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

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