ($cgi, $varHash);
2146    }
2147    
2148    =head3 ETracing
2149    
2150    C<< ETracing($parameter); >>
2151    
2152    Set up emergency tracing. Emergency tracing is tracing that is turned
2153    on automatically for any program that calls this method. The emergency
2154    tracing parameters are stored in a a file identified by a tracing key.
2155    If this method is called with a CGI object, then the tracing key is
2156    taken from a cookie. If it is called with no parameters, then the tracing
2157    key is taken from an environment variable. If it is called with a string,
2158    the tracing key is that string.
2159    
2160    =over 4
2161    
2162    =item parameter
2163    
2164    A parameter from which the tracing key is computed. If it is a scalar,
2165    that scalar is used as the tracing key. If it is a CGI object, the
2166    tracing key is taken from the C<IP> cookie. If it is omitted, the
2167    tracing key is taken from the C<TRACING> environment variable. If it
2168    is a CGI object and emergency tracing is not on, the C<Trace> and
2169    C<TF> parameters will be used to determine the type of tracing.
2170    
2171    =back
2172    
2173    =cut
2174    
2175    sub ETracing {
2176        # Get the parameter.
2177        my ($parameter) = @_;
2178        # Check for CGI mode.
2179        my $cgi = (ref $parameter eq 'CGI' ? $parameter : undef);
2180        # Default to no tracing except errors.
2181        my ($tracing, $dest) = ("0", "WARN");
2182        # Check for emergency tracing.
2183        my $tkey = EmergencyKey($parameter);
2184        my $emergencyFile = EmergencyFileName($tkey);
2185        if (-e $emergencyFile) {
2186            # We have the file. Read in the data.
2187            my @tracing = GetFile($emergencyFile);
2188            # Pull off the time limit.
2189            my $expire = shift @tracing;
2190            # Convert it to seconds.
2191            $expire *= 3600;
2192            # Check the file data.
2193            my $stat = stat($emergencyFile);
2194            my ($now) = gettimeofday;
2195            if ($now - $stat->mtime > $expire) {
2196                # Delete the expired file.
2197                unlink $emergencyFile;
2198                          } else {                          } else {
2199                                  $category = $package;              # Emergency tracing is on. Pull off the destination and
2200                # the trace level;
2201                $dest = shift @tracing;
2202                my $level = shift @tracing;
2203                # Convert the destination to a real tracing destination.
2204                # temp directory.
2205                $dest = EmergencyTracingDest($tkey, $dest);
2206                # Insure Tracer is specified.
2207                my %moduleHash = map { $_ => 1 } @tracing;
2208                $moduleHash{Tracer} = 1;
2209                # Set the trace parameter.
2210                $tracing = join(" ", $level, sort keys %moduleHash);
2211                          }                          }
2212        } elsif (defined $cgi) {
2213            # There's no emergency tracing, but we have a CGI object, so check
2214            # for tracing from the form parameters.
2215            if ($cgi->param('Trace')) {
2216                # Here the user has requested tracing via a form.
2217                $dest = ($cgi->param('TF') ? ">$FIG_Config::temp/Trace$$.log" : "QUEUE");
2218                $tracing = $cgi->param('Trace') . " Tracer";
2219                  }                  }
         # Save the category name.  
         $LastCategory = $category;  
                 # Use the category and tracelevel to compute the result.  
                 $retVal = ($traceLevel <= $TraceLevel && exists $Categories{$category});  
2220      }      }
2221          # Return the computed result.      # Setup the tracing we've determined from all the stuff above.
2222      return $retVal;      TSetup($tracing, $dest);
2223        # If we're a web script, trace the parameter and environment data.
2224        if (defined $cgi) {
2225            TraceParms($cgi);
2226        }
2227  }  }
2228    
2229  =head3 ParseCommand  =head3 EmergencyFileName
2230    
2231  C<< my ($options, @arguments) = Tracer::ParseCommand(\%optionTable, @inputList); >>  C<< my $fileName = Tracer::EmergencyFileName($tkey); >>
2232    
2233  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
2234  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.  
2235    
2236  C<< my ($options, @arguments) = ParseCommand({ errors => 0, logFile => 'trace.log'}, @words); >>  =over 4
2237    
2238  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  
2239    
2240  C<< -logFile=error.log apple orange rutabaga >>  Tracing key for the current program.
2241    
2242  then at the end of the invocation, C<$options> will be  =item RETURN
2243    
2244  C<< { errors => 0, logFile => 'error.log' } >>  Returns the name of the file to contain the emergency tracing information.
2245    
2246  and C<@arguments> will contain  =back
2247    
2248  C<< apple orange rutabaga >>  =cut
2249    
2250  The parser allows for some escape sequences. See L</UnEscape> for a description. There is no  sub EmergencyFileName {
2251  support for quote characters.      # Get the parameters.
2252        my ($tkey) = @_;
2253        # Compute the emergency tracing file name.
2254        return "$FIG_Config::temp/Emergency$tkey.txt";
2255    }
2256    
2257  =over 4  =head3 EmergencyFileTarget
2258    
2259  =item optionTable  C<< my $fileName = Tracer::EmergencyFileTarget($tkey); >>
2260    
2261  Table of default options.  Return the emergency tracing target file name. This is the file that receives
2262    the tracing output for file-based tracing.
2263    
2264  =item inputList  =over 4
2265    
2266  List of words on the command line.  =item tkey
2267    
2268    Tracing key for the current program.
2269    
2270  =item RETURN  =item RETURN
2271    
2272  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.
2273    
2274  =back  =back
2275    
2276  =cut  =cut
2277    
2278  sub ParseCommand {  sub EmergencyFileTarget {
2279          # Get the parameters.          # Get the parameters.
2280          my ($optionTable, @inputList) = @_;      my ($tkey) = @_;
2281          # Process any options in the input list.      # Compute the emergency tracing file name.
2282          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);  
2283  }  }
2284    
2285  =head3 Escape  =head3 EmergencyTracingDest
2286    
2287  C<< my $codedString = Tracer::Escape($realString); >>  C<< my $dest = Tracer::EmergencyTracingDest($tkey, $myDest); >>
2288    
2289  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
2290  tabs replaced by C<\t>, new-lines replaced by C<\n>, and backslashes will be  tracing destination. The main difference is that if the
2291  doubled. The effect is to exactly reverse the effect of L</UnEscape>.  destination is C<FILE> or C<APPEND>, we convert it to file
2292    output.
2293    
2294  =over 4  =over 4
2295    
2296  =item realString  =item tkey
2297    
2298  String to escape.  Tracing key for this environment.
2299    
2300    =item myDest
2301    
2302    Destination from the emergency tracing file.
2303    
2304  =item RETURN  =item RETURN
2305    
2306  Escaped equivalent of the real string.  Returns a destination that can be passed into L</TSetup>.
2307    
2308  =back  =back
2309    
2310  =cut  =cut
2311    
2312  sub Escape {  sub EmergencyTracingDest {
2313          # Get the parameter.      # Get the parameters.
2314          my ($realString) = @_;      my ($tkey, $myDest) = @_;
2315          # Initialize the return variable.      # Declare the return variable.
2316          my $retVal = "";      my $retVal;
2317          # Loop through the parameter string, looking for sequences to escape.      # Process according to the destination value.
2318          while (length $realString > 0) {      if ($myDest eq 'FILE') {
2319                  # Look for the first sequence to escape.          $retVal = ">" . EmergencyFileTarget($tkey);
2320                  if ($realString =~ /^(.*?)([ \n\t\\])/) {      } elsif ($myDest eq 'APPEND') {
2321                          # 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;  
2322                  } else {                  } else {
2323                          # Here there are no more escape sequences. The rest of the string is          $retVal = $myDest;
                         # transferred unmodified.  
                         $retVal .= $realString;  
                         $realString = "";  
                 }  
2324          }          }
2325          # Return the result.          # Return the result.
2326          return $retVal;          return $retVal;
2327  }  }
2328    
2329  =head3 UnEscape  =head3 Emergency
2330    
2331  C<< my $realString = Tracer::UnEscape($codedString); >>  C<< Emergency($key, $hours, $dest, $level, @modules); >>
2332    
2333  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
2334  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
2335    emergency in hours, the desired tracing destination, the trace level,
2336    and a list of the trace modules to activate. For the length of the duration, when a
2337    program in an environment with the specified tracing key active invokes a Sprout
2338    CGI script, tracing will be turned on automatically. See L</TSetup> for more
2339    about tracing setup and L</ETracing> for more about emergency tracing.
2340    
2341  =over 4  =over 4
2342    
2343  =item codedString  =item tkey
2344    
2345  String to un-escape.  The tracing key. This is used to identify the control file and the trace file.
2346    
2347  =item RETURN  =item hours
2348    
2349  Returns a copy of the original string with the escape sequences converted to their actual  Number of hours to keep emergency tracing alive.
2350  values.  
2351    =item dest
2352    
2353    Tracing destination. If no path information is specified for a file
2354    destination, it is put in the FIG temporary directory.
2355    
2356    =item level
2357    
2358    Tracing level. A higher level means more trace messages.
2359    
2360    =item modules
2361    
2362    A list of the tracing modules to activate.
2363    
2364  =back  =back
2365    
2366  =cut  =cut
2367    
2368  sub UnEscape {  sub Emergency {
2369          # Get the parameter.      # Get the parameters.
2370          my ($codedString) = @_;      my ($tkey, $hours, $dest, $level, @modules) = @_;
2371          # Initialize the return variable.      # Create the emergency file.
2372          my $retVal = "";      my $specFile = EmergencyFileName($tkey);
2373          # Only proceed if the incoming string is nonempty.      my $outHandle = Open(undef, ">$specFile");
2374          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;  
2375  }  }
2376    
2377  =head3 ParseRecord  =head3 EmergencyKey
2378    
2379  C<< my @fields = Tracer::ParseRecord($line); >>  C<< my $tkey = EmergencyKey($parameter); >>
2380    
2381  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,
2382  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.  
2383    
2384  =over 4  =over 4
2385    
2386  =item line  =item parameter
2387    
2388  Line of data containing the tab-delimited fields.  Parameter defining the method for finding the tracing key. If it is a scalar,
2389    then it is presumed to be the tracing key itself. If it is a CGI object, then
2390    the tracing key is taken from the C<IP> cookie. Otherwise, the tracing key is
2391    taken from the C<TRACING> environment variable.
2392    
2393  =item RETURN  =item RETURN
2394    
2395  Returns a list of the fields found in the data line.  Returns the key to be used for labels in emergency tracing.
2396    
2397  =back  =back
2398    
2399  =cut  =cut
2400    
2401  sub ParseRecord {  sub EmergencyKey {
2402          # Get the parameter.      # Get the parameters.
2403          my ($line) = @_;      my ($parameter) = @_;
2404          # Remove the trailing new-line, if any.      # Declare the return variable.
2405          chomp $line;      my $retVal;
2406          # Split the line read into pieces using the tab character.      # Determine the parameter type.
2407          my @retVal = split /\t/, $line;      if (! defined $parameter) {
2408          # Trim and fix the escapes in each piece.          # Here we're supposed to check the environment.
2409          for my $value (@retVal) {          $retVal = $ENV{TRACING};
2410                  # Trim leading whitespace.      } else {
2411                  $value =~ s/^\s+//;          my $ptype = ref $parameter;
2412                  # Trim trailing whitespace.          if ($ptype eq 'CGI') {
2413                  $value =~ s/\s+$//;              # Here we were invoked from a web page. Look for a cookie.
2414                  # Delete the carriage returns.              $retVal = $parameter->cookie('IP');
2415                  $value =~ s/\r//g;          } elsif (! $ptype) {
2416                  # Convert the escapes into their real values.              # Here the key was passed in.
2417                  $value =~ s/\\t/"\t"/ge;              $retVal = $parameter;
2418                  $value =~ s/\\n/"\n"/ge;          }
2419        }
2420        # If no luck finding a key, use the PID.
2421        if (! defined $retVal) {
2422            $retVal = $$;
2423          }          }
2424          # Return the result.          # Return the result.
2425          return @retVal;      return $retVal;
2426  }  }
2427    
 =head3 Merge  
   
 C<< my @mergedList = Tracer::Merge(@inputList); >>  
2428    
2429  Sort a list of strings and remove duplicates.  =head3 TraceParms
2430    
2431  =over 4  C<< Tracer::TraceParms($cgi); >>
2432    
2433  =item inputList  Trace the CGI parameters at trace level CGI => 3 and the environment variables
2434    at level CGI => 4.
2435    
2436  List of scalars to sort and merge.  =over 4
2437    
2438  =item RETURN  =item cgi
2439    
2440  Returns a list containing the same elements sorted in ascending order with duplicates  CGI query object containing the parameters to trace.
 removed.  
2441    
2442  =back  =back
2443    
2444  =cut  =cut
2445    
2446  sub Merge {  sub TraceParms {
2447          # Get the input list in sort order.      # Get the parameters.
2448          my @inputList = sort @_;      my ($cgi) = @_;
2449          # Only proceed if the list has at least two elements.      if (T(CGI => 3)) {
2450          if (@inputList > 1) {          # Here we want to trace the parameter data.
2451                  # Now we want to move through the list splicing out duplicates.          my @names = $cgi->param;
2452                  my $i = 0;          for my $parmName (sort @names) {
2453                  while ($i < @inputList) {              # Note we skip the Trace parameters, which are for our use only.
2454                          # Get the current entry.              if ($parmName ne 'Trace' && $parmName ne 'TF') {
2455                          my $thisEntry = $inputList[$i];                  my @values = $cgi->param($parmName);
2456                          # 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;  
2457                          }                          }
2458                          # Now the element at position $dup1 is different from the element before it          }
2459                          # at position $i. We push $i forward one position and start again.          # Display the request method.
2460                          $i++;          my $method = $cgi->request_method();
2461            Trace("Method: $method");
2462        }
2463        if (T(CGI => 4)) {
2464            # Here we want the environment data too.
2465            for my $envName (sort keys %ENV) {
2466                Trace("ENV: $envName = $ENV{$envName}");
2467                  }                  }
2468          }          }
         # Return the merged list.  
         return @inputList;  
2469  }  }
2470    
2471  =head3 GetFile  =head3 ScriptFinish
2472    
2473  C<< my @fileContents = Tracer::GetFile($fileName); >>  C<< ScriptFinish($webData, $varHash); >>
2474    
2475    Output a web page at the end of a script. Either the string to be output or the
2476    name of a template file can be specified. If the second parameter is omitted,
2477    it is assumed we have a string to be output; otherwise, it is assumed we have the
2478    name of a template file. The template should have the variable C<DebugData>
2479    specified in any form that invokes a standard script. If debugging mode is turned
2480    on, a form field will be put in that allows the user to enter tracing data.
2481    Trace messages will be placed immediately before the terminal C<BODY> tag in
2482    the output, formatted as a list.
2483    
2484    A typical standard script would loook like the following.
2485    
2486        BEGIN {
2487            # Print the HTML header.
2488            print "CONTENT-TYPE: text/html\n\n";
2489        }
2490        use Tracer;
2491        use CGI;
2492        use FIG;
2493        # ... more uses ...
2494    
2495        my ($cgi, $varHash) = ScriptSetup();
2496        eval {
2497            # ... get data from $cgi, put it in $varHash ...
2498        };
2499        if ($@) {
2500            Trace("Script Error: $@") if T(0);
2501        }
2502        ScriptFinish("Html/MyTemplate.html", $varHash);
2503    
2504  Return the entire contents of a file.  The idea here is that even if the script fails, you'll see trace messages and
2505    useful output.
2506    
2507  =over 4  =over 4
2508    
2509  =item fileName  =item webData
2510    
2511  Name of the file to read.  A string containing either the full web page to be written to the output or the
2512    name of a template file from which the page is to be constructed. If the name
2513    of a template file is specified, then the second parameter must be present;
2514    otherwise, it must be absent.
2515    
2516  =item RETURN  =item varHash (optional)
2517    
2518  In a list context, returns the entire file as a list with the line terminators removed.  If specified, then a reference to a hash mapping variable names for a template
2519  In a scalar context, returns the entire file as a string.  to their values. The template file will be read into memory, and variable markers
2520    will be replaced by data in this hash reference.
2521    
2522  =back  =back
2523    
2524  =cut  =cut
2525    
2526  sub GetFile {  sub ScriptFinish {
2527          # Get the parameters.          # Get the parameters.
2528          my ($fileName) = @_;      my ($webData, $varHash) = @_;
2529          # Declare the return variable.      # Check for a template file situation.
2530          my @retVal = ();      my $outputString;
2531          # Open the file for input.      if (defined $varHash) {
2532          my $ok = open INPUTFILE, "<$fileName";          # Here we have a template file. We need to determine the template type.
2533          if (!$ok) {          my $template;
2534                  # If we had an error, trace it. We will automatically return a null value.          if ($FIG_Config::template_url && $webData =~ /\.php$/) {
2535                  Trace("Could not open \"$fileName\" for input.") if T(0);              $template = "$FIG_Config::template_url/$webData";
2536          } else {          } else {
2537                  # 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;  
2538                  }                  }
2539                  # Close it.          $outputString = PageBuilder::Build($template, $varHash, "Html");
2540                  close INPUTFILE;      } else {
2541          my $actualLines = @retVal;          # Here the user gave us a raw string.
2542          Trace("$lineCount lines read from $fileName. $actualLines processed.") if T(3);          $outputString = $webData;
2543          }          }
2544          # Return the file's contents in the desired format.      # Check for trace messages.
2545      if (wantarray) {      if ($Destination ne "NONE" && $TraceLevel > 0) {
2546              return @retVal;          # We have trace messages, so we want to put them at the end of the body. This
2547            # is either at the end of the whole string or at the beginning of the BODY
2548            # end-tag.
2549            my $pos = length $outputString;
2550            if ($outputString =~ m#</body>#gi) {
2551                $pos = (pos $outputString) - 7;
2552            }
2553            # If the trace messages were queued, we unroll them. Otherwise, we display the
2554            # destination.
2555            my $traceHtml;
2556            if ($Destination eq "QUEUE") {
2557                $traceHtml = QTrace('Html');
2558            } elsif ($Destination =~ /^>>(.+)$/) {
2559                # Here the tracing output it to a file. We code it as a hyperlink so the user
2560                # can copy the file name into the clipboard easily.
2561                my $actualDest = $1;
2562                $traceHtml = "<p>Tracing output to $actualDest.</p>\n";
2563      } else {      } else {
2564          return join "\n", @retVal;              # Here we have one of the special destinations.
2565                $traceHtml = "<P>Tracing output type is $Destination.</p>\n";
2566      }      }
2567            substr $outputString, $pos, 0, $traceHtml;
2568        }
2569        # Write the output string.
2570        print $outputString;
2571  }  }
2572    
2573  =head3 QTrace  =head3 Insure
2574    
2575  C<< my $data = QTrace($format); >>  C<< Insure($dirName); >>
2576    
2577  Return the queued trace data in the specified format.  Insure a directory is present.
2578    
2579  =over 4  =over 4
2580    
2581  =item format  =item dirName
2582    
2583  C<html> to format the data as an HTML list, C<text> to format it as straight text.  Name of the directory to check. If it does not exist, it will be created.
2584    
2585  =back  =back
2586    
2587  =cut  =cut
2588    
2589  sub QTrace {  sub Insure {
2590          # Get the parameter.      my ($dirName) = @_;
2591          my ($format) = @_;      if (! -d $dirName) {
2592          # Create the return variable.          Trace("Creating $dirName directory.") if T(File => 2);
2593          my $retVal = "";          eval { mkpath $dirName; };
2594          # Process according to the format.          if ($@) {
2595          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";  
2596                  }                  }
                 $retVal .= "</ul>\n";  
         } elsif ($format =~ m/^TEXT$/i) {  
                 # Convert the queue into a list of text lines.  
                 $retVal = join("\n", @Queue) . "\n";  
2597          }          }
         # Clear the queue.  
         @Queue = ();  
         # Return the formatted list.  
         return $retVal;  
2598  }  }
2599    
2600  =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  
2601    
2602  C<< Assert($recNum >= 0) || Confess("Invalid record number $recNum."); >>  C<< ChDir($dirName); >>
2603    
2604  Will abort the program with a stack trace if the value of C<$recNum> is negative.  Change to the specified directory.
2605    
2606  =over 4  =over 4
2607    
2608  =item message  =item dirName
2609    
2610  Message to include in the trace.  Name of the directory to which we want to change.
2611    
2612  =back  =back
2613    
2614  =cut  =cut
2615    
2616  sub Confess {  sub ChDir {
2617          # Get the parameters.      my ($dirName) = @_;
2618          my ($message) = @_;      if (! -d $dirName) {
2619          # Trace the call stack.          Confess("Cannot change to directory $dirName: no such directory.");
2620          Cluck($message) if T(1);      } else {
2621          # Abort the program.          Trace("Changing to directory $dirName.") if T(File => 4);
2622          croak(">>> $message");          my $okFlag = chdir $dirName;
2623            if (! $okFlag) {
2624                Confess("Error switching to directory $dirName.");
2625            }
2626        }
2627  }  }
2628    
2629  =head3 Assert  =head3 SendSMS
   
 C<< Assert($condition1, $condition2, ... $conditionN); >>  
2630    
2631  Return TRUE if all the conditions are true. This method can be used in conjunction with  C<< my $msgID = Tracer::SendSMS($phoneNumber, $msg); >>
 the OR operator and the L</Confess> method, B<Assert> can function as a debugging assert.  
 So, for example  
2632    
2633  C<< Assert($recNum >= 0) || Confess("Invalid record number $recNum."); >>  Send a text message to a phone number using Clickatell. The FIG_Config file must contain the
2634    user name, password, and API ID for the relevant account in the hash reference variable
2635    I<$FIG_Config::phone>, using the keys C<user>, C<password>, and C<api_id>. For
2636    example, if the user name is C<BruceTheHumanPet>, the password is C<silly>, and the API ID
2637    is C<2561022>, then the FIG_Config file must contain
2638    
2639  Will abort the program with a stack trace if the value of C<$recNum> is negative.      $phone =  { user => 'BruceTheHumanPet',
2640                    password => 'silly',
2641                    api_id => '2561022' };
2642    
2643  =cut  The original purpose of this method was to insure Bruce would be notified immediately when the
2644  sub Assert {  Sprout Load terminates. Care should be taken if you do not wish Bruce to be notified immediately
2645      my $retVal = 1;  when you call this method.
     LOOP: for my $condition (@_) {  
         if (! $condition) {  
             $retVal = 0;  
             last LOOP;  
         }  
     }  
     return $retVal;  
 }  
2646    
2647  =head3 Cluck  The message ID will be returned if successful, and C<undef> if an error occurs.
2648    
2649  C<< Cluck($message); >>  =over 4
2650    
2651  Trace the call stack. Note that for best results, you should qualify the call with a  =item phoneNumber
 trace condition. For example,  
2652    
2653  C<< Cluck("Starting record parse.") if T(3); >>  Phone number to receive the message, in international format. A United States phone number
2654    would be prefixed by "1". A British phone number would be prefixed by "44".
2655    
2656  will only trace the stack if the trace level for the package is 3 or more.  =item msg
2657    
2658  =over 4  Message to send to the specified phone.
2659    
2660  =item message  =item RETURN
2661    
2662  Message to include in the trace.  Returns the message ID if successful, and C<undef> if the message could not be sent.
2663    
2664  =back  =back
2665    
2666  =cut  =cut
2667    
2668  sub Cluck {  sub SendSMS {
2669          # Get the parameters.          # Get the parameters.
2670          my ($message) = @_;      my ($phoneNumber, $msg) = @_;
2671      # Trace what's happening.      # Declare the return variable. If we do not change it, C<undef> will be returned.
2672      Trace("Stack trace for event: $message");      my $retVal;
2673          my $confession = longmess($message);      # Only proceed if we have phone support.
2674          # Convert the confession to a series of trace messages. Note we skip any      if (! defined $FIG_Config::phone) {
2675      # messages relating to calls into Tracer.          Trace("Phone support not present in FIG_Config.") if T(1);
2676          for my $line (split /\s*\n/, $confession) {      } else {
2677                  Trace($line) if ($line !~ /Tracer\.pm/);          # Get the phone data.
2678            my $parms = $FIG_Config::phone;
2679            # Get the Clickatell URL.
2680            my $url = "http://api.clickatell.com/http/";
2681            # Create the user agent.
2682            my $ua = LWP::UserAgent->new;
2683            # Request a Clickatell session.
2684            my $resp = $ua->post("$url/sendmsg", { user => $parms->{user},
2685                                         password => $parms->{password},
2686                                         api_id => $parms->{api_id},
2687                                         to => $phoneNumber,
2688                                         text => $msg});
2689            # Check for an error.
2690            if (! $resp->is_success) {
2691                Trace("Alert failed.") if T(1);
2692            } else {
2693                # Get the message ID.
2694                my $rstring = $resp->content;
2695                if ($rstring =~ /^ID:\s+(.*)$/) {
2696                    $retVal = $1;
2697                } else {
2698                    Trace("Phone attempt failed with $rstring") if T(1);
2699                }
2700          }          }
2701  }  }
2702        # Return the result.
2703        return $retVal;
2704    }
2705    
2706  =head3 Min  =head3 CommaFormat
2707    
2708  C<< my $min = Min($value1, $value2, ... $valueN); >>  C<< my $formatted = Tracer::CommaFormat($number); >>
2709    
2710  Return the minimum argument. The arguments are treated as numbers.  Insert commas into a number.
2711    
2712  =over 4  =over 4
2713    
2714  =item $value1, $value2, ... $valueN  =item number
2715    
2716  List of numbers to compare.  A sequence of digits.
2717    
2718  =item RETURN  =item RETURN
2719    
2720  Returns the lowest number in the list.  Returns the same digits with commas strategically inserted.
2721    
2722  =back  =back
2723    
2724  =cut  =cut
2725    
2726  sub Min {  sub CommaFormat {
2727          # Get the parameters. Note that we prime the return value with the first parameter.      # Get the parameters.
2728          my ($retVal, @values) = @_;      my ($number) = @_;
2729          # Loop through the remaining parameters, looking for the lowest.      # Pad the length up to a multiple of three.
2730          for my $value (@values) {      my $padded = "$number";
2731                  if ($value < $retVal) {      $padded = " " . $padded while length($padded) % 3 != 0;
2732                          $retVal = $value;      # This is a fancy PERL trick. The parentheses in the SPLIT pattern
2733                  }      # cause the delimiters to be included in the output stream. The
2734          }      # GREP removes the empty strings in between the delimiters.
2735          # Return the minimum found.      my $retVal = join(",", grep { $_ ne '' } split(/(...)/, $padded));
2736        # Clean out the spaces.
2737        $retVal =~ s/ //g;
2738        # Return the result.
2739          return $retVal;          return $retVal;
2740  }  }
2741    =head3 SetPermissions
2742    
2743  =head3 Max  C<< Tracer::SetPermissions($dirName, $group, $mask, %otherMasks); >>
2744    
2745  C<< my $max = Max($value1, $value2, ... $valueN); >>  Set the permissions for a directory and all the files and folders inside it.
2746    In addition, the group ownership will be changed to the specified value.
2747    
2748  Return the maximum argument. The arguments are treated as numbers.  This method is more vulnerable than most to permission and compatability
2749    problems, so it does internal error recovery.
2750    
2751  =over 4  =over 4
2752    
2753  =item $value1, $value2, ... $valueN  =item dirName
2754    
2755  List of numbers to compare.  Name of the directory to process.
2756    
2757  =item RETURN  =item group
2758    
2759  Returns the highest number in the list.  Name of the group to be assigned.
2760    
2761    =item mask
2762    
2763    Permission mask. Bits that are C<1> in this mask will be ORed into the
2764    permission bits of any file or directory that does not already have them
2765    set to 1.
2766    
2767    =item otherMasks
2768    
2769    Map of search patterns to permission masks. If a directory name matches
2770    one of the patterns, that directory and all its members and subdirectories
2771    will be assigned the new pattern. For example, the following would
2772    assign 01664 to most files, but would use 01777 for directories named C<tmp>.
2773    
2774        Tracer::SetPermissions($dirName, 'fig', 01664, '^tmp$' => 01777);
2775    
2776    The list is ordered, so the following would use 0777 for C<tmp1> and
2777    0666 for C<tmp>, C<tmp2>, or C<tmp3>.
2778    
2779        Tracer::SetPermissions($dirName, 'fig', 01664, '^tmp1' => 0777,
2780                                                       '^tmp' => 0666);
2781    
2782    Note that the pattern matches are all case-insensitive, and only directory
2783    names are matched, not file names.
2784    
2785  =back  =back
2786    
2787  =cut  =cut
2788    
2789  sub Max {  sub SetPermissions {
2790          # Get the parameters. Note that we prime the return value with the first parameter.      # Get the parameters.
2791          my ($retVal, @values) = @_;      my ($dirName, $group, $mask, @otherMasks) = @_;
2792          # Loop through the remaining parameters, looking for the highest.      # Set up for error recovery.
2793          for my $value (@values) {      eval {
2794                  if ($value > $retVal) {          # Switch to the specified directory.
2795                          $retVal = $value;          ChDir($dirName);
2796            # Get the group ID.
2797            my $gid = getgrnam($group);
2798            # Get the mask for tracing.
2799            my $traceMask = sprintf("%04o", $mask) . "($mask)";
2800            Trace("Fixing permissions for directory $dirName using group $group($gid) and mask $traceMask.") if T(File => 2);
2801            my $fixCount = 0;
2802            my $lookCount = 0;
2803            # @dirs will be a stack of directories to be processed.
2804            my @dirs = (getcwd());
2805            while (scalar(@dirs) > 0) {
2806                # Get the current directory.
2807                my $dir = pop @dirs;
2808                # Check for a match to one of the specified directory names. To do
2809                # that, we need to pull the individual part of the name off of the
2810                # whole path.
2811                my $simpleName = $dir;
2812                if ($dir =~ m!/([^/]+)$!) {
2813                    $simpleName = $1;
2814                }
2815                Trace("Simple directory name for $dir is $simpleName.") if T(File => 4);
2816                # Search for a match.
2817                my $match = 0;
2818                my $i;
2819                for ($i = 0; $i < $#otherMasks && ! $match; $i += 2) {
2820                    my $pattern = $otherMasks[$i];
2821                    if ($simpleName =~ /$pattern/i) {
2822                        $match = 1;
2823                    }
2824                }
2825                # Check for a match. Note we use $i-1 because the loop added 2
2826                # before terminating due to the match.
2827                if ($match && $otherMasks[$i-1] != $mask) {
2828                    # This directory matches one of the incoming patterns, and it's
2829                    # a different mask, so we process it recursively with that mask.
2830                    SetPermissions($dir, $group, $otherMasks[$i-1], @otherMasks);
2831                } else {
2832                    # Here we can process normally. Get all of the non-hidden members.
2833                    my @submems = OpenDir($dir, 1);
2834                    for my $submem (@submems) {
2835                        # Get the full name.
2836                        my $thisMem = "$dir/$submem";
2837                        Trace("Checking member $thisMem.") if T(4);
2838                        $lookCount++;
2839                        if ($lookCount % 1000 == 0) {
2840                            Trace("$lookCount members examined. Current is $thisMem. Mask is $traceMask") if T(File => 3);
2841                        }
2842                        # Fix the group.
2843                        chown -1, $gid, $thisMem;
2844                        # Insure this member is not a symlink.
2845                        if (! -l $thisMem) {
2846                            # Get its info.
2847                            my $fileInfo = stat $thisMem;
2848                            # Only proceed if we got the info. Otherwise, it's a hard link
2849                            # and we want to skip it anyway.
2850                            if ($fileInfo) {
2851                                my $fileMode = $fileInfo->mode;
2852                                if (($fileMode & $mask) != $mask) {
2853                                    # Fix this member.
2854                                    $fileMode |= $mask;
2855                                    chmod $fileMode, $thisMem;
2856                                    $fixCount++;
2857                                }
2858                                # If it's a subdirectory, stack it.
2859                                if (-d $thisMem) {
2860                                    push @dirs, $thisMem;
2861                                }
2862                  }                  }
2863          }          }
2864          # Return the maximum found.                  }
2865          return $retVal;              }
2866            }
2867            Trace("$lookCount files and directories processed, $fixCount fixed.") if T(File => 2);
2868        };
2869        # Check for an error.
2870        if ($@) {
2871            Confess("SetPermissions error: $@");
2872        }
2873  }  }
2874    
2875  =head3 AddToListMap  =head3 CompareLists
2876    
2877  C<< Tracer::AddToListMap(\%hash, $key, $value); >>  C<< my ($inserted, $deleted) = Tracer::CompareLists(\@newList, \@oldList, $keyIndex); >>
2878    
2879  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
2880  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 $keyIndex column.
2881    The return value contains a list of items that are only in the new list
2882    (inserted) and only in the old list (deleted).
2883    
2884  =over 4  =over 4
2885    
2886  =item hash  =item newList
2887    
2888  Reference to the target hash.  Reference to a list of new tuples.
2889    
2890  =item key  =item oldList
2891    
2892  Key for which the value is to be added.  Reference to a list of old tuples.
2893    
2894    =item keyIndex (optional)
2895    
2896  =item value  Index into each tuple of its key field. The default is 0.
2897    
2898  Value to add to the key's value list.  =item RETURN
2899    
2900    Returns a 2-tuple consisting of a reference to the list of items that are only in the new
2901    list (inserted) followed by a reference to the list of items that are only in the old
2902    list (deleted).
2903    
2904  =back  =back
2905    
2906  =cut  =cut
2907    
2908  sub AddToListMap {  sub CompareLists {
2909      # Get the parameters.      # Get the parameters.
2910      my ($hash, $key, $value) = @_;      my ($newList, $oldList, $keyIndex) = @_;
2911      # Process according to whether or not the key already has a value.      if (! defined $keyIndex) {
2912      if (! exists $hash->{$key}) {          $keyIndex = 0;
2913          $hash->{$key} = [$value];      }
2914        # Declare the return variables.
2915        my ($inserted, $deleted) = ([], []);
2916        # Loop through the two lists simultaneously.
2917        my ($newI, $oldI) = (0, 0);
2918        my ($newN, $oldN) = (scalar @{$newList}, scalar @{$oldList});
2919        while ($newI < $newN || $oldI < $oldN) {
2920            # Get the current object in each list. Note that if one
2921            # of the lists is past the end, we'll get undef.
2922            my $newItem = $newList->[$newI];
2923            my $oldItem = $oldList->[$oldI];
2924            if (! defined($newItem) || defined($oldItem) && $newItem->[$keyIndex] gt $oldItem->[$keyIndex]) {
2925                # The old item is not in the new list, so mark it deleted.
2926                push @{$deleted}, $oldItem;
2927                $oldI++;
2928            } elsif (! defined($oldItem) || $oldItem->[$keyIndex] gt $newItem->[$keyIndex]) {
2929                # The new item is not in the old list, so mark it inserted.
2930                push @{$inserted}, $newItem;
2931                $newI++;
2932      } else {      } else {
2933          push @{$hash->{$key}}, $value;              # The item is in both lists, so push forward.
2934                $oldI++;
2935                $newI++;
2936            }
2937      }      }
2938        # Return the result.
2939        return ($inserted, $deleted);
2940  }  }
2941    
2942  =head3 DebugMode  =head3 GetLine
2943    
2944  C<< if (Tracer::DebugMode) { ...code... } >>  C<< my @data = Tracer::GetLine($handle); >>
2945    
2946  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.  
2947    
2948  Certain CGI scripts are too dangerous to exist in the production  =over 4
2949  environment. This method provides a simple way to prevent them  
2950  from working unless they are explicitly turned on in the configuration  =item handle
2951  file by setting C<$FIG_Config::debug_mode> to 1. If debugging mode  
2952  is not turned on, an error web page will be output.  Open file handle from which to read.
2953    
2954    =item RETURN
2955    
2956    Returns a list of the fields in the record read. The fields are presumed to be
2957    tab-delimited. If we are at the end of the file, then an empty list will be
2958    returned. If an empty line is read, a single list item consisting of a null
2959    string will be returned.
2960    
2961    =back
2962    
2963  =cut  =cut
2964    
2965  sub DebugMode {  sub GetLine {
2966        # Get the parameters.
2967        my ($handle) = @_;
2968          # Declare the return variable.          # Declare the return variable.
2969          my $retVal;      my @retVal = ();
2970          # Check the debug configuration.      Trace("File position is " . tell($handle) . ". EOF flag is " . eof($handle) . ".") if T(File => 4);
2971          if ($FIG_Config::debug_mode) {      # Read from the file.
2972                  $retVal = 1;      my $line = <$handle>;
2973        # Only proceed if we found something.
2974        if (defined $line) {
2975            # Remove the new-line.
2976            chomp $line;
2977            Trace("Line read: $line") if T(File => 4);
2978            # If the line is empty, return a single empty string; otherwise, parse
2979            # it into fields.
2980            if ($line eq "") {
2981                push @retVal, "";
2982          } else {          } else {
2983                  # 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;  
2984          }          }
2985          # Return the determination indicator.      } else {
2986          return $retVal;          # Trace the reason the read failed.
2987            Trace("End of file: $!") if T(File => 3);
2988        }
2989        # Return the result.
2990        return @retVal;
2991  }  }
2992    
2993  =head3 Strip  =head3 PutLine
2994    
2995  C<< my $string = Tracer::Strip($line); >>  C<< Tracer::PutLine($handle, \@fields); >>
2996    
2997  Strip all line terminators off a string. This is necessary when dealing with files  Write a line of data to a tab-delimited file. The specified field values will be
2998  that may have been transferred back and forth several times among different  output in tab-separated form, with a trailing new-line.
 operating environments.  
2999    
3000  =over 4  =over 4
3001    
3002  =item line  =item handle
3003    
3004  Line of text to be stripped.  Output file handle.
3005    
3006  =item RETURN  =item fields
3007    
3008  The same line of text with all the line-ending characters chopped from the end.  List of field values.
3009    
3010  =back  =back
3011    
3012  =cut  =cut
3013    
3014  sub Strip {  sub PutLine {
3015          # Get a copy of the parameter string.      # Get the parameters.
3016          my ($string) = @_;      my ($handle, $fields) = @_;
3017          my $retVal = $string;      # Write the data.
3018      # Strip the line terminator characters.      print $handle join("\t", @{$fields}) . "\n";
     $retVal =~ s/(\r|\n)+$//g;  
         # Return the result.  
         return $retVal;  
3019  }  }
3020    
3021  =head3 Pad  =head3 GenerateURL
3022    
3023  C<< my $paddedString = Tracer::Pad($string, $len, $left, $padChar); >>  C<< my $queryUrl = Tracer::GenerateURL($page, %parameters); >>
3024    
3025  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
3026  space, and the padding will be on the right side unless specified  names and values. The values will be URL-escaped automatically. So, for
3027  in the third parameter.  example
3028    
3029  =over 4      Tracer::GenerateURL("form.cgi", type => 1, string => "\"high pass\" or highway")
3030    
3031  =item string  would return
3032    
3033  String to be padded.      form.cgi?type=1&string=%22high%20pass%22%20or%20highway
3034    
3035  =item len  =over 4
3036    
3037  Desired length of the padded string.  =item page
3038    
3039  =item left (optional)  Page URL.
3040    
3041  TRUE if the string is to be left-padded; otherwise it will be padded on the right.  =item parameters
3042    
3043  =item padChar (optional)  Hash mapping parameter names to parameter values.
3044    
3045  =item RETURN  =item RETURN
3046    
3047  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
3048  that it achieves the desired length.  specified parameters and values.
3049    
3050  =back  =back
3051    
3052  =cut  =cut
3053    
3054  sub Pad {  sub GenerateURL {
3055          # Get the parameters.          # Get the parameters.
3056          my ($string, $len, $left, $padChar) = @_;      my ($page, %parameters) = @_;
3057          # Compute the padding character.      # Prime the return variable with the page URL.
3058          if (! defined $padChar) {      my $retVal = $page;
3059                  $padChar = " ";      # Loop through the parameters, creating parameter elements in a list.
3060          }      my @parmList = map { "$_=" . uri_escape($parameters{$_}) } keys %parameters;
3061          # Compute the number of spaces needed.      # If the list is nonempty, tack it on.
3062          my $needed = $len - length $string;      if (@parmList) {
3063          # 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;  
                 }  
3064          }          }
3065          # Return the result.          # Return the result.
3066          return $retVal;          return $retVal;

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