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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    NOTE: to configure emergency tracing from the command line instead of the Debugging
190    Control Panel (see below), use the C<trace.pl> script.
191    
192    =head3 Debugging Control Panel
193    
194    The debugging control panel provides several tools to assist in development of
195    SEED and Sprout software. You access the debugging control panel from the URL
196    C</FIG/Html/SetPassword.html> in whichever seed instance you're using. (So,
197    for example, the panel access point for the development NMPDR system is
198    C<http://web-1.nmpdr.org/next/FIG/Html/SetPassword.html>. Contact Bruce to
199    find out what the password is. From this page, you can also specify a tracing
200    key. If you don't specify a key, one will be generated for you.
201    
202    =head4 Emergency Tracing Form
203    
204    At the bottom of the debugging control panel is a form that allows you to
205    specify a trace level and tracing categories. Special and common categories
206    are listed with check boxes. You can hold your mouse over a check box to see
207    what its category does. In general, however, a category name is the same as
208    the name of the package in which the trace message occurs.
209    
210    Additional categories can be entered in an input box, delimited by spaces or commas.
211    
212    The B<Activate> button turns on Emergency tracing at the level you specify with the
213    specified categories active. The B<Terminate> button turns tracing off. The
214    B<Show File> button displays the current contents of the trace file. The tracing
215    form at the bottom of the control panel is designed for emergency tracing, so it
216    will only affect programs that call L</ETracing>, L</StandardScript>,
217    or L</StandardSetup>.
218    
219    =head4 Script Form
220    
221    The top form of the debugging control panel allows you to enter a tiny script and
222    have the output generated in a formatted table. Certain object variables are
223    predefined in the script, including a FIG object (C<$fig>), a CGI object (C<$cgi>),
224    and-- if Sprout is active-- Sprout (C<$sprout>) and SFXlate (C<$sfx>) objects.
225    
226    The last line of the script must be a scalar, but it can be a reference to a hash,
227    a list, a list of lists, and various other combinations. If you select the appropriate
228    data type in the dropdown box, the output will be formatted accordingly. The form
229    also has controls for specifying tracing. These controls override any emergency
230    tracing in effect.
231    
232    =head4 Database Query Forms
233    
234    The forms between the script form and the emergency tracing form allow you to
235    make queries against the database. The FIG query form allows simple queries against
236    a single FIG table. The Sprout query form uses the B<GetAll> method to do a
237    multi-table query against the Sprout database. B<GetAll> is located in the B<ERDB>
238    package, and it takes five parameters.
239    
240        GetAll(\@objectNames, $filterClause, \@parameters, \@fields, $count);
241    
242    Each of the five parameters corresponds to a text box on the query form:
243    
244    =over 4
245    
246    =item Objects
247    
248    Comma-separated list containing the names of the entity and relationship objects to be retrieved.
249    
250    =item Filter
251    
252    WHERE/ORDER BY clause (without the WHERE) to be used to filter and sort the query. The WHERE clause can
253    be parameterized with parameter markers (C<?>). Each field used must be specified in the standard form
254    B<I<objectName>(I<fieldName>)> or B<$I<number>(I<fieldName>)> where I<fieldName> is the name of a
255    field, I<objectName> is the name of the entity or relationship object containing the field, and
256    I<number> is the 1-based position of the object in the object list. Any parameters
257    specified in the filter clause should be specified in the B<Params> field.
258    The fields in a filter clause can come from primary entity relations,
259    relationship relations, or secondary entity relations; however, all of the
260    entities and relationships involved must be included in the list of object names.
261    
262    =item Params
263    
264    List of the parameters to be substituted in for the parameters marks in the filter clause. This
265    is a comma-separated list without any quoting or escaping.
266    
267    =item fields
268    
269    Comma-separated list of the fields to be returned in each element of the list returned. Fields
270    are specified in the same manner as in the filter clause.
271    
272    =item count
273    
274    Maximum number of records to return. If omitted or 0, all available records will be returned.
275    
276    =back
277    
278    B<GetAll> automatically joins together the entities and relationships listed in the object
279    names. This simplifies the coding of the filter clause, but it means that some queries are
280    not possible, since they cannot be expressed in a linear sequence of joins. This is a limitation
281    that has yet to be addressed.
282    
283  =cut  =cut
284    
285  # Declare the configuration variables.  # Declare the configuration variables.
286    
287  my $Destination = "NONE";       # Description of where to send the trace output.  my $Destination = "NONE";       # Description of where to send the trace output.
288    my $TeeFlag = 0;            # TRUE if output is going to a file and to the
289                                # standard output
290  my %Categories = ( main => 1 );  my %Categories = ( main => 1 );
291                                                          # hash of active category names                                                          # hash of active category names
292  my $TraceLevel = 0;                     # trace level; a higher trace level produces more  my $TraceLevel = 0;                     # trace level; a higher trace level produces more
293                                                          # messages                                                          # messages
294  my @Queue = ();                         # queued list of trace messages.  my @Queue = ();                         # queued list of trace messages.
295  my $LastCategory = "main";  # name of the last category interrogated  my $LastCategory = "main";  # name of the last category interrogated
296    my $SetupCount = 0;         # number of times TSetup called
297    my $AllTrace = 0;           # TRUE if we are tracing all categories.
298    
299  =head2 Public Methods  =head2 Public Methods
300    
301  =head3 TSetup  =head3 TSetup
302    
303  C<< TSetup($categoryList, $target); >>      TSetup($categoryList, $target);
304    
305  This method is used to specify the trace options. The options are stored as package data  This method is used to specify the trace options. The options are stored as package data
306  and interrogated by the L</Trace> and L</T> methods.  and interrogated by the L</Trace> and L</T> methods.
# Line 93  Line 316 
316    
317  The destination for the trace output. To send the trace output to a file, specify the file  The destination for the trace output. To send the trace output to a file, specify the file
318  name preceded by a ">" symbol. If a double symbol is used (">>"), then the data is appended  name preceded by a ">" symbol. If a double symbol is used (">>"), then the data is appended
319  to the file. Otherwise the file is cleared before tracing begins. In addition to sending  to the file. Otherwise the file is cleared before tracing begins. Precede the first ">"
320  the trace messages to a file, you can specify a special destination. C<HTML> will cause  symbol with a C<+> to echo output to a file AND to the standard output. In addition to
321  tracing to the standard output with each line formatted as an HTML paragraph. C<TEXT>  sending the trace messages to a file, you can specify a special destination. C<HTML> will
322    cause tracing to the standard output with each line formatted as an HTML paragraph. C<TEXT>
323  will cause tracing to the standard output as ordinary text. C<ERROR> will cause trace  will cause tracing to the standard output as ordinary text. C<ERROR> will cause trace
324  messages to be sent to the standard error output as ordinary text. C<QUEUE> will cause trace  messages to be sent to the standard error output as ordinary text. C<QUEUE> will cause trace
325  messages to be stored in a queue for later retrieval by the L</QTrace> method. C<WARN> will  messages to be stored in a queue for later retrieval by the L</QTrace> method. C<WARN> will
# Line 113  Line 337 
337          my @categoryData = split /\s+/, $categoryList;          my @categoryData = split /\s+/, $categoryList;
338          # Extract the trace level.          # Extract the trace level.
339          $TraceLevel = shift @categoryData;          $TraceLevel = shift @categoryData;
340          # Build the category hash.      # Presume category-based tracing until we learn otherwise.
341        $AllTrace = 0;
342        # Build the category hash. Note that if we find a "*", we turn on non-category
343        # tracing. We must also clear away any pre-existing data.
344        %Categories = ( main => 1 );
345          for my $category (@categoryData) {          for my $category (@categoryData) {
346                  $Categories{$category} = 1;          if ($category eq '*') {
347                $AllTrace = 1;
348            } else {
349                $Categories{lc $category} = 1;
350            }
351          }          }
352          # Now we need to process the destination information. The most important special          # Now we need to process the destination information. The most important special
353          # case is the single ">", which requires we clear the file first. After doing      # cases are the single ">", which requires we clear the file first, and the
354          # so, we tack on another ">" sign so that future trace messages are appended.      # "+" prefix which indicates a double echo.
355        if ($target =~ m/^\+?>>?/) {
356            if ($target =~ m/^\+/) {
357                $TeeFlag = 1;
358                $target = substr($target, 1);
359            }
360          if ($target =~ m/^>[^>]/) {          if ($target =~ m/^>[^>]/) {
361                  open TRACEFILE, $target;                  open TRACEFILE, $target;
362                  print TRACEFILE Now() . " Tracing initialized.\n";              print TRACEFILE "[" . Now() . "] <Tracer>: Tracing initialized.\n";
363                  close TRACEFILE;                  close TRACEFILE;
364                  $Destination = ">$target";                  $Destination = ">$target";
365          } else {          } else {
366                $Destination = $target;
367            }
368        } else {
369                  $Destination = uc($target);                  $Destination = uc($target);
370          }          }
371        # Increment the setup counter.
372        $SetupCount++;
373  }  }
374    
375  =head3 SetLevel  =head3 StandardSetup
376    
377  C<< Tracer::SetLevel($newLevel); >>      my ($options, @parameters) = StandardSetup(\@categories, \%options, $parmHelp, @ARGV);
378    
379  Modify the trace level. A higher trace level will cause more messages to appear.  This method performs standard command-line parsing and tracing setup. The return
380    values are a hash of the command-line options and a list of the positional
381    parameters. Tracing is automatically set up and the command-line options are
382    validated.
383    
384    This is a complex method that does a lot of grunt work. The parameters can
385    be more easily understood, however, once they are examined individually.
386    
387    The I<categories> parameter is the most obtuse. It is a reference to a list of
388    special-purpose tracing categories. Most tracing categories are PERL package
389    names. So, for example, if you wanted to turn on tracing inside the B<Sprout>,
390    B<ERDB>, and B<SproutLoad> packages, you would specify the categories
391    
392        ["Sprout", "SproutLoad", "ERDB"]
393    
394    This would cause trace messages in the specified three packages to appear in
395    the output. There are two special tracing categories that are automatically
396    handled by this method. In other words, if you used L</TSetup> you would need
397    to include these categories manually, but if you use this method they are turned
398    on automatically.
399    
400  =over 4  =over 4
401    
402  =item newLevel  =item SQL
403    
404  Proposed new trace level.  Traces SQL commands and activity.
405    
406    =item Tracer
407    
408    Traces error messages and call stacks.
409    
410  =back  =back
411    
412  =cut  C<SQL> is only turned on if the C<-sql> option is specified in the command line.
413    The trace level is specified using the C<-trace> command-line option. For example,
414    the following command line for C<TransactFeatures> turns on SQL tracing and runs
415    all tracing at level 3.
416    
417  sub SetLevel {      TransactFeatures -trace=3 -sql register ../xacts IDs.tbl
     $TraceLevel = $_[0];  
 }  
418    
419  =head3 Now  Standard tracing is output to the standard output and echoed to the file
420    C<trace>I<$$>C<.log> in the FIG temporary directory, where I<$$> is the
421    process ID. You can also specify the C<user> parameter to put a user ID
422    instead of a process ID in the trace file name. So, for example
423    
424  C<< my $string = Tracer::Now(); >>  The default trace level is 2. To get all messages, specify a trace level of 4.
425    For a genome-by-genome update, use 3.
426    
427  Return a displayable time stamp containing the local time.      TransactFeatures -trace=3 -sql -user=Bruce register ../xacts IDs.tbl
428    
429  =cut  would send the trace output to C<traceBruce.log> in the temporary directory.
430    
431  sub Now {  The I<options> parameter is a reference to a hash containing the command-line
432          my ($sec,$min,$hour,$mday,$mon,$year,$wday,$yday,$isdst) = localtime(time);  options, their default values, and an explanation of what they mean. Command-line
433          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
434                                   _p2($hour) . ":" . _p2($min) . ":" . _p2($sec);  option value is 1 if it is specified and 0 if it is not specified. In the case
435          return $retVal;  of a keyword, the value is separated from the option name by an equal sign. You
436  }  can see this last in the command-line example above.
437    
438  # Pad a number to 2 digits.  You can specify a different default trace level by setting C<$options->{trace}>
439  sub _p2 {  prior to calling this method.
         my ($value) = @_;  
         $value = "0$value" if ($value < 10);  
         return $value;  
 }  
440    
441  =head3 LogErrors  An example at this point would help. Consider, for example, the command-line utility
442    C<TransactFeatures>. It accepts a list of positional parameters plus the options
443    C<safe>, C<noAlias>, C<start>, and C<tblFiles>. To start up this command, we execute
444    the following code.
445    
446  C<< Tracer::LogErrors($fileName); >>      my ($options, @parameters) = Tracer::StandardSetup(["DocUtils"],
447                            { safe => [0, "use database transactions"],
448                              noAlias => [0, "do not expect aliases in CHANGE transactions"],
449                              start => [' ', "start with this genome"],
450                              tblFiles => [0, "output TBL files containing the corrected IDs"] },
451                            "<command> <transactionDirectory> <IDfile>",
452                          @ARGV);
453    
 Route the standard error output to a log file.  
454    
455  =over 4  The call to C<ParseCommand> specifies the default values for the options and
456    stores the actual options in a hash that is returned as C<$options>. The
457    positional parameters are returned in C<@parameters>.
458    
459  =item fileName  The following is a sample command line for C<TransactFeatures>.
460    
461  Name of the file to receive the error output.      TransactFeatures -trace=2 -noAlias register ../xacts IDs.tbl
462    
463  =back  Single and double hyphens are equivalent. So, you could also code the
464    above command as
465    
466  =cut      TransactFeatures --trace=2 --noAlias register ../xacts IDs.tbl
467    
468  sub LogErrors {  In this case, C<register>, C<../xacts>, and C<IDs.tbl> are the positional
469          # Get the file name.  parameters, and would find themselves in I<@parameters> after executing the
470          my ($fileName) = @_;  above code fragment. The tracing would be set to level 2, and the categories
471          # Open the file as the standard error output.  would be C<Tracer>, and <DocUtils>. C<Tracer> is standard,
472          open STDERR, '>', $fileName;  and C<DocUtils> was included because it came in within the first parameter
473  }  to this method. The I<$options> hash would be
474    
475  =head3 ReadOptions      { trace => 2, sql => 0, safe => 0,
476          noAlias => 1, start => ' ', tblFiles => 0 }
477    
478  C<< my %options = Tracer::ReadOptions($fileName); >>  Use of C<StandardSetup> in this way provides a simple way of performing
479    standard tracing setup and command-line parsing. Note that the caller is
480    not even aware of the command-line switches C<-trace> and C<-sql>, which
481    are used by this method to control the tracing. If additional tracing features
482    need to be added in the future, they can be processed by this method without
483    upsetting the command-line utilities.
484    
485  Read a set of options from a file. Each option is encoded in a line of text that has the  If the C<background> option is specified on the command line, then the
486  format  standard and error outputs will be directed to files in the temporary
487    directory, using the same suffix as the trace file. So, if the command
488    line specified
489    
490  I<optionName>C<=>I<optionValue>C<; >I<comment>      -user=Bruce -background
491    
492  The option name must consist entirely of letters, digits, and the punctuation characters  then the trace output would go to C<traceBruce.log>, the standard output to
493  C<.> and C<_>, and is case sensitive. Blank lines and lines in which the first nonblank  C<outBruce.log>, and the error output to C<errBruce.log>. This is designed to
494  character is a semi-colon will be ignored. The return hash will map each option name to  simplify starting a command in the background.
495  the corresponding option value.  
496    The user name is also used as the tracing key for L</Emergency Tracing>.
497    Specifying a value of C<E> for the trace level causes emergency tracing to
498    be used instead of custom tracing. If the user name is not specified,
499    the tracing key is taken from the C<Tracing> environment variable. If there
500    is no value for that variable, the tracing key will be computed from the PID.
501    
502    Finally, if the special option C<-help> is specified, the option
503    names will be traced at level 0 and the program will exit without processing.
504    This provides a limited help capability. For example, if the user enters
505    
506        TransactFeatures -help
507    
508    he would see the following output.
509    
510        TransactFeatures [options] <command> <transactionDirectory> <IDfile>
511            -trace    tracing level (default E)
512            -sql      trace SQL commands
513            -safe     use database transactions
514            -noAlias  do not expect aliases in CHANGE transactions
515            -start    start with this genome
516            -tblFiles output TBL files containing the corrected IDs
517    
518    The caller has the option of modifying the tracing scheme by placing a value
519    for C<trace> in the incoming options hash. The default value can be overridden,
520    or the tracing to the standard output can be turned off by suffixing a minus
521    sign to the trace level. So, for example,
522    
523        { trace => [0, "tracing level (default 0)"],
524           ...
525    
526    would set the default trace level to 0 instead of E, while
527    
528        { trace => ["2-", "tracing level (default 2)"],
529           ...
530    
531    would set the default to 2, but trace only to the log file, not to the
532    standard output.
533    
534    The parameters to this method are as follows.
535    
536  =over 4  =over 4
537    
538  =item fileName  =item categories
539    
540  Name of the file containing the option data.  Reference to a list of tracing category names. These should be names of
541    packages whose internal workings will need to be debugged to get the
542    command working.
543    
544    =item options
545    
546    Reference to a hash containing the legal options for the current command mapped
547    to their default values and descriptions. The user can override the defaults
548    by specifying the options as command-line switches prefixed by a hyphen.
549    Tracing-related options may be added to this hash. If the C<-h> option is
550    specified on the command line, the option descriptions will be used to
551    explain the options. To turn off tracing to the standard output, add a
552    minus sign to the value for C<trace> (see above).
553    
554    =item parmHelp
555    
556    A string that vaguely describes the positional parameters. This is used
557    if the user specifies the C<-h> option.
558    
559    =item argv
560    
561    List of command line parameters, including the option switches, which must
562    precede the positional parameters and be prefixed by a hyphen.
563    
564  =item RETURN  =item RETURN
565    
566  Returns a 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
567  value.  maps the command-line option switches to their values. These will either be the
568    default values or overrides specified on the command line. The remaining
569    elements of the list are the position parameters, in order.
570    
571  =back  =back
572    
573  =cut  =cut
574    
575  sub ReadOptions {  sub StandardSetup {
576          # Get the parameters.          # Get the parameters.
577          my ($fileName) = @_;      my ($categories, $options, $parmHelp, @argv) = @_;
578          # Open the file.      # Get the default tracing key.
579          (open CONFIGFILE, "<$fileName") || Confess("Could not open option file $fileName.");      my $tkey = EmergencyKey();
580          # Count the number of records read.      # Add the tracing options.
581          my ($records, $comments) = 0;      if (! exists $options->{trace}) {
582          # Create the return hash.          $options->{trace} = ['2', "tracing level (E for emergency tracing)"];
583          my %retVal = ();      }
584          # Loop through the file, accumulating key-value pairs.      $options->{sql} = [0, "turn on SQL tracing"];
585          while (my $line = <CONFIGFILE>) {      $options->{help} = [0, "display command-line options"];
586                  # Denote we've read a line.      $options->{user} = [$tkey, "tracing key"];
587                  $records++;      $options->{background} = [0, "spool standard and error output"];
588                  # Determine the line type.      # Create a parsing hash from the options hash. The parsing hash
589                  if ($line =~ /^\s*[\n\r]/) {      # contains the default values rather than the default value
590                          # A blank line is a comment.      # and the description. While we're at it, we'll memorize the
591                          $comments++;      # length of the longest option name.
592                  } elsif ($line =~ /^\s*([A-Za-z0-9_\.]+)=([^;]*);/) {      my $longestName = 0;
593                          # Here we have an option assignment.      my %parseOptions = ();
594                          retVal{$1} = $2;      for my $key (keys %{$options}) {
595                  } elsif ($line =~ /^\s*;/) {          if (length $key > $longestName) {
596                          # Here we have a text comment.              $longestName = length $key;
597                          $comments++;          }
598            $parseOptions{$key} = $options->{$key}->[0];
599        }
600        # Parse the command line.
601        my ($retOptions, @retParameters) = ParseCommand(\%parseOptions, @argv);
602        # Get the logfile suffix.
603        my $suffix = $retOptions->{user};
604        # Check for background mode.
605        if ($retOptions->{background}) {
606            my $outFileName = "$FIG_Config::temp/out$suffix.log";
607            my $errFileName = "$FIG_Config::temp/err$suffix.log";
608            open STDOUT, ">$outFileName";
609            open STDERR, ">$errFileName";
610            # Check for phone support. If we have phone support and a phone number,
611            # we want to turn it on.
612            if ($ENV{PHONE} && defined($FIG_Config::phone)) {
613                $retOptions->{phone} = $ENV{PHONE};
614            }
615        }
616        # Now we want to set up tracing. First, we need to know if the user
617        # wants emergency tracing.
618        if ($retOptions->{trace} eq 'E') {
619            ETracing($retOptions->{user});
620                  } else {                  } else {
621                          # Here we have an invalid line.          # Here the tracing is controlled from the command line.
622                          Trace("Invalid option statement in record $records.") if T(0);          my @cats = @{$categories};
623            if ($retOptions->{sql}) {
624                push @cats, "SQL";
625            }
626            # Add the default categories.
627            push @cats, "Tracer";
628            # Next, we create the category string by joining the categories.
629            my $cats = join(" ", @cats);
630            # Check to determine whether or not the caller wants to turn off tracing
631            # to the standard output.
632            my $traceLevel = $retOptions->{trace};
633            my $textOKFlag = 1;
634            if ($traceLevel =~ /^(.)-/) {
635                $traceLevel = $1;
636                $textOKFlag = 0;
637            }
638            # Now we set up the trace mode.
639            my $traceMode;
640            # Verify that we can open a file in the FIG temporary directory.
641            my $traceFileName = "$FIG_Config::temp/trace$suffix.log";
642            if (open TESTTRACE, ">$traceFileName") {
643                # Here we can trace to a file.
644                $traceMode = ">$traceFileName";
645                if ($textOKFlag) {
646                    # Echo to standard output if the text-OK flag is set.
647                    $traceMode = "+$traceMode";
648                  }                  }
649                # Close the test file.
650                close TESTTRACE;
651            } else {
652                # Here we can't trace to a file. We trace to the standard output if it's
653                # okay, and the error log otherwise.
654                if ($textOKFlag) {
655                    $traceMode = "TEXT";
656                } else {
657                    $traceMode = "WARN";
658          }          }
659          # Return the hash created.          }
660          return %retVal;          # Now set up the tracing.
661            TSetup("$traceLevel $cats", $traceMode);
662        }
663        # Check for the "help" option. If it is specified, dump the command-line
664        # options and exit the program.
665        if ($retOptions->{help}) {
666            $0 =~ m#[/\\](\w+)(\.pl)?$#i;
667            print "$1 [options] $parmHelp\n";
668            for my $key (sort keys %{$options}) {
669                my $name = Pad($key, $longestName, 0, ' ');
670                my $desc = $options->{$key}->[1];
671                if ($options->{$key}->[0]) {
672                    $desc .= " (default " . $options->{$key}->[0] . ")";
673                }
674                print "  $name $desc\n";
675            }
676            exit(0);
677        }
678        # Trace the options, if applicable.
679        if (T(3)) {
680            my @parms = grep { $retOptions->{$_} } keys %{$retOptions};
681            Trace("Selected options: " . join(", ", sort @parms) . ".");
682        }
683        # Return the parsed parameters.
684        return ($retOptions, @retParameters);
685  }  }
686    
687  =head3 GetOptions  =head3 Setups
688    
689  C<< Tracer::GetOptions(\%defaults, \%options); >>      my $count = Tracer::Setups();
690    
691  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.  
692    
693  Consider the following example.  This method allows for the creation of conditional tracing setups where, for example, we
694    may want to set up tracing if nobody else has done it before us.
695    
696  C<< my $optionTable = GetOptions({ dbType => 'mySQL', trace => 0 }, $options); >>  =cut
697    
698  In this example, the variable B<$options> is expected to contain at most two options-- B<dbType> and  sub Setups {
699  B<trace>. The default database type is C<mySQL> and the default trace level is C<0>. If the value of      return $SetupCount;
700  B<$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  
701    
702  C<< {databaseType => 'Oracle'} >>  =head3 Open
703    
704  an error will occur because the B<databaseType> option does not exist.      my $handle = Open($fileHandle, $fileSpec, $message);
705    
706    Open a file.
707    
708    The I<$fileSpec> is essentially the second argument of the PERL C<open>
709    function. The mode is specified using Unix-like shell information. So, for
710    example,
711    
712        Open(\*LOGFILE, '>>/usr/spool/news/twitlog', "Could not open twit log.");
713    
714    would open for output appended to the specified file, and
715    
716        Open(\*DATASTREAM, "| sort -u >$outputFile", "Could not open $outputFile.");
717    
718    would open a pipe that sorts the records written and removes duplicates. Note
719    the use of file handle syntax in the Open call. To use anonymous file handles,
720    code as follows.
721    
722        my $logFile = Open(undef, '>>/usr/spool/news/twitlog', "Could not open twit log.");
723    
724    The I<$message> parameter is used if the open fails. If it is set to C<0>, then
725    the open returns TRUE if successful and FALSE if an error occurred. Otherwise, a
726    failed open will throw an exception and the third parameter will be used to construct
727    an error message. If the parameter is omitted, a standard message is constructed
728    using the file spec.
729    
730        Could not open "/usr/spool/news/twitlog"
731    
732    Note that the mode characters are automatically cleaned from the file name.
733    The actual error message from the file system will be captured and appended to the
734    message in any case.
735    
736        Could not open "/usr/spool/news/twitlog": file not found.
737    
738    In some versions of PERL the only error message we get is a number, which
739    corresponds to the C++ C<errno> value.
740    
741        Could not open "/usr/spool/news/twitlog": 6.
742    
743  =over 4  =over 4
744    
745  =item defaults  =item fileHandle
746    
747  Table of default option values.  File handle. If this parameter is C<undef>, a file handle will be generated
748    and returned as the value of this method.
749    
750  =item options  =item fileSpec
751    
752  Table of overrides, if any.  File name and mode, as per the PERL C<open> function.
753    
754    =item message (optional)
755    
756    Error message to use if the open fails. If omitted, a standard error message
757    will be generated. In either case, the error information from the file system
758    is appended to the message. To specify a conditional open that does not throw
759    an error if it fails, use C<0>.
760    
761  =item RETURN  =item RETURN
762    
763  Returns a reference to the default table passed in as the first parameter.  Returns the name of the file handle assigned to the file, or C<undef> if the
764    open failed.
765    
766  =back  =back
767    
768  =cut  =cut
769    
770  sub GetOptions {  sub Open {
771          # Get the parameters.          # Get the parameters.
772          my ($defaults, $options) = @_;      my ($fileHandle, $fileSpec, $message) = @_;
773          # Check for overrides.      # Attempt to open the file.
774          if ($options) {      my $rv = open $fileHandle, $fileSpec;
775                  # Loop through the overrides.      # If the open failed, generate an error message.
776                  while (my ($option, $setting) = each %{$options}) {      if (! $rv) {
777                          # Insure this override exists.          # Save the system error message.
778                          if (!exists $defaults->{$option}) {          my $sysMessage = $!;
779                                  croak "Unrecognized option $option encountered.";          # See if we need a default message.
780                          } else {          if (!$message) {
781                                  # Apply the override.              # Clean any obvious mode characters and leading spaces from the
782                                  $defaults->{$option} = $setting;              # filename.
783                my ($fileName) = FindNamePart($fileSpec);
784                $message = "Could not open \"$fileName\"";
785                          }                          }
786            # Terminate with an error using the supplied message and the
787            # error message from the file system.
788            Confess("$message: $!");
789                  }                  }
790          }      # Return the file handle.
791          # Return the merged table.      return $fileHandle;
         return $defaults;  
792  }  }
793    
794  =head3 MergeOptions  =head3 FindNamePart
795    
796  C<< Tracer::MergeOptions(\%table, \%defaults); >>      my ($fileName, $start, $len) = Tracer::FindNamePart($fileSpec);
797    
798  Merge default values into a hash table. This method looks at the key-value pairs in the  Extract the portion of a file specification that contains the file name.
799  second (default) hash, and if a matching key is not found in the first hash, the default  
800  pair is copied in. The process is similar to L</GetOptions>, but there is no error-  A file specification is the string passed to an C<open> call. It specifies the file
801  checking and no return value.  mode and name. In a truly complex situation, it can specify a pipe sequence. This
802    method assumes that the file name is whatever follows the first angle bracket
803    sequence.  So, for example, in the following strings the file name is
804    C</usr/fig/myfile.txt>.
805    
806        >>/usr/fig/myfile.txt
807        </usr/fig/myfile.txt
808        | sort -u > /usr/fig/myfile.txt
809    
810    If the method cannot find a file name using its normal methods, it will return the
811    whole incoming string.
812    
813  =over 4  =over 4
814    
815  =item table  =item fileSpec
816    
817  Hash table to be updated with the default values.  File specification string from which the file name is to be extracted.
818    
819  =item defaults  =item RETURN
820    
821  Default values to be merged into the first hash table if they are not already present.  Returns a three-element list. The first element contains the file name portion of
822    the specified string, or the whole string if a file name cannot be found via normal
823    methods. The second element contains the start position of the file name portion and
824    the third element contains the length.
825    
826  =back  =back
827    
828  =cut  =cut
829    #: Return Type $;
830  sub MergeOptions {  sub FindNamePart {
831          # Get the parameters.          # Get the parameters.
832          my ($table, $defaults) = @_;      my ($fileSpec) = @_;
833          # Loop through the defaults.      # Default to the whole input string.
834          while (my ($key, $value) = each %{$defaults}) {      my ($retVal, $pos, $len) = ($fileSpec, 0, length $fileSpec);
835                  if (!exists $table->{$key}) {      # Parse out the file name if we can.
836                          $table->{$key} = $value;      if ($fileSpec =~ m/(<|>>?)(.+?)(\s*)$/) {
837                  }          $retVal = $2;
838            $len = length $retVal;
839            $pos = (length $fileSpec) - (length $3) - $len;
840          }          }
841        # Return the result.
842        return ($retVal, $pos, $len);
843  }  }
844    
845  =head3 Trace  =head3 OpenDir
846    
847  C<< Trace($message); >>      my @files = OpenDir($dirName, $filtered, $flag);
848    
849  Write a trace message to the target location specified in L</TSetup>. If there has not been  Open a directory and return all the file names. This function essentially performs
850  any prior call to B<TSetup>.  the functions of an C<opendir> and C<readdir>. If the I<$filtered> parameter is
851    set to TRUE, all filenames beginning with a period (C<.>), dollar sign (C<$>),
852    or pound sign (C<#>) and all filenames ending with a tilde C<~>) will be
853    filtered out of the return list. If the directory does not open and I<$flag> is not
854    set, an exception is thrown. So, for example,
855    
856  =over 4      my @files = OpenDir("/Volumes/fig/contigs", 1);
857    
858  =item message  is effectively the same as
859    
860  Message to write.      opendir(TMP, "/Volumes/fig/contigs") || Confess("Could not open /Volumes/fig/contigs.");
861        my @files = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir(TMP);
862    
863  =back  Similarly, the following code
864    
865        my @files = grep { $_ =~ /^\d/ } OpenDir("/Volumes/fig/orgs", 0, 1);
866    
867    Returns the names of all files in C</Volumes/fig/orgs> that begin with digits and
868    automatically returns an empty list if the directory fails to open.
869    
870    =over 4
871    
872    =item dirName
873    
874    Name of the directory to open.
875    
876    =item filtered
877    
878    TRUE if files whose names begin with a period (C<.>) should be automatically removed
879    from the list, else FALSE.
880    
881    =item flag
882    
883    TRUE if a failure to open is okay, else FALSE
884    
885    =back
886    
887    =cut
888    #: Return Type @;
889    sub OpenDir {
890        # Get the parameters.
891        my ($dirName, $filtered, $flag) = @_;
892        # Declare the return variable.
893        my @retVal = ();
894        # Open the directory.
895        if (opendir(my $dirHandle, $dirName)) {
896            # The directory opened successfully. Get the appropriate list according to the
897            # strictures of the filter parameter.
898            if ($filtered) {
899                @retVal = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir $dirHandle;
900            } else {
901                @retVal = readdir $dirHandle;
902            }
903        } elsif (! $flag) {
904            # Here the directory would not open and it's considered an error.
905            Confess("Could not open directory $dirName.");
906        }
907        # Return the result.
908        return @retVal;
909    }
910    
911    =head3 SetLevel
912    
913        Tracer::SetLevel($newLevel);
914    
915    Modify the trace level. A higher trace level will cause more messages to appear.
916    
917    =over 4
918    
919    =item newLevel
920    
921    Proposed new trace level.
922    
923    =back
924    
925    =cut
926    
927    sub SetLevel {
928        $TraceLevel = $_[0];
929    }
930    
931    =head3 Now
932    
933        my $string = Tracer::Now();
934    
935    Return a displayable time stamp containing the local time.
936    
937    =cut
938    
939    sub Now {
940        my ($sec,$min,$hour,$mday,$mon,$year,$wday,$yday,$isdst) = localtime(time);
941        my $retVal = _p2($mon+1) . "/" . _p2($mday) . "/" . ($year + 1900) . " " .
942                     _p2($hour) . ":" . _p2($min) . ":" . _p2($sec);
943        return $retVal;
944    }
945    
946    # Pad a number to 2 digits.
947    sub _p2 {
948        my ($value) = @_;
949        $value = "0$value" if ($value < 10);
950        return $value;
951    }
952    
953    =head3 ParseTraceDate
954    
955        my $time = Tracer::ParseTraceDate($dateString);
956    
957    Convert a date from the trace file into a PERL timestamp.
958    
959    =over 4
960    
961    =item dateString
962    
963    The date string from the trace file. The format of the string is determined by the
964    L</Now> method.
965    
966    =item RETURN
967    
968    Returns a PERL time, that is, a number of seconds since the epoch, or C<undef> if
969    the time string is invalid.
970    
971    =back
972    
973    =cut
974    
975    sub ParseTraceDate {
976        # Get the parameters.
977        my ($dateString) = @_;
978        # Declare the return variable.
979        my $retVal;
980        # Parse the date.
981        if ($dateString =~ m#(\d+)/(\d+)/(\d+)\s+(\d+):(\d+):(\d+)#) {
982            # Create a time object. Note we need to convert the day, month,
983            # and year to a different base. Years count from 1900, and
984            # the internal month value is relocated to January = 0.
985            $retVal = timelocal($6, $5, $4, $2, $1 - 1, $3 - 1900);
986        }
987        # Return the result.
988        return $retVal;
989    }
990    
991    =head3 LogErrors
992    
993        Tracer::LogErrors($fileName);
994    
995    Route the standard error output to a log file.
996    
997    =over 4
998    
999    =item fileName
1000    
1001    Name of the file to receive the error output.
1002    
1003    =back
1004    
1005    =cut
1006    
1007    sub LogErrors {
1008        # Get the file name.
1009        my ($fileName) = @_;
1010        # Open the file as the standard error output.
1011        open STDERR, '>', $fileName;
1012    }
1013    
1014    =head3 ReadOptions
1015    
1016        my %options = Tracer::ReadOptions($fileName);
1017    
1018    Read a set of options from a file. Each option is encoded in a line of text that has the
1019    format
1020    
1021    I<optionName>C<=>I<optionValue>C<; >I<comment>
1022    
1023    The option name must consist entirely of letters, digits, and the punctuation characters
1024    C<.> and C<_>, and is case sensitive. Blank lines and lines in which the first nonblank
1025    character is a semi-colon will be ignored. The return hash will map each option name to
1026    the corresponding option value.
1027    
1028    =over 4
1029    
1030    =item fileName
1031    
1032    Name of the file containing the option data.
1033    
1034    =item RETURN
1035    
1036    Returns a hash mapping the option names specified in the file to their corresponding option
1037    value.
1038    
1039    =back
1040    
1041    =cut
1042    
1043    sub ReadOptions {
1044        # Get the parameters.
1045        my ($fileName) = @_;
1046        # Open the file.
1047        (open CONFIGFILE, "<$fileName") || Confess("Could not open option file $fileName.");
1048        # Count the number of records read.
1049        my ($records, $comments) = 0;
1050        # Create the return hash.
1051        my %retVal = ();
1052        # Loop through the file, accumulating key-value pairs.
1053        while (my $line = <CONFIGFILE>) {
1054            # Denote we've read a line.
1055            $records++;
1056            # Determine the line type.
1057            if ($line =~ /^\s*[\n\r]/) {
1058                # A blank line is a comment.
1059                $comments++;
1060            } elsif ($line =~ /^\s*([A-Za-z0-9_\.]+)=([^;]*);/) {
1061                # Here we have an option assignment.
1062                retVal{$1} = $2;
1063            } elsif ($line =~ /^\s*;/) {
1064                # Here we have a text comment.
1065                $comments++;
1066            } else {
1067                # Here we have an invalid line.
1068                Trace("Invalid option statement in record $records.") if T(0);
1069            }
1070        }
1071        # Return the hash created.
1072        return %retVal;
1073    }
1074    
1075    =head3 GetOptions
1076    
1077        Tracer::GetOptions(\%defaults, \%options);
1078    
1079    Merge a specified set of options into a table of defaults. This method takes two hash references
1080    as input and uses the data from the second to update the first. If the second does not exist,
1081    there will be no effect. An error will be thrown if one of the entries in the second hash does not
1082    exist in the first.
1083    
1084    Consider the following example.
1085    
1086        my $optionTable = GetOptions({ dbType => 'mySQL', trace => 0 }, $options);
1087    
1088    In this example, the variable B<$options> is expected to contain at most two options-- B<dbType> and
1089    B<trace>. The default database type is C<mySQL> and the default trace level is C<0>. If the value of
1090    B<$options> is C<< {dbType => 'Oracle'} >>, then the database type will be changed to C<Oracle> and
1091    the trace level will remain at 0. If B<$options> is undefined, then the database type and trace level
1092    will remain C<mySQL> and C<0>. If, on the other hand, B<$options> is defined as
1093    
1094        {databaseType => 'Oracle'}
1095    
1096    an error will occur because the B<databaseType> option does not exist.
1097    
1098    =over 4
1099    
1100    =item defaults
1101    
1102    Table of default option values.
1103    
1104    =item options
1105    
1106    Table of overrides, if any.
1107    
1108    =item RETURN
1109    
1110    Returns a reference to the default table passed in as the first parameter.
1111    
1112    =back
1113    
1114    =cut
1115    
1116    sub GetOptions {
1117        # Get the parameters.
1118        my ($defaults, $options) = @_;
1119        # Check for overrides.
1120        if ($options) {
1121            # Loop through the overrides.
1122            while (my ($option, $setting) = each %{$options}) {
1123                # Insure this override exists.
1124                if (!exists $defaults->{$option}) {
1125                    croak "Unrecognized option $option encountered.";
1126                } else {
1127                    # Apply the override.
1128                    $defaults->{$option} = $setting;
1129                }
1130            }
1131        }
1132        # Return the merged table.
1133        return $defaults;
1134    }
1135    
1136    =head3 MergeOptions
1137    
1138        Tracer::MergeOptions(\%table, \%defaults);
1139    
1140    Merge default values into a hash table. This method looks at the key-value pairs in the
1141    second (default) hash, and if a matching key is not found in the first hash, the default
1142    pair is copied in. The process is similar to L</GetOptions>, but there is no error-
1143    checking and no return value.
1144    
1145    =over 4
1146    
1147    =item table
1148    
1149    Hash table to be updated with the default values.
1150    
1151    =item defaults
1152    
1153    Default values to be merged into the first hash table if they are not already present.
1154    
1155    =back
1156    
1157    =cut
1158    
1159    sub MergeOptions {
1160        # Get the parameters.
1161        my ($table, $defaults) = @_;
1162        # Loop through the defaults.
1163        while (my ($key, $value) = each %{$defaults}) {
1164            if (!exists $table->{$key}) {
1165                $table->{$key} = $value;
1166            }
1167        }
1168    }
1169    
1170    =head3 Trace
1171    
1172        Trace($message);
1173    
1174    Write a trace message to the target location specified in L</TSetup>. If there has not been
1175    any prior call to B<TSetup>.
1176    
1177    =over 4
1178    
1179    =item message
1180    
1181    Message to write.
1182    
1183    =back
1184    
1185    =cut
1186    
1187    sub Trace {
1188        # Get the parameters.
1189        my ($message) = @_;
1190        # Get the timestamp.
1191        my $timeStamp = Now();
1192        # Format the message. Note we strip off any line terminators at the end.
1193        my $prefix = "[$timeStamp] <$LastCategory>: ";
1194        my $formatted = $prefix . Strip($message);
1195        # Process according to the destination.
1196        if ($Destination eq "TEXT") {
1197            # Write the message to the standard output.
1198            print "$formatted\n";
1199        } elsif ($Destination eq "ERROR") {
1200            # Write the message to the error output.
1201            print STDERR "$formatted\n";
1202        } elsif ($Destination eq "QUEUE") {
1203            # Push the message into the queue.
1204            push @Queue, "$formatted";
1205        } elsif ($Destination eq "HTML") {
1206            # Convert the message to HTML and write it to the standard output.
1207            my $escapedMessage = CGI::escapeHTML($message);
1208            print "<p>$timeStamp $LastCategory: $escapedMessage</p>\n";
1209        } elsif ($Destination eq "WARN") {
1210           # Emit the message as a warning.
1211           warn $message;
1212        } elsif ($Destination =~ m/^>>/) {
1213            # Write the trace message to an output file.
1214            (open TRACING, $Destination) || die "Tracing open for \"$Destination\" failed: $!";
1215            print TRACING "$formatted\n";
1216            close TRACING;
1217            # If the Tee flag is on, echo it to the standard output.
1218            if ($TeeFlag) {
1219                print "$formatted\n";
1220            }
1221        }
1222    }
1223    
1224    =head3 T
1225    
1226        my $switch = T($category, $traceLevel);
1227    
1228        or
1229    
1230        my $switch = T($traceLevel);
1231    
1232    Return TRUE if the trace level is at or above a specified value and the specified category
1233    is active, else FALSE. If no category is specified, the caller's package name is used.
1234    
1235    =over 4
1236    
1237    =item category
1238    
1239    Category to which the message belongs. If not specified, the caller's package name is
1240    used.
1241    
1242    =item traceLevel
1243    
1244    Relevant tracing level.
1245    
1246    =item RETURN
1247    
1248    TRUE if a message at the specified trace level would appear in the trace, else FALSE.
1249    
1250    =back
1251    
1252    =cut
1253    
1254    sub T {
1255        # Declare the return variable.
1256        my $retVal = 0;
1257        # Only proceed if tracing is turned on.
1258        if ($Destination ne "NONE") {
1259            # Get the parameters.
1260            my ($category, $traceLevel) = @_;
1261            if (!defined $traceLevel) {
1262                # Here we have no category, so we need to get the calling package.
1263                # The calling package is normally the first parameter. If it is
1264                # omitted, the first parameter will be the tracelevel. So, the
1265                # first thing we do is shift the so-called category into the
1266                # $traceLevel variable where it belongs.
1267                $traceLevel = $category;
1268                my ($package, $fileName, $line) = caller;
1269                # If there is no calling package, we default to "main".
1270                if (!$package) {
1271                    $category = "main";
1272                } else {
1273                    my @cats = split /::/, $package;
1274                    $category = $cats[$#cats];
1275                }
1276            }
1277            # Save the category name.
1278            $LastCategory = $category;
1279            # Convert it to lower case before we hash it.
1280            $category = lc $category;
1281            # Use the category and tracelevel to compute the result.
1282            if (ref $traceLevel) {
1283                Confess("Bad trace level.");
1284            } elsif (ref $TraceLevel) {
1285                Confess("Bad trace config.");
1286            }
1287            $retVal = ($traceLevel <= $TraceLevel && ($AllTrace || exists $Categories{$category}));
1288        }
1289        # Return the computed result.
1290        return $retVal;
1291    }
1292    
1293    =head3 ParseCommand
1294    
1295        my ($options, @arguments) = Tracer::ParseCommand(\%optionTable, @inputList);
1296    
1297    Parse a command line consisting of a list of parameters. The initial parameters may be option
1298    specifiers of the form C<->I<option> or C<->I<option>C<=>I<value>. The options are stripped
1299    off and merged into a table of default options. The remainder of the command line is
1300    returned as a list of positional arguments. For example, consider the following invocation.
1301    
1302        my ($options, @arguments) = ParseCommand({ errors => 0, logFile => 'trace.log'}, @words);
1303    
1304    In this case, the list @words will be treated as a command line and there are two options available,
1305    B<errors> and B<logFile>. If @words has the following format
1306    
1307        -logFile=error.log apple orange rutabaga
1308    
1309    then at the end of the invocation, C<$options> will be
1310    
1311        { errors => 0, logFile => 'error.log' }
1312    
1313    and C<@arguments> will contain
1314    
1315        apple orange rutabaga
1316    
1317    The parser allows for some escape sequences. See L</UnEscape> for a description. There is no
1318    support for quote characters. Options can be specified with single or double hyphens.
1319    
1320    =over 4
1321    
1322    =item optionTable
1323    
1324    Table of default options.
1325    
1326    =item inputList
1327    
1328    List of words on the command line.
1329    
1330    =item RETURN
1331    
1332    Returns a reference to the option table and a list of the positional arguments.
1333    
1334    =back
1335    
1336    =cut
1337    
1338    sub ParseCommand {
1339        # Get the parameters.
1340        my ($optionTable, @inputList) = @_;
1341        # Process any options in the input list.
1342        my %overrides = ();
1343        while ((@inputList > 0) && ($inputList[0] =~ /^--?/)) {
1344            # Get the current option.
1345            my $arg = shift @inputList;
1346            # Pull out the option name.
1347            $arg =~ /^--?([^=]*)/g;
1348            my $name = $1;
1349            # Check for an option value.
1350            if ($arg =~ /\G=(.*)$/g) {
1351                # Here we have a value for the option.
1352                $overrides{$name} = UnEscape($1);
1353            } else {
1354                # Here there is no value, so we use 1.
1355                $overrides{$name} = 1;
1356            }
1357        }
1358        # Merge the options into the defaults.
1359        GetOptions($optionTable, \%overrides);
1360        # Translate the remaining parameters.
1361        my @retVal = ();
1362        for my $inputParm (@inputList) {
1363            push @retVal, UnEscape($inputParm);
1364        }
1365        # Return the results.
1366        return ($optionTable, @retVal);
1367    }
1368    
1369    =head3 Escape
1370    
1371        my $codedString = Tracer::Escape($realString);
1372    
1373    Escape a string for use in a command length. Tabs will be replaced by C<\t>, new-lines
1374    replaced by C<\n>, carriage returns will be deleted, and backslashes will be doubled. The
1375    result is to reverse the effect of L</UnEscape>.
1376    
1377    =over 4
1378    
1379    =item realString
1380    
1381    String to escape.
1382    
1383    =item RETURN
1384    
1385    Escaped equivalent of the real string.
1386    
1387    =back
1388    
1389    =cut
1390    
1391    sub Escape {
1392        # Get the parameter.
1393        my ($realString) = @_;
1394        # Initialize the return variable.
1395        my $retVal = "";
1396        # Loop through the parameter string, looking for sequences to escape.
1397        while (length $realString > 0) {
1398            # Look for the first sequence to escape.
1399            if ($realString =~ /^(.*?)([\n\t\r\\])/) {
1400                # Here we found it. The text preceding the sequence is in $1. The sequence
1401                # itself is in $2. First, move the clear text to the return variable.
1402                $retVal .= $1;
1403                # Strip the processed section off the real string.
1404                $realString = substr $realString, (length $2) + (length $1);
1405                # Get the matched character.
1406                my $char = $2;
1407                # If we have a CR, we are done.
1408                if ($char ne "\r") {
1409                    # It's not a CR, so encode the escape sequence.
1410                    $char =~ tr/\t\n/tn/;
1411                    $retVal .= "\\" . $char;
1412                }
1413            } else {
1414                # Here there are no more escape sequences. The rest of the string is
1415                # transferred unmodified.
1416                $retVal .= $realString;
1417                $realString = "";
1418            }
1419        }
1420        # Return the result.
1421        return $retVal;
1422    }
1423    
1424    =head3 UnEscape
1425    
1426        my $realString = Tracer::UnEscape($codedString);
1427    
1428    Replace escape sequences with their actual equivalents. C<\t> will be replaced by
1429    a tab, C<\n> by a new-line character, and C<\\> by a backslash. C<\r> codes will
1430    be deleted.
1431    
1432    =over 4
1433    
1434    =item codedString
1435    
1436    String to un-escape.
1437    
1438    =item RETURN
1439    
1440    Returns a copy of the original string with the escape sequences converted to their actual
1441    values.
1442    
1443    =back
1444    
1445    =cut
1446    
1447    sub UnEscape {
1448        # Get the parameter.
1449        my ($codedString) = @_;
1450        # Initialize the return variable.
1451        my $retVal = "";
1452        # Only proceed if the incoming string is nonempty.
1453        if (defined $codedString) {
1454            # Loop through the parameter string, looking for escape sequences. We can't do
1455            # translating because it causes problems with the escaped slash. ("\\t" becomes
1456            # "\<tab>" no matter what we do.)
1457            while (length $codedString > 0) {
1458                # Look for the first escape sequence.
1459                if ($codedString =~ /^(.*?)\\(\\|n|t|r)/) {
1460                    # Here we found it. The text preceding the sequence is in $1. The sequence
1461                    # itself is in $2. First, move the clear text to the return variable.
1462                    $retVal .= $1;
1463                    $codedString = substr $codedString, (2 + length $1);
1464                    # Get the escape value.
1465                    my $char = $2;
1466                    # If we have a "\r", we are done.
1467                    if ($char ne 'r') {
1468                        # Here it's not an 'r', so we convert it.
1469                        $char =~ tr/\\tn/\\\t\n/;
1470                        $retVal .= $char;
1471                    }
1472                } else {
1473                    # Here there are no more escape sequences. The rest of the string is
1474                    # transferred unmodified.
1475                    $retVal .= $codedString;
1476                    $codedString = "";
1477                }
1478            }
1479        }
1480        # Return the result.
1481        return $retVal;
1482    }
1483    
1484    =head3 ParseRecord
1485    
1486        my @fields = Tracer::ParseRecord($line);
1487    
1488    Parse a tab-delimited data line. The data line is split into field values. Embedded tab
1489    and new-line characters in the data line must be represented as C<\t> and C<\n>, respectively.
1490    These will automatically be converted.
1491    
1492    =over 4
1493    
1494    =item line
1495    
1496    Line of data containing the tab-delimited fields.
1497    
1498    =item RETURN
1499    
1500    Returns a list of the fields found in the data line.
1501    
1502    =back
1503    
1504    =cut
1505    
1506    sub ParseRecord {
1507        # Get the parameter.
1508        my ($line) = @_;
1509        # Remove the trailing new-line, if any.
1510        chomp $line;
1511        # Split the line read into pieces using the tab character.
1512        my @retVal = split /\t/, $line;
1513        # Trim and fix the escapes in each piece.
1514        for my $value (@retVal) {
1515            # Trim leading whitespace.
1516            $value =~ s/^\s+//;
1517            # Trim trailing whitespace.
1518            $value =~ s/\s+$//;
1519            # Delete the carriage returns.
1520            $value =~ s/\r//g;
1521            # Convert the escapes into their real values.
1522            $value =~ s/\\t/"\t"/ge;
1523            $value =~ s/\\n/"\n"/ge;
1524        }
1525        # Return the result.
1526        return @retVal;
1527    }
1528    
1529    =head3 Merge
1530    
1531        my @mergedList = Tracer::Merge(@inputList);
1532    
1533    Sort a list of strings and remove duplicates.
1534    
1535    =over 4
1536    
1537    =item inputList
1538    
1539    List of scalars to sort and merge.
1540    
1541    =item RETURN
1542    
1543    Returns a list containing the same elements sorted in ascending order with duplicates
1544    removed.
1545    
1546    =back
1547    
1548    =cut
1549    
1550    sub Merge {
1551        # Get the input list in sort order.
1552        my @inputList = sort @_;
1553        # Only proceed if the list has at least two elements.
1554        if (@inputList > 1) {
1555            # Now we want to move through the list splicing out duplicates.
1556            my $i = 0;
1557            while ($i < @inputList) {
1558                # Get the current entry.
1559                my $thisEntry = $inputList[$i];
1560                # Find out how many elements duplicate the current entry.
1561                my $j = $i + 1;
1562                my $dup1 = $i + 1;
1563                while ($j < @inputList && $inputList[$j] eq $thisEntry) { $j++; };
1564                # If the number is nonzero, splice out the duplicates found.
1565                if ($j > $dup1) {
1566                    splice @inputList, $dup1, $j - $dup1;
1567                }
1568                # Now the element at position $dup1 is different from the element before it
1569                # at position $i. We push $i forward one position and start again.
1570                $i++;
1571            }
1572        }
1573        # Return the merged list.
1574        return @inputList;
1575    }
1576    
1577    =head3 Percent
1578    
1579        my $percent = Tracer::Percent($number, $base);
1580    
1581    Returns the percent of the base represented by the given number. If the base
1582    is zero, returns zero.
1583    
1584    =over 4
1585    
1586    =item number
1587    
1588    Percent numerator.
1589    
1590    =item base
1591    
1592    Percent base.
1593    
1594    =item RETURN
1595    
1596    Returns the percentage of the base represented by the numerator.
1597    
1598    =back
1599    
1600    =cut
1601    
1602    sub Percent {
1603        # Get the parameters.
1604        my ($number, $base) = @_;
1605        # Declare the return variable.
1606        my $retVal = 0;
1607        # Compute the percent.
1608        if ($base != 0) {
1609            $retVal = $number * 100 / $base;
1610        }
1611        # Return the result.
1612        return $retVal;
1613    }
1614    
1615    =head3 GetFile
1616    
1617        my @fileContents = Tracer::GetFile($fileName);
1618    
1619        or
1620    
1621        my $fileContents = Tracer::GetFile($fileName);
1622    
1623    Return the entire contents of a file. In list context, line-ends are removed and
1624    each line is a list element. In scalar context, line-ends are replaced by C<\n>.
1625    
1626    =over 4
1627    
1628    =item fileName
1629    
1630    Name of the file to read.
1631    
1632    =item RETURN
1633    
1634    In a list context, returns the entire file as a list with the line terminators removed.
1635    In a scalar context, returns the entire file as a string. If an error occurs opening
1636    the file, an empty list will be returned.
1637    
1638    =back
1639    
1640    =cut
1641    
1642    sub GetFile {
1643        # Get the parameters.
1644        my ($fileName) = @_;
1645        # Declare the return variable.
1646        my @retVal = ();
1647        # Open the file for input.
1648        my $handle = Open(undef, "<$fileName");
1649        # Read the whole file into the return variable, stripping off any terminator
1650        # characters.
1651        my $lineCount = 0;
1652        while (my $line = <$handle>) {
1653            $lineCount++;
1654            $line = Strip($line);
1655            push @retVal, $line;
1656        }
1657        # Close it.
1658        close $handle;
1659        my $actualLines = @retVal;
1660        Trace("$actualLines lines read from file $fileName.") if T(File => 2);
1661        # Return the file's contents in the desired format.
1662        if (wantarray) {
1663            return @retVal;
1664        } else {
1665            return join "\n", @retVal;
1666        }
1667    }
1668    
1669    =head3 PutFile
1670    
1671        Tracer::PutFile($fileName, \@lines);
1672    
1673    Write out a file from a list of lines of text.
1674    
1675    =over 4
1676    
1677    =item fileName
1678    
1679    Name of the output file.
1680    
1681    =item lines
1682    
1683    Reference to a list of text lines. The lines will be written to the file in order, with trailing
1684    new-line characters. Alternatively, may be a string, in which case the string will be written without
1685    modification.
1686    
1687    =back
1688    
1689    =cut
1690    
1691    sub PutFile {
1692        # Get the parameters.
1693        my ($fileName, $lines) = @_;
1694        # Open the output file.
1695        my $handle = Open(undef, ">$fileName");
1696        # Count the lines written.
1697        if (ref $lines ne 'ARRAY') {
1698            # Here we have a scalar, so we write it raw.
1699            print $handle $lines;
1700            Trace("Scalar put to file $fileName.") if T(File => 3);
1701        } else {
1702            # Write the lines one at a time.
1703            my $count = 0;
1704            for my $line (@{$lines}) {
1705                print $handle "$line\n";
1706                $count++;
1707            }
1708            Trace("$count lines put to file $fileName.") if T(File => 3);
1709        }
1710        # Close the output file.
1711        close $handle;
1712    }
1713    
1714    =head3 QTrace
1715    
1716        my $data = QTrace($format);
1717    
1718    Return the queued trace data in the specified format.
1719    
1720    =over 4
1721    
1722    =item format
1723    
1724    C<html> to format the data as an HTML list, C<text> to format it as straight text.
1725    
1726    =back
1727    
1728    =cut
1729    
1730    sub QTrace {
1731        # Get the parameter.
1732        my ($format) = @_;
1733        # Create the return variable.
1734        my $retVal = "";
1735        # Only proceed if there is an actual queue.
1736        if (@Queue) {
1737            # Process according to the format.
1738            if ($format =~ m/^HTML$/i) {
1739                # Convert the queue into an HTML list.
1740                $retVal = "<ul>\n";
1741                for my $line (@Queue) {
1742                    my $escapedLine = CGI::escapeHTML($line);
1743                    $retVal .= "<li>$escapedLine</li>\n";
1744                }
1745                $retVal .= "</ul>\n";
1746            } elsif ($format =~ m/^TEXT$/i) {
1747                # Convert the queue into a list of text lines.
1748                $retVal = join("\n", @Queue) . "\n";
1749            }
1750            # Clear the queue.
1751            @Queue = ();
1752        }
1753        # Return the formatted list.
1754        return $retVal;
1755    }
1756    
1757    =head3 Confess
1758    
1759        Confess($message);
1760    
1761    Trace the call stack and abort the program with the specified message. When used with
1762    the OR operator and the L</Assert> method, B<Confess> can function as a debugging assert.
1763    So, for example
1764    
1765        Assert($recNum >= 0) || Confess("Invalid record number $recNum.");
1766    
1767    Will abort the program with a stack trace if the value of C<$recNum> is negative.
1768    
1769    =over 4
1770    
1771    =item message
1772    
1773    Message to include in the trace.
1774    
1775    =back
1776    
1777    =cut
1778    
1779    sub Confess {
1780        # Get the parameters.
1781        my ($message) = @_;
1782        if (! defined($FIG_Config::no_tool_hdr)) {
1783            # Here we have a tool header. Display its length so that the user can adjust the line numbers.
1784            my $toolHeaderFile = "$FIG_Config::fig_disk/dist/releases/current/$FIG_Config::arch/tool_hdr";
1785            # Only proceed if the tool header file is actually present.
1786            if (-f $toolHeaderFile) {
1787                my @lines = GetFile($toolHeaderFile);
1788                Trace("Tool header has " . scalar(@lines) . " lines.");
1789            }
1790        }
1791        # Trace the call stack.
1792        Cluck($message);
1793        # Abort the program.
1794        croak(">>> $message");
1795    }
1796    
1797    =head3 Assert
1798    
1799        Assert($condition1, $condition2, ... $conditionN);
1800    
1801    Return TRUE if all the conditions are true. This method can be used in conjunction with
1802    the OR operator and the L</Confess> method as a debugging assert.
1803    So, for example
1804    
1805        Assert($recNum >= 0) || Confess("Invalid record number $recNum.");
1806    
1807    Will abort the program with a stack trace if the value of C<$recNum> is negative.
1808    
1809    =cut
1810    sub Assert {
1811        my $retVal = 1;
1812        LOOP: for my $condition (@_) {
1813            if (! $condition) {
1814                $retVal = 0;
1815                last LOOP;
1816            }
1817        }
1818        return $retVal;
1819    }
1820    
1821    =head3 Cluck
1822    
1823        Cluck($message);
1824    
1825    Trace the call stack. Note that for best results, you should qualify the call with a
1826    trace condition. For example,
1827    
1828        Cluck("Starting record parse.") if T(3);
1829    
1830    will only trace the stack if the trace level for the package is 3 or more.
1831    
1832    =over 4
1833    
1834    =item message
1835    
1836    Message to include in the trace.
1837    
1838    =back
1839    
1840    =cut
1841    
1842    sub Cluck {
1843        # Get the parameters.
1844        my ($message) = @_;
1845        # Trace what's happening.
1846        Trace("Stack trace for event: $message");
1847        my $confession = longmess($message);
1848        # Convert the confession to a series of trace messages. Note we skip any
1849        # messages relating to calls into Tracer.
1850        for my $line (split /\s*\n/, $confession) {
1851            Trace($line) if ($line !~ /Tracer\.pm/);
1852        }
1853    }
1854    
1855    =head3 Min
1856    
1857        my $min = Min($value1, $value2, ... $valueN);
1858    
1859    Return the minimum argument. The arguments are treated as numbers.
1860    
1861    =over 4
1862    
1863    =item $value1, $value2, ... $valueN
1864    
1865    List of numbers to compare.
1866    
1867    =item RETURN
1868    
1869    Returns the lowest number in the list.
1870    
1871    =back
1872    
1873  =cut  =cut
1874    
1875  sub Trace {  sub Min {
1876        # Get the parameters. Note that we prime the return value with the first parameter.
1877        my ($retVal, @values) = @_;
1878        # Loop through the remaining parameters, looking for the lowest.
1879        for my $value (@values) {
1880            if ($value < $retVal) {
1881                $retVal = $value;
1882            }
1883        }
1884        # Return the minimum found.
1885        return $retVal;
1886    }
1887    
1888    =head3 Max
1889    
1890        my $max = Max($value1, $value2, ... $valueN);
1891    
1892    Return the maximum argument. The arguments are treated as numbers.
1893    
1894    =over 4
1895    
1896    =item $value1, $value2, ... $valueN
1897    
1898    List of numbers to compare.
1899    
1900    =item RETURN
1901    
1902    Returns the highest number in the list.
1903    
1904    =back
1905    
1906    =cut
1907    
1908    sub Max {
1909        # Get the parameters. Note that we prime the return value with the first parameter.
1910        my ($retVal, @values) = @_;
1911        # Loop through the remaining parameters, looking for the highest.
1912        for my $value (@values) {
1913            if ($value > $retVal) {
1914                $retVal = $value;
1915            }
1916        }
1917        # Return the maximum found.
1918        return $retVal;
1919    }
1920    
1921    =head3 AddToListMap
1922    
1923        Tracer::AddToListMap(\%hash, $key, $value1, $value2, ... valueN);
1924    
1925    Add a key-value pair to a hash of lists. If no value exists for the key, a singleton list
1926    is created for the key. Otherwise, the new value is pushed onto the list.
1927    
1928    =over 4
1929    
1930    =item hash
1931    
1932    Reference to the target hash.
1933    
1934    =item key
1935    
1936    Key for which the value is to be added.
1937    
1938    =item value1, value2, ... valueN
1939    
1940    List of values to add to the key's value list.
1941    
1942    =back
1943    
1944    =cut
1945    
1946    sub AddToListMap {
1947          # Get the parameters.          # Get the parameters.
1948          my ($message) = @_;      my ($hash, $key, @values) = @_;
1949          # Get the timestamp.      # Process according to whether or not the key already has a value.
1950          my $timeStamp = Now();      if (! exists $hash->{$key}) {
1951          # Format the message. Note we strip off any line terminators at the end.          $hash->{$key} = [@values];
1952          my $formatted = "$timeStamp <$LastCategory>: " . Strip($message);      } else {
1953          # Process according to the destination.          push @{$hash->{$key}}, @values;
1954          if ($Destination eq "TEXT") {      }
1955                  # Write the message to the standard output.  }
1956                  print "$formatted\n";  
1957          } elsif ($Destination eq "ERROR") {  =head3 DebugMode
1958                  # Write the message to the error output.  
1959                  print STDERR "$formatted\n";      if (Tracer::DebugMode) { ...code... }
1960          } elsif ($Destination eq "QUEUE") {  
1961                  # Push the message into the queue.  Return TRUE if debug mode has been turned on, else abort.
1962                  push @Queue, "$formatted";  
1963          } elsif ($Destination eq "HTML") {  Certain CGI scripts are too dangerous to exist in the production
1964                  # Convert the message to HTML and write it to the standard output.  environment. This method provides a simple way to prevent them
1965                  my $escapedMessage = CGI::escapeHTML($message);  from working unless they are explicitly turned on by creating a password
1966                  print "<p>$formatted</p>\n";  cookie via the B<SetPassword> script.  If debugging mode
1967      } elsif ($Destination eq "WARN") {  is not turned on, an error will occur.
1968         # Emit the message as a warning.  
1969         warn $message;  =cut
1970          } elsif ($Destination =~ m/^>>/) {  
1971                  # Write the trace message to an output file.  sub DebugMode {
1972                  open TRACING, $Destination;      # Declare the return variable.
1973                  print TRACING "$formatted\n";      my $retVal = 0;
1974                  close TRACING;      # Check the debug configuration.
1975        my $password = CGI::cookie("DebugMode");
1976        my $encrypted = Digest::MD5::md5_hex($password);
1977        if ($encrypted eq "252dec43280e0c0d6a75ffcec486e61d") {
1978            $retVal = 1;
1979        } else {
1980            # Here debug mode is off, so we generate an error.
1981            Confess("Cannot use this facility without logging in.");
1982        }
1983        # Return the determination indicator.
1984        return $retVal;
1985    }
1986    
1987    =head3 Strip
1988    
1989        my $string = Tracer::Strip($line);
1990    
1991    Strip all line terminators off a string. This is necessary when dealing with files
1992    that may have been transferred back and forth several times among different
1993    operating environments.
1994    
1995    =over 4
1996    
1997    =item line
1998    
1999    Line of text to be stripped.
2000    
2001    =item RETURN
2002    
2003    The same line of text with all the line-ending characters chopped from the end.
2004    
2005    =back
2006    
2007    =cut
2008    
2009    sub Strip {
2010        # Get a copy of the parameter string.
2011        my ($string) = @_;
2012        my $retVal = (defined $string ? $string : "");
2013        # Strip the line terminator characters.
2014        $retVal =~ s/(\r|\n)+$//g;
2015        # Return the result.
2016        return $retVal;
2017    }
2018    
2019    =head3 Pad
2020    
2021        my $paddedString = Tracer::Pad($string, $len, $left, $padChar);
2022    
2023    Pad a string to a specified length. The pad character will be a
2024    space, and the padding will be on the right side unless specified
2025    in the third parameter.
2026    
2027    =over 4
2028    
2029    =item string
2030    
2031    String to be padded.
2032    
2033    =item len
2034    
2035    Desired length of the padded string.
2036    
2037    =item left (optional)
2038    
2039    TRUE if the string is to be left-padded; otherwise it will be padded on the right.
2040    
2041    =item padChar (optional)
2042    
2043    Character to use for padding. The default is a space.
2044    
2045    =item RETURN
2046    
2047    Returns a copy of the original string with the pad character added to the
2048    specified end so that it achieves the desired length.
2049    
2050    =back
2051    
2052    =cut
2053    
2054    sub Pad {
2055        # Get the parameters.
2056        my ($string, $len, $left, $padChar) = @_;
2057        # Compute the padding character.
2058        if (! defined $padChar) {
2059            $padChar = " ";
2060        }
2061        # Compute the number of spaces needed.
2062        my $needed = $len - length $string;
2063        # Copy the string into the return variable.
2064        my $retVal = $string;
2065        # Only proceed if padding is needed.
2066        if ($needed > 0) {
2067            # Create the pad string.
2068            my $pad = $padChar x $needed;
2069            # Affix it to the return value.
2070            if ($left) {
2071                $retVal = $pad . $retVal;
2072            } else {
2073                $retVal .= $pad;
2074            }
2075        }
2076        # Return the result.
2077        return $retVal;
2078    }
2079    
2080    =head3 EOF
2081    
2082    This is a constant that is lexically greater than any useful string.
2083    
2084    =cut
2085    
2086    sub EOF {
2087        return "\xFF\xFF\xFF\xFF\xFF";
2088    }
2089    
2090    =head3 TICK
2091    
2092        my @results = TICK($commandString);
2093    
2094    Perform a back-tick operation on a command. If this is a Windows environment, any leading
2095    dot-slash (C<./> will be removed. So, for example, if you were doing
2096    
2097        `./protein.cgi`
2098    
2099    from inside a CGI script, it would work fine in Unix, but would issue an error message
2100    in Windows complaining that C<'.'> is not a valid command. If instead you code
2101    
2102        TICK("./protein.cgi")
2103    
2104    it will work correctly in both environments.
2105    
2106    =over 4
2107    
2108    =item commandString
2109    
2110    The command string to pass to the system.
2111    
2112    =item RETURN
2113    
2114    Returns the standard output from the specified command, as a list.
2115    
2116    =back
2117    
2118    =cut
2119    #: Return Type @;
2120    sub TICK {
2121        # Get the parameters.
2122        my ($commandString) = @_;
2123        # Chop off the dot-slash if this is Windows.
2124        if ($FIG_Config::win_mode) {
2125            $commandString =~ s!^\./!!;
2126        }
2127        # Activate the command and return the result.
2128        return `$commandString`;
2129          }          }
2130    
2131    =head3 ScriptSetup
2132    
2133        my ($cgi, $varHash) = ScriptSetup($noTrace);
2134    
2135    Perform standard tracing and debugging setup for scripts. The value returned is
2136    the CGI object followed by a pre-built variable hash. At the end of the script,
2137    the client should call L</ScriptFinish> to output the web page.
2138    
2139    This method calls L</ETracing> to configure tracing, which allows the tracing
2140    to be configured via the emergency tracing form on the debugging control panel.
2141    Tracing will then be turned on automatically for all programs that use the L</ETracing>
2142    method, which includes every program that uses this method or L</StandardSetup>.
2143    
2144    =over 4
2145    
2146    =item noTrace (optional)
2147    
2148    If specified, tracing will be suppressed. This is useful if the script wants to set up
2149    tracing manually.
2150    
2151    =item RETURN
2152    
2153    Returns a two-element list consisting of a CGI query object and a variable hash for
2154    the output page.
2155    
2156    =back
2157    
2158    =cut
2159    
2160    sub ScriptSetup {
2161        # Get the parameters.
2162        my ($noTrace) = @_;
2163        # Get the CGI query object.
2164        my $cgi = CGI->new();
2165        # Set up tracing if it's not suppressed.
2166        ETracing($cgi) unless $noTrace;
2167        # Create the variable hash.
2168        my $varHash = { results => '' };
2169        # Return the query object and variable hash.
2170        return ($cgi, $varHash);
2171  }  }
2172    
2173  =head3 T  =head3 ETracing
2174    
2175        ETracing($parameter);
2176    
2177  C<< my $switch = T($category, $traceLevel); >>  Set up emergency tracing. Emergency tracing is tracing that is turned
2178    on automatically for any program that calls this method. The emergency
2179    tracing parameters are stored in a a file identified by a tracing key.
2180    If this method is called with a CGI object, then the tracing key is
2181    taken from a cookie. If it is called with no parameters, then the tracing
2182    key is taken from an environment variable. If it is called with a string,
2183    the tracing key is that string.
2184    
2185          or  =over 4
2186    
2187  C<< my $switch = T($traceLevel); >>  =item parameter
2188    
2189  Return TRUE if the trace level is at or above a specified value and the specified category  A parameter from which the tracing key is computed. If it is a scalar,
2190  is active, else FALSE. If no category is specified, the caller's package name is used.  that scalar is used as the tracing key. If it is a CGI object, the
2191    tracing key is taken from the C<IP> cookie. If it is omitted, the
2192    tracing key is taken from the C<TRACING> environment variable. If it
2193    is a CGI object and emergency tracing is not on, the C<Trace> and
2194    C<TF> parameters will be used to determine the type of tracing.
2195    
2196  =over 4  =back
2197    
2198  =item category  =cut
2199    
2200  Category to which the message belongs. If not specified, the caller's package name is  sub ETracing {
2201  used.      # Get the parameter.
2202        my ($parameter) = @_;
2203        # Check for CGI mode.
2204        my $cgi = (ref $parameter eq 'CGI' ? $parameter : undef);
2205        # Default to no tracing except errors.
2206        my ($tracing, $dest) = ("0", "WARN");
2207        # Check for emergency tracing.
2208        my $tkey = EmergencyKey($parameter);
2209        my $emergencyFile = EmergencyFileName($tkey);
2210        if (-e $emergencyFile) {
2211            # We have the file. Read in the data.
2212            my @tracing = GetFile($emergencyFile);
2213            # Pull off the time limit.
2214            my $expire = shift @tracing;
2215            # Convert it to seconds.
2216            $expire *= 3600;
2217            # Check the file data.
2218            my $stat = stat($emergencyFile);
2219            my ($now) = gettimeofday;
2220            if ($now - $stat->mtime > $expire) {
2221                # Delete the expired file.
2222                unlink $emergencyFile;
2223            } else {
2224                # Emergency tracing is on. Pull off the destination and
2225                # the trace level;
2226                $dest = shift @tracing;
2227                my $level = shift @tracing;
2228                # Convert the destination to a real tracing destination.
2229                # temp directory.
2230                $dest = EmergencyTracingDest($tkey, $dest);
2231                # Insure Tracer is specified.
2232                my %moduleHash = map { $_ => 1 } @tracing;
2233                $moduleHash{Tracer} = 1;
2234                # Set the trace parameter.
2235                $tracing = join(" ", $level, sort keys %moduleHash);
2236            }
2237        } elsif (defined $cgi) {
2238            # There's no emergency tracing, but we have a CGI object, so check
2239            # for tracing from the form parameters.
2240            if ($cgi->param('Trace')) {
2241                # Here the user has requested tracing via a form.
2242                $dest = ($cgi->param('TF') ? ">$FIG_Config::temp/Trace$$.log" : "QUEUE");
2243                $tracing = $cgi->param('Trace') . " Tracer";
2244            }
2245        }
2246        # Setup the tracing we've determined from all the stuff above.
2247        TSetup($tracing, $dest);
2248        # If we're a web script, trace the parameter and environment data.
2249        if (defined $cgi) {
2250            TraceParms($cgi);
2251        }
2252    }
2253    
2254  =item traceLevel  =head3 EmergencyFileName
2255    
2256  Relevant tracing level.      my $fileName = Tracer::EmergencyFileName($tkey);
2257    
2258    Return the emergency tracing file name. This is the file that specifies
2259    the tracing information.
2260    
2261    =over 4
2262    
2263    =item tkey
2264    
2265    Tracing key for the current program.
2266    
2267  =item RETURN  =item RETURN
2268    
2269  TRUE if a message at the specified trace level would appear in the trace, else FALSE.  Returns the name of the file to contain the emergency tracing information.
2270    
2271  =back  =back
2272    
2273  =cut  =cut
2274    
2275  sub T {  sub EmergencyFileName {
         # Declare the return variable.  
         my $retVal = 0;  
         # Only proceed if tracing is turned on.  
         if ($Destination ne "NONE") {  
2276                  # Get the parameters.                  # Get the parameters.
2277                  my ($category, $traceLevel) = @_;      my ($tkey) = @_;
2278                  if (!defined $traceLevel) {      # Compute the emergency tracing file name.
2279                          # Here we have no category, so we need to get the calling package.      return "$FIG_Config::temp/Emergency$tkey.txt";
                         $traceLevel = $category;  
                         my ($package, $fileName, $line) = caller;  
             # If there is no calling package, we default to "main".  
                         if (!$package) {  
                 $category = "main";  
                         } else {  
                                 $category = $package;  
                         }  
                 }  
         # Save the category name.  
         $LastCategory = $category;  
                 # Use the category and tracelevel to compute the result.  
                 $retVal = ($traceLevel <= $TraceLevel && exists $Categories{$category});  
     }  
         # Return the computed result.  
     return $retVal;  
2280  }  }
2281    
2282  =head3 ParseCommand  =head3 EmergencyFileTarget
2283    
2284  C<< my ($options, @arguments) = Tracer::ParseCommand(\%optionTable, @inputList); >>      my $fileName = Tracer::EmergencyFileTarget($tkey);
2285    
2286  Parse a command line consisting of a list of parameters. The initial parameters may be option  Return the emergency tracing target file name. This is the file that receives
2287  specifiers of the form C<->I<option> or C<->I<option>C<=>I<value>. The options are stripped  the tracing output for file-based tracing.
 off and merged into a table of default options. The remainder of the command line is  
 returned as a list of positional arguments. For example, consider the following invocation.  
2288    
2289  C<< my ($options, @arguments) = ParseCommand({ errors => 0, logFile => 'trace.log'}, @words); >>  =over 4
2290    
2291  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  
2292    
2293  C<< -logFile=error.log apple orange rutabaga >>  Tracing key for the current program.
2294    
2295  then at the end of the invocation, C<$options> will be  =item RETURN
2296    
2297  C<< { errors => 0, logFile => 'error.log' } >>  Returns the name of the file to contain the trace output.
2298    
2299  and C<@arguments> will contain  =back
2300    
2301    =cut
2302    
2303  C<< apple orange rutabaga >>  sub EmergencyFileTarget {
2304        # Get the parameters.
2305        my ($tkey) = @_;
2306        # Compute the emergency tracing file name.
2307        return "$FIG_Config::temp/trace$tkey.log";
2308    }
2309    
2310  The parser allows for some escape sequences. See L</UnEscape> for a description. There is no  =head3 EmergencyTracingDest
2311  support for quote characters.  
2312        my $dest = Tracer::EmergencyTracingDest($tkey, $myDest);
2313    
2314    This method converts an emergency tracing destination to a real
2315    tracing destination. The main difference is that if the
2316    destination is C<FILE> or C<APPEND>, we convert it to file
2317    output. If the destination is C<DUAL>, we convert it to file
2318    and standard output.
2319    
2320  =over 4  =over 4
2321    
2322  =item optionTable  =item tkey
2323    
2324  Table of default options.  Tracing key for this environment.
2325    
2326  =item inputList  =item myDest
2327    
2328  List of words on the command line.  Destination from the emergency tracing file.
2329    
2330  =item RETURN  =item RETURN
2331    
2332  Returns a reference to the option table and a list of the positional arguments.  Returns a destination that can be passed into L</TSetup>.
2333    
2334  =back  =back
2335    
2336  =cut  =cut
2337    
2338  sub ParseCommand {  sub EmergencyTracingDest {
2339          # Get the parameters.          # Get the parameters.
2340          my ($optionTable, @inputList) = @_;      my ($tkey, $myDest) = @_;
2341          # Process any options in the input list.      # Declare the return variable.
2342          my %overrides = ();      my $retVal = $myDest;
2343          while ((@inputList > 0) && ($inputList[0] =~ /^-/)) {      # Process according to the destination value.
2344                  # Get the current option.      if ($myDest eq 'FILE') {
2345                  my $arg = shift @inputList;          $retVal = ">" . EmergencyFileTarget($tkey);
2346                  # Pull out the option name.      } elsif ($myDest eq 'APPEND') {
2347                  $arg =~ /^-([^=]*)/g;          $retVal = ">>" . EmergencyFileTarget($tkey);
2348                  my $name = $1;      } elsif ($myDest eq 'DUAL') {
2349                  # Check for an option value.          $retVal = "+>" . EmergencyFileTarget($tkey);
                 if ($arg =~ /\G=(.*)$/g) {  
                         # Here we have a value for the option.  
                         $overrides{$name} = UnEscape($1);  
                 } else {  
                         # Here there is no value, so we use 1.  
                         $overrides{$name} = 1;  
                 }  
2350          }          }
2351          # Merge the options into the defaults.      # Return the result.
2352          GetOptions($optionTable, \%overrides);      return $retVal;
         # Translate the remaining parameters.  
         my @retVal = ();  
         for my $inputParm (@inputList) {  
                 push @retVal, UnEscape($inputParm);  
2353          }          }
2354          # Return the results.  
2355          return ($optionTable, @retVal);  =head3 Emergency
2356    
2357        Emergency($key, $hours, $dest, $level, @modules);
2358    
2359    Turn on emergency tracing. This method is normally invoked over the web from
2360    a debugging console, but it can also be called by the C<trace.pl> script.
2361    The caller specifies the duration of the emergency in hours, the desired tracing
2362    destination, the trace level, and a list of the trace modules to activate.
2363    For the length of the duration, when a program in an environment with the
2364    specified tracing key active invokes a Sprout CGI script, tracing will be
2365    turned on automatically. See L</TSetup> for more about tracing setup and
2366    L</ETracing> for more about emergency tracing.
2367    
2368    =over 4
2369    
2370    =item tkey
2371    
2372    The tracing key. This is used to identify the control file and the trace file.
2373    
2374    =item hours
2375    
2376    Number of hours to keep emergency tracing alive.
2377    
2378    =item dest
2379    
2380    Tracing destination. If no path information is specified for a file
2381    destination, it is put in the FIG temporary directory.
2382    
2383    =item level
2384    
2385    Tracing level. A higher level means more trace messages.
2386    
2387    =item modules
2388    
2389    A list of the tracing modules to activate.
2390    
2391    =back
2392    
2393    =cut
2394    
2395    sub Emergency {
2396        # Get the parameters.
2397        my ($tkey, $hours, $dest, $level, @modules) = @_;
2398        # Create the emergency file.
2399        my $specFile = EmergencyFileName($tkey);
2400        my $outHandle = Open(undef, ">$specFile");
2401        print $outHandle join("\n", $hours, $dest, $level, @modules, "");
2402  }  }
2403    
2404  =head3 Escape  =head3 EmergencyKey
2405    
2406  C<< my $codedString = Tracer::Escape($realString); >>      my $tkey = EmergencyKey($parameter);
2407    
2408  Escape a string for use in a command length. Spaces will be replaced by C<\b>,  Return the Key to be used for emergency tracing. This could be an IP address,
2409  tabs replaced by C<\t>, new-lines replaced by C<\n>, and backslashes will be   a session ID, or a user name, depending on the environment.
 doubled. The effect is to exactly reverse the effect of L</UnEscape>.  
2410    
2411  =over 4  =over 4
2412    
2413  =item realString  =item parameter
2414    
2415  String to escape.  Parameter defining the method for finding the tracing key. If it is a scalar,
2416    then it is presumed to be the tracing key itself. If it is a CGI object, then
2417    the tracing key is taken from the C<IP> cookie. Otherwise, the tracing key is
2418    taken from the C<TRACING> environment variable.
2419    
2420  =item RETURN  =item RETURN
2421    
2422  Escaped equivalent of the real string.  Returns the key to be used for labels in emergency tracing.
2423    
2424  =back  =back
2425    
2426  =cut  =cut
2427    
2428  sub Escape {  sub EmergencyKey {
2429          # Get the parameter.      # Get the parameters.
2430          my ($realString) = @_;      my ($parameter) = @_;
2431          # Initialize the return variable.      # Declare the return variable.
2432          my $retVal = "";      my $retVal;
2433          # Loop through the parameter string, looking for sequences to escape.      # Determine the parameter type.
2434          while (length $realString > 0) {      if (! defined $parameter) {
2435                  # Look for the first sequence to escape.          # Here we're supposed to check the environment.
2436                  if ($realString =~ /^(.*?)([ \n\t\\])/) {          $retVal = $ENV{TRACING};
                         # Here we found it. The text preceding the sequence is in $1. The sequence  
                         # itself is in $2. First, move the clear text to the return variable.  
                         $retVal .= $1;  
                         $realString = substr $realString, (length $2 + length $1);  
                         # Encode the escape sequence.  
                         my $char = $2;  
                         $char =~ tr/ \t\n/btn/;  
                         $retVal .= "\\" . $char;  
2437                  } else {                  } else {
2438                          # Here there are no more escape sequences. The rest of the string is          my $ptype = ref $parameter;
2439                          # transferred unmodified.          if ($ptype eq 'CGI') {
2440                          $retVal .= $realString;              # Here we were invoked from a web page. Look for a cookie.
2441                          $realString = "";              $retVal = $parameter->cookie('IP');
2442            } elsif (! $ptype) {
2443                # Here the key was passed in.
2444                $retVal = $parameter;
2445            }
2446                  }                  }
2447        # If no luck finding a key, use the PID.
2448        if (! defined $retVal) {
2449            $retVal = $$;
2450          }          }
2451          # Return the result.          # Return the result.
2452          return $retVal;          return $retVal;
2453  }  }
2454    
 =head3 UnEscape  
   
 C<< my $realString = Tracer::UnEscape($codedString); >>  
2455    
2456  Replace escape sequences with their actual equivalents. C<\b> will be replaced by a space,  =head3 TraceParms
 C<\t> by a tab, C<\n> by a new-line character, and C<\\> by a back-slash.  
2457    
2458  =over 4      Tracer::TraceParms($cgi);
2459    
2460  =item codedString  Trace the CGI parameters at trace level CGI => 3 and the environment variables
2461    at level CGI => 4.
2462    
2463  String to un-escape.  =over 4
2464    
2465  =item RETURN  =item cgi
2466    
2467  Returns a copy of the original string with the escape sequences converted to their actual  CGI query object containing the parameters to trace.
 values.  
2468    
2469  =back  =back
2470    
2471  =cut  =cut
2472    
2473  sub UnEscape {  sub TraceParms {
2474          # Get the parameter.      # Get the parameters.
2475          my ($codedString) = @_;      my ($cgi) = @_;
2476          # Initialize the return variable.      if (T(CGI => 3)) {
2477          my $retVal = "";          # Here we want to trace the parameter data.
2478          # Only proceed if the incoming string is nonempty.          my @names = $cgi->param;
2479          if (defined $codedString) {          for my $parmName (sort @names) {
2480                  # Loop through the parameter string, looking for escape sequences. We can't do              # Note we skip the Trace parameters, which are for our use only.
2481                  # translating because it causes problems with the escaped slash. ("\\b" becomes              if ($parmName ne 'Trace' && $parmName ne 'TF') {
2482                  # "\ " no matter what we do.)                  my @values = $cgi->param($parmName);
2483                  while (length $codedString > 0) {                  Trace("CGI: $parmName = " . join(", ", @values));
                         # Look for the first escape sequence.  
                         if ($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 = "";  
2484                          }                          }
2485                  }                  }
2486            # Display the request method.
2487            my $method = $cgi->request_method();
2488            Trace("Method: $method");
2489        }
2490        if (T(CGI => 4)) {
2491            # Here we want the environment data too.
2492            for my $envName (sort keys %ENV) {
2493                Trace("ENV: $envName = $ENV{$envName}");
2494            }
2495          }          }
         # Return the result.  
         return $retVal;  
2496  }  }
2497    
2498  =head3 ParseRecord  =head3 ScriptFinish
2499    
2500  C<< my @fields = Tracer::ParseRecord($line); >>      ScriptFinish($webData, $varHash);
2501    
2502  Parse a tab-delimited data line. The data line is split into field values. Embedded tab  Output a web page at the end of a script. Either the string to be output or the
2503  and new-line characters in the data line must be represented as C<\t> and C<\n>, respectively.  name of a template file can be specified. If the second parameter is omitted,
2504  These will automatically be converted.  it is assumed we have a string to be output; otherwise, it is assumed we have the
2505    name of a template file. The template should have the variable C<DebugData>
2506    specified in any form that invokes a standard script. If debugging mode is turned
2507    on, a form field will be put in that allows the user to enter tracing data.
2508    Trace messages will be placed immediately before the terminal C<BODY> tag in
2509    the output, formatted as a list.
2510    
2511    A typical standard script would loook like the following.
2512    
2513        BEGIN {
2514            # Print the HTML header.
2515            print "CONTENT-TYPE: text/html\n\n";
2516        }
2517        use Tracer;
2518        use CGI;
2519        use FIG;
2520        # ... more uses ...
2521    
2522        my ($cgi, $varHash) = ScriptSetup();
2523        eval {
2524            # ... get data from $cgi, put it in $varHash ...
2525        };
2526        if ($@) {
2527            Trace("Script Error: $@") if T(0);
2528        }
2529        ScriptFinish("Html/MyTemplate.html", $varHash);
2530    
2531    The idea here is that even if the script fails, you'll see trace messages and
2532    useful output.
2533    
2534  =over 4  =over 4
2535    
2536  =item line  =item webData
2537    
2538  Line of data containing the tab-delimited fields.  A string containing either the full web page to be written to the output or the
2539    name of a template file from which the page is to be constructed. If the name
2540    of a template file is specified, then the second parameter must be present;
2541    otherwise, it must be absent.
2542    
2543  =item RETURN  =item varHash (optional)
2544    
2545  Returns a list of the fields found in the data line.  If specified, then a reference to a hash mapping variable names for a template
2546    to their values. The template file will be read into memory, and variable markers
2547    will be replaced by data in this hash reference.
2548    
2549  =back  =back
2550    
2551  =cut  =cut
2552    
2553  sub ParseRecord {  sub ScriptFinish {
2554          # Get the parameter.      # Get the parameters.
2555          my ($line) = @_;      my ($webData, $varHash) = @_;
2556          # Remove the trailing new-line, if any.      # Check for a template file situation.
2557          chomp $line;      my $outputString;
2558          # Split the line read into pieces using the tab character.      if (defined $varHash) {
2559          my @retVal = split /\t/, $line;          # Here we have a template file. We need to determine the template type.
2560          # Trim and fix the escapes in each piece.          my $template;
2561          for my $value (@retVal) {          if ($FIG_Config::template_url && $webData =~ /\.php$/) {
2562                  # Trim leading whitespace.              $template = "$FIG_Config::template_url/$webData";
2563                  $value =~ s/^\s+//;          } else {
2564                  # Trim trailing whitespace.              $template = "<<$webData";
                 $value =~ s/\s+$//;  
                 # Delete the carriage returns.  
                 $value =~ s/\r//g;  
                 # Convert the escapes into their real values.  
                 $value =~ s/\\t/"\t"/ge;  
                 $value =~ s/\\n/"\n"/ge;  
2565          }          }
2566          # Return the result.          $outputString = PageBuilder::Build($template, $varHash, "Html");
2567          return @retVal;      } else {
2568            # Here the user gave us a raw string.
2569            $outputString = $webData;
2570        }
2571        # Check for trace messages.
2572        if ($Destination ne "NONE" && $TraceLevel > 0) {
2573            # We have trace messages, so we want to put them at the end of the body. This
2574            # is either at the end of the whole string or at the beginning of the BODY
2575            # end-tag.
2576            my $pos = length $outputString;
2577            if ($outputString =~ m#</body>#gi) {
2578                $pos = (pos $outputString) - 7;
2579            }
2580            # If the trace messages were queued, we unroll them. Otherwise, we display the
2581            # destination.
2582            my $traceHtml;
2583            if ($Destination eq "QUEUE") {
2584                $traceHtml = QTrace('Html');
2585            } elsif ($Destination =~ /^>>(.+)$/) {
2586                # Here the tracing output it to a file. We code it as a hyperlink so the user
2587                # can copy the file name into the clipboard easily.
2588                my $actualDest = $1;
2589                $traceHtml = "<p>Tracing output to $actualDest.</p>\n";
2590            } else {
2591                # Here we have one of the special destinations.
2592                $traceHtml = "<P>Tracing output type is $Destination.</p>\n";
2593            }
2594            substr $outputString, $pos, 0, $traceHtml;
2595        }
2596        # Write the output string.
2597        print $outputString;
2598  }  }
2599    
2600  =head3 Merge  =head3 Insure
2601    
2602  C<< my @mergedList = Tracer::Merge(@inputList); >>      Insure($dirName, $chmod);
2603    
2604  Sort a list of strings and remove duplicates.  Insure a directory is present.
2605    
2606  =over 4  =over 4
2607    
2608  =item inputList  =item dirName
2609    
2610  List of scalars to sort and merge.  Name of the directory to check. If it does not exist, it will be created.
2611    
2612  =item RETURN  =item chmod (optional)
2613    
2614  Returns a list containing the same elements sorted in ascending order with duplicates  Security privileges to be given to the directory if it is created.
 removed.  
2615    
2616  =back  =back
2617    
2618  =cut  =cut
2619    
2620  sub Merge {  sub Insure {
2621          # Get the input list in sort order.      my ($dirName, $chmod) = @_;
2622          my @inputList = sort @_;      if (! -d $dirName) {
2623          # Only proceed if the list has at least two elements.          Trace("Creating $dirName directory.") if T(2);
2624          if (@inputList > 1) {          eval {
2625                  # Now we want to move through the list splicing out duplicates.              mkpath $dirName;
2626                  my $i = 0;              # If we have permissions specified, set them here.
2627                  while ($i < @inputList) {              if (defined($chmod)) {
2628                          # Get the current entry.                  chmod $chmod, $dirName;
                         my $thisEntry = $inputList[$i];  
                         # Find out how many elements duplicate the current entry.  
                         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;  
2629                          }                          }
2630                          # Now the element at position $dup1 is different from the element before it          };
2631                          # at position $i. We push $i forward one position and start again.          if ($@) {
2632                          $i++;              Confess("Error creating $dirName: $@");
2633                  }                  }
2634          }          }
         # Return the merged list.  
         return @inputList;  
2635  }  }
2636    
2637  =head3 GetFile  =head3 ChDir
2638    
2639  C<< my @fileContents = Tracer::GetFile($fileName); >>      ChDir($dirName);
2640    
2641  Return the entire contents of a file.  Change to the specified directory.
2642    
2643  =over 4  =over 4
2644    
2645  =item fileName  =item dirName
   
 Name of the file to read.  
   
 =item RETURN  
2646    
2647  In a list context, returns the entire file as a list with the line terminators removed.  Name of the directory to which we want to change.
 In a scalar context, returns the entire file as a string.  
2648    
2649  =back  =back
2650    
2651  =cut  =cut
2652    
2653  sub GetFile {  sub ChDir {
2654          # Get the parameters.      my ($dirName) = @_;
2655          my ($fileName) = @_;      if (! -d $dirName) {
2656          # Declare the return variable.          Confess("Cannot change to directory $dirName: no such directory.");
         my @retVal = ();  
         # Open the file for input.  
         my $ok = open INPUTFILE, "<$fileName";  
         if (!$ok) {  
                 # If we had an error, trace it. We will automatically return a null value.  
                 Trace("Could not open \"$fileName\" for input.") if T(0);  
2657          } else {          } else {
2658                  # Read the whole file into the return variable, stripping off any terminator          Trace("Changing to directory $dirName.") if T(File => 4);
2659          # characters.          my $okFlag = chdir $dirName;
2660          my $lineCount = 0;          if (! $okFlag) {
2661                  while (my $line = <INPUTFILE>) {              Confess("Error switching to directory $dirName.");
             $lineCount++;  
             $line = Strip($line);  
                         push @retVal, $line;  
                 }  
                 # Close it.  
                 close INPUTFILE;  
         my $actualLines = @retVal;  
         Trace("$lineCount lines read from $fileName. $actualLines processed.") if T(3);  
2662          }          }
         # Return the file's contents in the desired format.  
     if (wantarray) {  
             return @retVal;  
     } else {  
         return join "\n", @retVal;  
2663      }      }
2664  }  }
2665    
2666  =head3 QTrace  =head3 SendSMS
2667    
2668  C<< my $data = QTrace($format); >>      my $msgID = Tracer::SendSMS($phoneNumber, $msg);
2669    
2670  Return the queued trace data in the specified format.  Send a text message to a phone number using Clickatell. The FIG_Config file must contain the
2671    user name, password, and API ID for the relevant account in the hash reference variable
2672    I<$FIG_Config::phone>, using the keys C<user>, C<password>, and C<api_id>. For
2673    example, if the user name is C<BruceTheHumanPet>, the password is C<silly>, and the API ID
2674    is C<2561022>, then the FIG_Config file must contain
2675    
2676        $phone =  { user => 'BruceTheHumanPet',
2677                    password => 'silly',
2678                    api_id => '2561022' };
2679    
2680    The original purpose of this method was to insure Bruce would be notified immediately when the
2681    Sprout Load terminates. Care should be taken if you do not wish Bruce to be notified immediately
2682    when you call this method.
2683    
2684    The message ID will be returned if successful, and C<undef> if an error occurs.
2685    
2686  =over 4  =over 4
2687    
2688  =item format  =item phoneNumber
2689    
2690  C<html> to format the data as an HTML list, C<text> to format it as straight text.  Phone number to receive the message, in international format. A United States phone number
2691    would be prefixed by "1". A British phone number would be prefixed by "44".
2692    
2693    =item msg
2694    
2695    Message to send to the specified phone.
2696    
2697    =item RETURN
2698    
2699    Returns the message ID if successful, and C<undef> if the message could not be sent.
2700    
2701  =back  =back
2702    
2703  =cut  =cut
2704    
2705  sub QTrace {  sub SendSMS {
2706          # Get the parameter.      # Get the parameters.
2707          my ($format) = @_;      my ($phoneNumber, $msg) = @_;
2708          # Create the return variable.      # Declare the return variable. If we do not change it, C<undef> will be returned.
2709          my $retVal = "";      my $retVal;
2710          # Process according to the format.      # Only proceed if we have phone support.
2711          if ($format =~ m/^HTML$/i) {      if (! defined $FIG_Config::phone) {
2712                  # Convert the queue into an HTML list.          Trace("Phone support not present in FIG_Config.") if T(1);
2713                  $retVal = "<ul>\n";      } else {
2714                  for my $line (@Queue) {          # Get the phone data.
2715                          my $escapedLine = CGI::escapeHTML($line);          my $parms = $FIG_Config::phone;
2716                          $retVal .= "<li>$escapedLine</li>\n";          # Get the Clickatell URL.
2717            my $url = "http://api.clickatell.com/http/";
2718            # Create the user agent.
2719            my $ua = LWP::UserAgent->new;
2720            # Request a Clickatell session.
2721            my $resp = $ua->post("$url/sendmsg", { user => $parms->{user},
2722                                         password => $parms->{password},
2723                                         api_id => $parms->{api_id},
2724                                         to => $phoneNumber,
2725                                         text => $msg});
2726            # Check for an error.
2727            if (! $resp->is_success) {
2728                Trace("Alert failed.") if T(1);
2729            } else {
2730                # Get the message ID.
2731                my $rstring = $resp->content;
2732                if ($rstring =~ /^ID:\s+(.*)$/) {
2733                    $retVal = $1;
2734                } else {
2735                    Trace("Phone attempt failed with $rstring") if T(1);
2736                  }                  }
                 $retVal .= "</ul>\n";  
         } elsif ($format =~ m/^TEXT$/i) {  
                 # Convert the queue into a list of text lines.  
                 $retVal = join("\n", @Queue) . "\n";  
2737          }          }
2738          # Clear the queue.      }
2739          @Queue = ();      # Return the result.
         # Return the formatted list.  
2740          return $retVal;          return $retVal;
2741  }  }
2742    
2743  =head3 Confess  =head3 CommaFormat
2744    
2745  C<< Confess($message); >>      my $formatted = Tracer::CommaFormat($number);
2746    
2747  Trace the call stack and abort the program with the specified message. The stack  Insert commas into a number.
 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  
2748    
2749  C<< Assert($recNum >= 0) || Confess("Invalid record number $recNum."); >>  =over 4
2750    
2751  Will abort the program with a stack trace if the value of C<$recNum> is negative.  =item number
2752    
2753  =over 4  A sequence of digits.
2754    
2755  =item message  =item RETURN
2756    
2757  Message to include in the trace.  Returns the same digits with commas strategically inserted.
2758    
2759  =back  =back
2760    
2761  =cut  =cut
2762    
2763  sub Confess {  sub CommaFormat {
2764          # Get the parameters.          # Get the parameters.
2765          my ($message) = @_;      my ($number) = @_;
2766          # Trace the call stack.      # Pad the length up to a multiple of three.
2767          Cluck($message) if T(1);      my $padded = "$number";
2768          # Abort the program.      $padded = " " . $padded while length($padded) % 3 != 0;
2769          croak(">>> $message");      # This is a fancy PERL trick. The parentheses in the SPLIT pattern
2770        # cause the delimiters to be included in the output stream. The
2771        # GREP removes the empty strings in between the delimiters.
2772        my $retVal = join(",", grep { $_ ne '' } split(/(...)/, $padded));
2773        # Clean out the spaces.
2774        $retVal =~ s/ //g;
2775        # Return the result.
2776        return $retVal;
2777  }  }
2778    =head3 SetPermissions
2779    
2780  =head3 Assert      Tracer::SetPermissions($dirName, $group, $mask, %otherMasks);
2781    
2782  C<< Assert($condition1, $condition2, ... $conditionN); >>  Set the permissions for a directory and all the files and folders inside it.
2783    In addition, the group ownership will be changed to the specified value.
2784    
2785  Return TRUE if all the conditions are true. This method can be used in conjunction with  This method is more vulnerable than most to permission and compatability
2786  the OR operator and the L</Confess> method, B<Assert> can function as a debugging assert.  problems, so it does internal error recovery.
 So, for example  
2787    
2788  C<< Assert($recNum >= 0) || Confess("Invalid record number $recNum."); >>  =over 4
2789    
2790  Will abort the program with a stack trace if the value of C<$recNum> is negative.  =item dirName
2791    
2792  =cut  Name of the directory to process.
 sub Assert {  
     my $retVal = 1;  
     LOOP: for my $condition (@_) {  
         if (! $condition) {  
             $retVal = 0;  
             last LOOP;  
         }  
     }  
     return $retVal;  
 }  
2793    
2794  =head3 Cluck  =item group
2795    
2796  C<< Cluck($message); >>  Name of the group to be assigned.
2797    
2798  Trace the call stack. Note that for best results, you should qualify the call with a  =item mask
 trace condition. For example,  
2799    
2800  C<< Cluck("Starting record parse.") if T(3); >>  Permission mask. Bits that are C<1> in this mask will be ORed into the
2801    permission bits of any file or directory that does not already have them
2802    set to 1.
2803    
2804  will only trace the stack if the trace level for the package is 3 or more.  =item otherMasks
2805    
2806  =over 4  Map of search patterns to permission masks. If a directory name matches
2807    one of the patterns, that directory and all its members and subdirectories
2808    will be assigned the new pattern. For example, the following would
2809    assign 01664 to most files, but would use 01777 for directories named C<tmp>.
2810    
2811  =item message      Tracer::SetPermissions($dirName, 'fig', 01664, '^tmp$' => 01777);
2812    
2813  Message to include in the trace.  The list is ordered, so the following would use 0777 for C<tmp1> and
2814    0666 for C<tmp>, C<tmp2>, or C<tmp3>.
2815    
2816        Tracer::SetPermissions($dirName, 'fig', 01664, '^tmp1' => 0777,
2817                                                       '^tmp' => 0666);
2818    
2819    Note that the pattern matches are all case-insensitive, and only directory
2820    names are matched, not file names.
2821    
2822  =back  =back
2823    
2824  =cut  =cut
2825    
2826  sub Cluck {  sub SetPermissions {
2827          # Get the parameters.          # Get the parameters.
2828          my ($message) = @_;      my ($dirName, $group, $mask, @otherMasks) = @_;
2829      # Trace what's happening.      # Set up for error recovery.
2830      Trace("Stack trace for event: $message");      eval {
2831          my $confession = longmess($message);          # Switch to the specified directory.
2832          # Convert the confession to a series of trace messages. Note we skip any          ChDir($dirName);
2833      # messages relating to calls into Tracer.          # Get the group ID.
2834          for my $line (split /\s*\n/, $confession) {          my $gid = getgrnam($group);
2835                  Trace($line) if ($line !~ /Tracer\.pm/);          # Get the mask for tracing.
2836            my $traceMask = sprintf("%04o", $mask) . "($mask)";
2837            Trace("Fixing permissions for directory $dirName using group $group($gid) and mask $traceMask.") if T(File => 2);
2838            my $fixCount = 0;
2839            my $lookCount = 0;
2840            # @dirs will be a stack of directories to be processed.
2841            my @dirs = (getcwd());
2842            while (scalar(@dirs) > 0) {
2843                # Get the current directory.
2844                my $dir = pop @dirs;
2845                # Check for a match to one of the specified directory names. To do
2846                # that, we need to pull the individual part of the name off of the
2847                # whole path.
2848                my $simpleName = $dir;
2849                if ($dir =~ m!/([^/]+)$!) {
2850                    $simpleName = $1;
2851                }
2852                Trace("Simple directory name for $dir is $simpleName.") if T(File => 4);
2853                # Search for a match.
2854                my $match = 0;
2855                my $i;
2856                for ($i = 0; $i < $#otherMasks && ! $match; $i += 2) {
2857                    my $pattern = $otherMasks[$i];
2858                    if ($simpleName =~ /$pattern/i) {
2859                        $match = 1;
2860                    }
2861                }
2862                # Check for a match. Note we use $i-1 because the loop added 2
2863                # before terminating due to the match.
2864                if ($match && $otherMasks[$i-1] != $mask) {
2865                    # This directory matches one of the incoming patterns, and it's
2866                    # a different mask, so we process it recursively with that mask.
2867                    SetPermissions($dir, $group, $otherMasks[$i-1], @otherMasks);
2868                } else {
2869                    # Here we can process normally. Get all of the non-hidden members.
2870                    my @submems = OpenDir($dir, 1);
2871                    for my $submem (@submems) {
2872                        # Get the full name.
2873                        my $thisMem = "$dir/$submem";
2874                        Trace("Checking member $thisMem.") if T(4);
2875                        $lookCount++;
2876                        if ($lookCount % 1000 == 0) {
2877                            Trace("$lookCount members examined. Current is $thisMem. Mask is $traceMask") if T(File => 3);
2878                        }
2879                        # Fix the group.
2880                        chown -1, $gid, $thisMem;
2881                        # Insure this member is not a symlink.
2882                        if (! -l $thisMem) {
2883                            # Get its info.
2884                            my $fileInfo = stat $thisMem;
2885                            # Only proceed if we got the info. Otherwise, it's a hard link
2886                            # and we want to skip it anyway.
2887                            if ($fileInfo) {
2888                                my $fileMode = $fileInfo->mode;
2889                                if (($fileMode & $mask) != $mask) {
2890                                    # Fix this member.
2891                                    $fileMode |= $mask;
2892                                    chmod $fileMode, $thisMem;
2893                                    $fixCount++;
2894                                }
2895                                # If it's a subdirectory, stack it.
2896                                if (-d $thisMem) {
2897                                    push @dirs, $thisMem;
2898                                }
2899                            }
2900                        }
2901                    }
2902                }
2903            }
2904            Trace("$lookCount files and directories processed, $fixCount fixed.") if T(File => 2);
2905        };
2906        # Check for an error.
2907        if ($@) {
2908            Confess("SetPermissions error: $@");
2909          }          }
2910  }  }
2911    
2912  =head3 Min  =head3 CompareLists
2913    
2914  C<< my $min = Min($value1, $value2, ... $valueN); >>      my ($inserted, $deleted) = Tracer::CompareLists(\@newList, \@oldList, $keyIndex);
2915    
2916  Return the minimum argument. The arguments are treated as numbers.  Compare two lists of tuples, and return a hash analyzing the differences. The lists
2917    are presumed to be sorted alphabetically by the value in the $keyIndex column.
2918    The return value contains a list of items that are only in the new list
2919    (inserted) and only in the old list (deleted).
2920    
2921  =over 4  =over 4
2922    
2923  =item $value1, $value2, ... $valueN  =item newList
2924    
2925  List of numbers to compare.  Reference to a list of new tuples.
2926    
2927    =item oldList
2928    
2929    Reference to a list of old tuples.
2930    
2931    =item keyIndex (optional)
2932    
2933    Index into each tuple of its key field. The default is 0.
2934    
2935  =item RETURN  =item RETURN
2936    
2937  Returns the lowest number in the list.  Returns a 2-tuple consisting of a reference to the list of items that are only in the new
2938    list (inserted) followed by a reference to the list of items that are only in the old
2939    list (deleted).
2940    
2941  =back  =back
2942    
2943  =cut  =cut
2944    
2945  sub Min {  sub CompareLists {
2946          # Get the parameters. Note that we prime the return value with the first parameter.      # Get the parameters.
2947          my ($retVal, @values) = @_;      my ($newList, $oldList, $keyIndex) = @_;
2948          # Loop through the remaining parameters, looking for the lowest.      if (! defined $keyIndex) {
2949          for my $value (@values) {          $keyIndex = 0;
2950                  if ($value < $retVal) {      }
2951                          $retVal = $value;      # Declare the return variables.
2952        my ($inserted, $deleted) = ([], []);
2953        # Loop through the two lists simultaneously.
2954        my ($newI, $oldI) = (0, 0);
2955        my ($newN, $oldN) = (scalar @{$newList}, scalar @{$oldList});
2956        while ($newI < $newN || $oldI < $oldN) {
2957            # Get the current object in each list. Note that if one
2958            # of the lists is past the end, we'll get undef.
2959            my $newItem = $newList->[$newI];
2960            my $oldItem = $oldList->[$oldI];
2961            if (! defined($newItem) || defined($oldItem) && $newItem->[$keyIndex] gt $oldItem->[$keyIndex]) {
2962                # The old item is not in the new list, so mark it deleted.
2963                push @{$deleted}, $oldItem;
2964                $oldI++;
2965            } elsif (! defined($oldItem) || $oldItem->[$keyIndex] gt $newItem->[$keyIndex]) {
2966                # The new item is not in the old list, so mark it inserted.
2967                push @{$inserted}, $newItem;
2968                $newI++;
2969            } else {
2970                # The item is in both lists, so push forward.
2971                $oldI++;
2972                $newI++;
2973                  }                  }
2974          }          }
2975          # Return the minimum found.      # Return the result.
2976          return $retVal;      return ($inserted, $deleted);
2977  }  }
2978    
2979  =head3 Max  =head3 GetLine
2980    
2981  C<< my $max = Max($value1, $value2, ... $valueN); >>      my @data = Tracer::GetLine($handle);
2982    
2983  Return the maximum argument. The arguments are treated as numbers.  Read a line of data from a tab-delimited file.
2984    
2985  =over 4  =over 4
2986    
2987  =item $value1, $value2, ... $valueN  =item handle
2988    
2989  List of numbers to compare.  Open file handle from which to read.
2990    
2991  =item RETURN  =item RETURN
2992    
2993  Returns the highest number in the list.  Returns a list of the fields in the record read. The fields are presumed to be
2994    tab-delimited. If we are at the end of the file, then an empty list will be
2995    returned. If an empty line is read, a single list item consisting of a null
2996    string will be returned.
2997    
2998  =back  =back
2999    
3000  =cut  =cut
3001    
3002  sub Max {  sub GetLine {
3003          # Get the parameters. Note that we prime the return value with the first parameter.      # Get the parameters.
3004          my ($retVal, @values) = @_;      my ($handle) = @_;
3005          # Loop through the remaining parameters, looking for the highest.      # Declare the return variable.
3006          for my $value (@values) {      my @retVal = ();
3007                  if ($value > $retVal) {      Trace("File position is " . tell($handle) . ". EOF flag is " . eof($handle) . ".") if T(File => 4);
3008                          $retVal = $value;      # Read from the file.
3009        my $line = <$handle>;
3010        # Only proceed if we found something.
3011        if (defined $line) {
3012            # Remove the new-line. We are a bit over-cautious here because the file may be coming in via an
3013            # upload control and have a nonstandard EOL combination.
3014            $line =~ s/(\r|\n)+$//;
3015            # Here we do some fancy tracing to help in debugging complicated EOL marks.
3016            if (T(File => 4)) {
3017                my $escapedLine = $line;
3018                $escapedLine =~ s/\n/\\n/g;
3019                $escapedLine =~ s/\r/\\r/g;
3020                $escapedLine =~ s/\t/\\t/g;
3021                Trace("Line read: -->$escapedLine<--");
3022            }
3023            # If the line is empty, return a single empty string; otherwise, parse
3024            # it into fields.
3025            if ($line eq "") {
3026                push @retVal, "";
3027            } else {
3028                push @retVal, split /\t/,$line;
3029                  }                  }
3030        } else {
3031            # Trace the reason the read failed.
3032            Trace("End of file: $!") if T(File => 3);
3033          }          }
3034          # Return the maximum found.      # Return the result.
3035          return $retVal;      return @retVal;
3036  }  }
3037    
3038  =head3 AddToListMap  =head3 PutLine
3039    
3040  C<< Tracer::AddToListMap(\%hash, $key, $value); >>      Tracer::PutLine($handle, \@fields, $eol);
3041    
3042  Add a key-value pair to a hash of lists. If no value exists for the key, a singleton list  Write a line of data to a tab-delimited file. The specified field values will be
3043  is created for the key. Otherwise, the new value is pushed onto the list.  output in tab-separated form, with a trailing new-line.
3044    
3045  =over 4  =over 4
3046    
3047  =item hash  =item handle
3048    
3049  Reference to the target hash.  Output file handle.
3050    
3051  =item key  =item fields
3052    
3053  Key for which the value is to be added.  List of field values.
3054    
3055  =item value  =item eol (optional)
3056    
3057  Value to add to the key's value list.  End-of-line character (default is "\n").
3058    
3059  =back  =back
3060    
3061  =cut  =cut
3062    
3063  sub AddToListMap {  sub PutLine {
3064      # Get the parameters.      # Get the parameters.
3065      my ($hash, $key, $value) = @_;      my ($handle, $fields, $eol) = @_;
3066      # Process according to whether or not the key already has a value.      # Write the data.
3067      if (! exists $hash->{$key}) {      print $handle join("\t", @{$fields}) . ($eol || "\n");
         $hash->{$key} = [$value];  
     } else {  
         push @{$hash->{$key}}, $value;  
     }  
3068  }  }
3069    
3070  =head3 DebugMode  =head3 GenerateURL
   
 C<< if (Tracer::DebugMode) { ...code... } >>  
3071    
3072  Return TRUE if debug mode has been turned on in FIG_Config, else output      my $queryUrl = Tracer::GenerateURL($page, %parameters);
 an error page and return FALSE.  
3073    
3074  Certain CGI scripts are too dangerous to exist in the production  Generate a GET-style URL for the specified page with the specified parameter
3075  environment. This method provides a simple way to prevent them  names and values. The values will be URL-escaped automatically. So, for
3076  from working unless they are explicitly turned on in the configuration  example
 file by setting C<$FIG_Config::debug_mode> to 1. If debugging mode  
 is not turned on, an error web page will be output.  
3077    
3078  =cut      Tracer::GenerateURL("form.cgi", type => 1, string => "\"high pass\" or highway")
3079    
3080  sub DebugMode {  would return
         # Declare the return variable.  
         my $retVal;  
         # Check the debug configuration.  
         if ($FIG_Config::debug_mode) {  
                 $retVal = 1;  
         } else {  
                 # Here debug mode is off, so we generate an error page.  
         my $pageString = PageBuilder::Build("<Html/ErrorPage.html", {}, "Html");  
                 print $pageString;  
         }  
         # Return the determination indicator.  
         return $retVal;  
 }  
3081    
3082  =head3 Strip      form.cgi?type=1;string=%22high%20pass%22%20or%20highway
3083    
3084  C<< my $string = Tracer::Strip($line); >>  =over 4
3085    
3086  Strip all line terminators off a string. This is necessary when dealing with files  =item page
 that may have been transferred back and forth several times among different  
 operating environments.  
3087    
3088  =over 4  Page URL.
3089    
3090  =item line  =item parameters
3091    
3092  Line of text to be stripped.  Hash mapping parameter names to parameter values.
3093    
3094  =item RETURN  =item RETURN
3095    
3096  The same line of text with all the line-ending characters chopped from the end.  Returns a GET-style URL that goes to the specified page and passes in the
3097    specified parameters and values.
3098    
3099  =back  =back
3100    
3101  =cut  =cut
3102    
3103  sub Strip {  sub GenerateURL {
3104          # Get a copy of the parameter string.      # Get the parameters.
3105          my ($string) = @_;      my ($page, %parameters) = @_;
3106          my $retVal = $string;      # Prime the return variable with the page URL.
3107      # Strip the line terminator characters.      my $retVal = $page;
3108      $retVal =~ s/(\r|\n)+$//g;      # Loop through the parameters, creating parameter elements in a list.
3109        my @parmList = map { "$_=" . uri_escape($parameters{$_}) } keys %parameters;
3110        # If the list is nonempty, tack it on.
3111        if (@parmList) {
3112            $retVal .= "?" . join(";", @parmList);
3113        }
3114          # Return the result.          # Return the result.
3115          return $retVal;          return $retVal;
3116  }  }
3117    
3118  =head3 Pad  =head3 ApplyURL
3119    
3120  C<< my $paddedString = Tracer::Pad($string, $len, $left, $padChar); >>      Tracer::ApplyURL($table, $target, $url);
3121    
3122  Pad a string to a specified length. The pad character will be a  Run through a two-dimensional table (or more accurately, a list of lists), converting the
3123  space, and the padding will be on the right side unless specified  I<$target> column to HTML text having a hyperlink to a URL in the I<$url> column. The
3124  in the third parameter.  URL column will be deleted by this process and the target column will be HTML-escaped.
3125    
3126    This provides a simple way to process the results of a database query into something
3127    displayable by combining a URL with text.
3128    
3129  =over 4  =over 4
3130    
3131  =item string  =item table
3132    
3133  String to be padded.  Reference to a list of lists. The elements in the containing list will be updated by
3134    this method.
3135    
3136  =item len  =item target
3137    
3138  Desired length of the padded string.  The index of the column to be converted into HTML.
3139    
3140  =item left (optional)  =item url
3141    
3142  TRUE if the string is to be left-padded; otherwise it will be padded on the right.  The index of the column containing the URL. Note that the URL must have a recognizable
3143    C<http:> at the beginning.
3144    
3145  =item padChar (optional)  =back
3146    
3147    =cut
3148    
3149    sub ApplyURL {
3150        # Get the parameters.
3151        my ($table, $target, $url) = @_;
3152        # Loop through the table.
3153        for my $row (@{$table}) {
3154            # Apply the URL to the target cell.
3155            $row->[$target] = CombineURL($row->[$target], $row->[$url]);
3156            # Delete the URL from the row.
3157            delete $row->[$url];
3158        }
3159    }
3160    
3161    =head3 CombineURL
3162    
3163        my $combinedHtml = Tracer::CombineURL($text, $url);
3164    
3165    This method will convert the specified text into HTML hyperlinked to the specified
3166    URL. The hyperlinking will only take place if the URL looks legitimate: that is, it
3167    is defined and begins with an C<http:> header.
3168    
3169    =over 4
3170    
3171    =item text
3172    
3173    Text to return. This will be HTML-escaped automatically.
3174    
3175    =item url
3176    
3177    A URL to be hyperlinked to the text. If it does not look like a URL, then the text
3178    will be returned without any hyperlinking.
3179    
3180  =item RETURN  =item RETURN
3181    
3182  Returns a copy of the original string with the spaces added to the specified end so  Returns the original text, HTML-escaped, with the URL hyperlinked to it. If the URL
3183  that it achieves the desired length.  doesn't look right, the HTML-escaped text will be returned without any further
3184    modification.
3185    
3186  =back  =back
3187    
3188  =cut  =cut
3189    
3190  sub Pad {  sub CombineURL {
3191          # Get the parameters.          # Get the parameters.
3192          my ($string, $len, $left, $padChar) = @_;      my ($text, $url) = @_;
3193          # Compute the padding character.      # Declare the return variable.
3194          if (! defined $padChar) {      my $retVal = CGI::escapeHTML($text);
3195                  $padChar = " ";      # Verify the URL.
3196          }      if (defined($url) && $url =~ m!http://!i) {
3197          # Compute the number of spaces needed.          # It's good, so we apply it to the text.
3198          my $needed = $len - length $string;          $retVal = "<a href=\"$url\">$retVal</a>";
         # Copy the string into the return variable.  
         my $retVal = $string;  
         # Only proceed if padding is needed.  
         if ($needed > 0) {  
                 # Create the pad string.  
                 my $pad = $padChar x $needed;  
                 # Affix it to the return value.  
                 if ($left) {  
                         $retVal = $pad . $retVal;  
                 } else {  
                         $retVal .= $pad;  
                 }  
3199          }          }
3200          # Return the result.          # Return the result.
3201          return $retVal;          return $retVal;
3202  }  }
3203    
3204    
3205  1;  1;

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