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revision 1.69, Mon Oct 2 02:59:47 2006 UTC revision 1.96, Fri Apr 18 18:40:51 2008 UTC
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1  #  # -*- perl -*-
2    ########################################################################
3  # Copyright (c) 2003-2006 University of Chicago and Fellowship  # Copyright (c) 2003-2006 University of Chicago and Fellowship
4  # for Interpretations of Genomes. All Rights Reserved.  # for Interpretations of Genomes. All Rights Reserved.
5  #  #
# Line 13  Line 14 
14  # at info@ci.uchicago.edu or the Fellowship for Interpretation of  # at info@ci.uchicago.edu or the Fellowship for Interpretation of
15  # Genomes at veronika@thefig.info or download a copy from  # Genomes at veronika@thefig.info or download a copy from
16  # http://www.theseed.org/LICENSE.TXT.  # http://www.theseed.org/LICENSE.TXT.
17  #  ########################################################################
18    
19  package Tracer;  package Tracer;
20    
21      require Exporter;      require Exporter;
22      @ISA = ('Exporter');      @ISA = ('Exporter');
23      @EXPORT = qw(Trace T TSetup QTrace Confess Cluck Min Max Assert Open OpenDir TICK StandardSetup EmergencyIP ScriptSetup ScriptFinish Insure ChDir Emergency);      @EXPORT = qw(Trace T TSetup QTrace Confess Cluck Min Max Assert Open OpenDir TICK StandardSetup EmergencyKey ETracing ScriptSetup ScriptFinish Insure ChDir Emergency);
24      @EXPORT_OK = qw(GetFile GetOptions Merge MergeOptions ParseCommand ParseRecord UnEscape Escape);      @EXPORT_OK = qw(GetFile GetOptions Merge MergeOptions ParseCommand ParseRecord UnEscape Escape);
25      use strict;      use strict;
26      use Carp qw(longmess croak);      use Carp qw(longmess croak carp);
27      use CGI;      use CGI;
28      use Cwd;      use Cwd;
29      use FIG_Config;      use FIG_Config;
# Line 34  Line 35 
35      use LWP::UserAgent;      use LWP::UserAgent;
36      use Time::HiRes 'gettimeofday';      use Time::HiRes 'gettimeofday';
37      use URI::Escape;      use URI::Escape;
38        use Time::Local;
39    
40  =head1 Tracing and Debugging Helpers  =head1 Tracing and Debugging Helpers
41    
42  =head2 Introduction  =head2 Tracing
43    
44  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
45  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.
46  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,
47  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
48  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
49  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
50  is less likely to be seen. A higher trace level passed to B<TSetup> 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
51  appear. To generate a trace message, use the following syntax.  appear.
52    
53    =head3 Putting Trace Messages in Your Code
54    
55    To generate a trace message, use the following syntax.
56    
57  C<< Trace($message) if T(errors => 4); >>      Trace($message) if T(errors => 4);
58    
59  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>
60  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
61    
62  C<< Trace($message) if T(main => 4); >>      Trace($message) if T(main => 4);
63    
64  will trace if the trace level is 4 or more.  will trace if the trace level is 4 or more.
65    
# Line 61  Line 67 
67  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
68  active and the trace level is 2 or more.  active and the trace level is 2 or more.
69    
70  C<< Trace($message) if T(2); >>      Trace($message) if T(2);
71    
72  To set up tracing, you call the L</TSetup> method. The method takes as input a trace level, a list  In scripts, where no package name is available, the category defaults to C<main>.
73  of category names, and a set of options. The trace level and list of category names are  
74    =head3 Custom Tracing
75    
76    Many programs have customized tracing configured using the L</TSetup> method. This is no longer
77    the preferred method, but a knowledge of how custom tracing works can make the more modern
78    L</Emergency Tracing> easier to understand.
79    
80    To set up custom tracing, you call the L</TSetup> method. The method takes as input a trace level,
81    a list of category names, and a destination. The trace level and list of category names are
82  specified as a space-delimited string. Thus  specified as a space-delimited string. Thus
83    
84  C<< TSetup('3 errors Sprout ERDB', 'HTML'); >>      TSetup('3 errors Sprout ERDB', 'TEXT');
85    
86  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
87  specifies that messages should be output as HTML paragraphs.  specifies that messages should be sent to the standard output.
88    
89  To turn on tracing for ALL categories, use an asterisk. The call below sets every category to  To turn on tracing for ALL categories, use an asterisk. The call below sets every category to
90  level 3 and writes the output to the standard error output. This sort of thing might be  level 3 and writes the output to the standard error output. This sort of thing might be
91  useful in a CGI environment.  useful in a CGI environment.
92    
93  C<< TSetup('3 *', 'WARN'); >>      TSetup('3 *', 'WARN');
94    
95  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
96  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
97  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
98  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
99  it easier to debug page formatting problems.  it easier to debug page formatting problems.
100    
101  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
102    a file at the same time. To trace to a file, specify the filename with an output character in front
103    of it.
104    
105        TSetup('4 SQL', ">$fileName");
106    
107    To trace to the standard output and a file at the same time, put a C<+> in front of the angle
108    bracket.
109    
110        TSetup('3 *', "+>$fileName");
111    
112  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>.
113  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.
114  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
115  being used out in the field.  being used out in the field.
116    
117    =head3 Trace Levels
118    
119  There is no hard and fast rule on how to use trace levels. The following is therefore only  There is no hard and fast rule on how to use trace levels. The following is therefore only
120  a suggestion.  a suggestion.
121    
# Line 122  Line 147 
147  =back  =back
148    
149  The format of trace messages is important because some utilities analyze trace files.  The format of trace messages is important because some utilities analyze trace files.
150  The time stamp is between square brackets, the module name between angle brackets,  There are three fields-- the time stamp, the category name, and the text.
151  a colon (C<:>), and the message text after that. If the square brackets or angle  The time stamp is between square brackets and the category name between angle brackets.
152  brackets are missing, then the trace management utilities assume that they  After the category name there is a colon (C<:>) followed by the message text.
153  are encountering a set of pre-formatted lines.  If the square brackets or angle brackets are missing, then the trace management
154    utilities assume that they are encountering a set of pre-formatted lines.
155    
156    Note, however, that this formatting is done automatically by the tracing functions. You
157    only need to know about it if you want to parse a trace file.
158    
159    =head3 Emergency Tracing
160    
161    Sometimes, you need a way for tracing to happen automatically without putting parameters
162    in a form or on the command line. Emergency tracing does this. You invoke emergency tracing
163    from the debug form, which is accessed from I<MySeedInstance>C</FIG/Html/SetPassword.html>.
164    Emergency tracing requires you specify a tracing key. For command-line tools, the key is
165    taken from the C<TRACING> environment variable. For web services, the key is taken from
166    a cookie. Either way, the key tells the tracing facility who you are, so that you control
167    the tracing in your environment without stepping on other users.
168    
169    The key can be anything you want. If you don't have a key, the C<SetPassword> page will
170    generate one for you.
171    
172    You can activate and de-activate emergency tracing from the debugging control panel, as
173    well as display the trace file itself.
174    
175    To enable emergency tracing in your code, call
176    
177        ETracing($cgi)
178    
179    from a web script and
180    
181        ETracing()
182    
183    from a command-line script.
184    
185    The web script will look for the tracing key in the cookies, and the command-line
186    script will look for it in the C<TRACING> environment variable. If you are
187    using the L</StandardScript> or L</StandardSetup> methods, emergency tracing
188    will be configured automatically.
189    
190    NOTE: to configure emergency tracing from the command line instead of the Debugging
191    Control Panel (see below), use the C<trace.pl> script.
192    
193    =head3 Debugging Control Panel
194    
195    The debugging control panel provides several tools to assist in development of
196    SEED and Sprout software. You access the debugging control panel from the URL
197    C</FIG/Html/SetPassword.html> in whichever seed instance you're using. (So,
198    for example, the panel access point for the development NMPDR system is
199    C<http://web-1.nmpdr.org/next/FIG/Html/SetPassword.html>. Contact Bruce to
200    find out what the password is. From this page, you can also specify a tracing
201    key. If you don't specify a key, one will be generated for you.
202    
203    =head4 Emergency Tracing Form
204    
205    At the bottom of the debugging control panel is a form that allows you to
206    specify a trace level and tracing categories. Special and common categories
207    are listed with check boxes. You can hold your mouse over a check box to see
208    what its category does. In general, however, a category name is the same as
209    the name of the package in which the trace message occurs.
210    
211    Additional categories can be entered in an input box, delimited by spaces or commas.
212    
213    The B<Activate> button turns on Emergency tracing at the level you specify with the
214    specified categories active. The B<Terminate> button turns tracing off. The
215    B<Show File> button displays the current contents of the trace file. The tracing
216    form at the bottom of the control panel is designed for emergency tracing, so it
217    will only affect programs that call L</ETracing>, L</StandardScript>,
218    or L</StandardSetup>.
219    
220    =head4 Script Form
221    
222    The top form of the debugging control panel allows you to enter a tiny script and
223    have the output generated in a formatted table. Certain object variables are
224    predefined in the script, including a FIG object (C<$fig>), a CGI object (C<$cgi>),
225    and-- if Sprout is active-- Sprout (C<$sprout>) and SFXlate (C<$sfx>) objects.
226    
227    The last line of the script must be a scalar, but it can be a reference to a hash,
228    a list, a list of lists, and various other combinations. If you select the appropriate
229    data type in the dropdown box, the output will be formatted accordingly. The form
230    also has controls for specifying tracing. These controls override any emergency
231    tracing in effect.
232    
233    =head4 Database Query Forms
234    
235    The forms between the script form and the emergency tracing form allow you to
236    make queries against the database. The FIG query form allows simple queries against
237    a single FIG table. The Sprout query form uses the B<GetAll> method to do a
238    multi-table query against the Sprout database. B<GetAll> is located in the B<ERDB>
239    package, and it takes five parameters.
240    
241        GetAll(\@objectNames, $filterClause, \@parameters, \@fields, $count);
242    
243    Each of the five parameters corresponds to a text box on the query form:
244    
245    =over 4
246    
247    =item Objects
248    
249    Comma-separated list containing the names of the entity and relationship objects to be retrieved.
250    
251    =item Filter
252    
253    WHERE/ORDER BY clause (without the WHERE) to be used to filter and sort the query. The WHERE clause can
254    be parameterized with parameter markers (C<?>). Each field used must be specified in the standard form
255    B<I<objectName>(I<fieldName>)> or B<$I<number>(I<fieldName>)> where I<fieldName> is the name of a
256    field, I<objectName> is the name of the entity or relationship object containing the field, and
257    I<number> is the 1-based position of the object in the object list. Any parameters
258    specified in the filter clause should be specified in the B<Params> field.
259    The fields in a filter clause can come from primary entity relations,
260    relationship relations, or secondary entity relations; however, all of the
261    entities and relationships involved must be included in the list of object names.
262    
263    =item Params
264    
265    List of the parameters to be substituted in for the parameters marks in the filter clause. This
266    is a comma-separated list without any quoting or escaping.
267    
268    =item fields
269    
270    Comma-separated list of the fields to be returned in each element of the list returned. Fields
271    are specified in the same manner as in the filter clause.
272    
273    =item count
274    
275    Maximum number of records to return. If omitted or 0, all available records will be returned.
276    
277    =back
278    
279    B<GetAll> automatically joins together the entities and relationships listed in the object
280    names. This simplifies the coding of the filter clause, but it means that some queries are
281    not possible, since they cannot be expressed in a linear sequence of joins. This is a limitation
282    that has yet to be addressed.
283    
284  =cut  =cut
285    
286  # Declare the configuration variables.  # Declare the configuration variables.
287    
288  my $Destination = "NONE";   # Description of where to send the trace output.  my $Destination = "WARN";   # Description of where to send the trace output.
289  my $TeeFlag = 0;            # TRUE if output is going to a file and to the  my $TeeFlag = 0;            # TRUE if output is going to a file and to the
290                              # standard output                              # standard output
291  my %Categories = ( main => 1 );  my %Categories = ( main => 1 );
# Line 143  Line 297 
297  my $SetupCount = 0;         # number of times TSetup called  my $SetupCount = 0;         # number of times TSetup called
298  my $AllTrace = 0;           # TRUE if we are tracing all categories.  my $AllTrace = 0;           # TRUE if we are tracing all categories.
299    
300  =head2 Public Methods  =head2 Tracing Methods
301    
302    =head3 Setups
303    
304        my $count = Tracer::Setups();
305    
306    Return the number of times L</TSetup> has been called.
307    
308    This method allows for the creation of conditional tracing setups where, for example, we
309    may want to set up tracing if nobody else has done it before us.
310    
311    =cut
312    
313    sub Setups {
314        return $SetupCount;
315    }
316    
317  =head3 TSetup  =head3 TSetup
318    
319  C<< TSetup($categoryList, $target); >>      TSetup($categoryList, $target);
320    
321  This method is used to specify the trace options. The options are stored as package data  This method is used to specify the trace options. The options are stored as package data
322  and interrogated by the L</Trace> and L</T> methods.  and interrogated by the L</Trace> and L</T> methods.
# Line 219  Line 388 
388      $SetupCount++;      $SetupCount++;
389  }  }
390    
391  =head3 StandardSetup  =head3 SetLevel
392    
393  C<< my ($options, @parameters) = StandardSetup(\@categories, \%options, $parmHelp, @ARGV); >>      Tracer::SetLevel($newLevel);
394    
395  This method performs standard command-line parsing and tracing setup. The return  Modify the trace level. A higher trace level will cause more messages to appear.
 values are a hash of the command-line options and a list of the positional  
 parameters. Tracing is automatically set up and the command-line options are  
 validated.  
396    
397  This is a complex method that does a lot of grunt work. The parameters can  =over 4
 be more easily understood, however, once they are examined individually.  
398    
399  The I<categories> parameter is the most obtuse. It is a reference to a list of  =item newLevel
 special-purpose tracing categories. Most tracing categories are PERL package  
 names. So, for example, if you wanted to turn on tracing inside the B<Sprout>,  
 B<ERDB>, and B<SproutLoad> packages, you would specify the categories  
400    
401      ["Sprout", "SproutLoad", "ERDB"]  Proposed new trace level.
402    
403  This would cause trace messages in the specified three packages to appear in  =back
 the output. There are two special tracing categories that are automatically  
 handled by this method. In other words, if you used L</TSetup> you would need  
 to include these categories manually, but if you use this method they are turned  
 on automatically.  
404    
405  =over 4  =cut
406    
407  =item SQL  sub SetLevel {
408        $TraceLevel = $_[0];
409    }
410    
411  Traces SQL commands and activity.  =head3 ParseTraceDate
412    
413  =item Tracer      my $time = Tracer::ParseTraceDate($dateString);
414    
415  Traces error messages and call stacks.  Convert a date from the trace file into a PERL timestamp.
416    
417  =back  =over 4
418    
419  C<SQL> is only turned on if the C<-sql> option is specified in the command line.  =item dateString
 The trace level is specified using the C<-trace> command-line option. For example,  
 the following command line for C<TransactFeatures> turns on SQL tracing and runs  
 all tracing at level 3.  
420    
421      TransactFeatures -trace=3 -sql register ../xacts IDs.tbl  The date string from the trace file. The format of the string is determined by the
422    L</Now> method.
423    
424  Standard tracing is output to the standard output and echoed to the file  =item RETURN
 C<trace>I<$$>C<.log> in the FIG temporary directory, where I<$$> is the  
 process ID. You can also specify the C<user> parameter to put a user ID  
 instead of a process ID in the trace file name. So, for example  
425    
426  The default trace level is 2. To get all messages, specify a trace level of 4.  Returns a PERL time, that is, a number of seconds since the epoch, or C<undef> if
427  For a genome-by-genome update, use 3.  the time string is invalid.
428    
429      TransactFeatures -trace=3 -sql -user=Bruce register ../xacts IDs.tbl  =back
430    
431  would send the trace output to C<traceBruce.log> in the temporary directory.  =cut
432    
433  The I<options> parameter is a reference to a hash containing the command-line  sub ParseTraceDate {
434  options, their default values, and an explanation of what they mean. Command-line      # Get the parameters.
435  options may be in the form of switches or keywords. In the case of a switch, the      my ($dateString) = @_;
436  option value is 1 if it is specified and 0 if it is not specified. In the case      # Declare the return variable.
437  of a keyword, the value is separated from the option name by an equal sign. You      my $retVal;
438  can see this last in the command-line example above.      # Parse the date.
439        if ($dateString =~ m#(\d+)/(\d+)/(\d+)\s+(\d+):(\d+):(\d+)#) {
440            # Create a time object. Note we need to convert the day, month,
441            # and year to a different base. Years count from 1900, and
442            # the internal month value is relocated to January = 0.
443            $retVal = timelocal($6, $5, $4, $2, $1 - 1, $3 - 1900);
444        }
445        # Return the result.
446        return $retVal;
447    }
448    
449  You can specify a different default trace level by setting C<$options->{trace}>  =head3 LogErrors
 prior to calling this method.  
450    
451  An example at this point would help. Consider, for example, the command-line utility      Tracer::LogErrors($fileName);
 C<TransactFeatures>. It accepts a list of positional parameters plus the options  
 C<safe>, C<noAlias>, C<start>, and C<tblFiles>. To start up this command, we execute  
 the following code.  
452    
453      my ($options, @parameters) = Tracer::StandardSetup(["DocUtils"],  Route the standard error output to a log file.
                         { safe => [0, "use database transactions"],  
                           noAlias => [0, "do not expect aliases in CHANGE transactions"],  
                           start => [' ', "start with this genome"],  
                           tblFiles => [0, "output TBL files containing the corrected IDs"] },  
                         "command transactionDirectory IDfile",  
                       @ARGV);  
454    
455    =over 4
456    
457  The call to C<ParseCommand> specifies the default values for the options and  =item fileName
 stores the actual options in a hash that is returned as C<$options>. The  
 positional parameters are returned in C<@parameters>.  
458    
459  The following is a sample command line for C<TransactFeatures>.  Name of the file to receive the error output.
460    
461      TransactFeatures -trace=2 -noAlias register ../xacts IDs.tbl  =back
462    
463  In this case, C<register>, C<../xacts>, and C<IDs.tbl> are the positional  =cut
 parameters, and would find themselves in I<@parameters> after executing the  
 above code fragment. The tracing would be set to level 2, and the categories  
 would be C<Tracer>, and <DocUtils>. C<Tracer> is standard,  
 and C<DocUtils> was included because it came in within the first parameter  
 to this method. The I<$options> hash would be  
464    
465      { trace => 2, sql => 0, safe => 0,  sub LogErrors {
466        noAlias => 1, start => ' ', tblFiles => 0 }      # Get the file name.
467        my ($fileName) = @_;
468        # Open the file as the standard error output.
469        open STDERR, '>', $fileName;
470    }
471    
472  Use of C<StandardSetup> in this way provides a simple way of performing  =head3 Trace
 standard tracing setup and command-line parsing. Note that the caller is  
 not even aware of the command-line switches C<-trace> and C<-sql>, which  
 are used by this method to control the tracing. If additional tracing features  
 need to be added in the future, they can be processed by this method without  
 upsetting the command-line utilities.  
473    
474  If the C<background> option is specified on the command line, then the      Trace($message);
 standard and error outputs will be directed to files in the temporary  
 directory, using the same suffix as the trace file. So, if the command  
 line specified  
475    
476      -user=Bruce -background  Write a trace message to the target location specified in L</TSetup>. If there has not been
477    any prior call to B<TSetup>.
478    
479  then the trace output would go to C<traceBruce.log>, the standard output to  =over 4
 C<outBruce.log>, and the error output to C<errBruce.log>. This is designed to  
 simplify starting a command in the background.  
480    
481  Finally, if the special option C<-h> is specified, the option names will  =item message
 be traced at level 0 and the program will exit without processing.  
 This provides a limited help capability. For example, if the user enters  
482    
483      TransactFeatures -h  Message to write.
484    
485  he would see the following output.  =back
486    
487      TransactFeatures [options] command transactionDirectory IDfile  =cut
         -trace    tracing level (default 2)  
         -sql      trace SQL commands  
         -safe     use database transactions  
         -noAlias  do not expect aliases in CHANGE transactions  
         -start    start with this genome  
         -tblFiles output TBL files containing the corrected IDs  
488    
489  The caller has the option of modifying the tracing scheme by placing a value  sub Trace {
490  for C<trace> in the incoming options hash. The default value can be overridden,      # Get the parameters.
491  or the tracing to the standard output can be turned off by suffixing a minus      my ($message) = @_;
492  sign to the trace level. So, for example,      # Get the timestamp.
493        my $timeStamp = Now();
494        # Format the message. Note we strip off any line terminators at the end.
495        my $prefix = "[$timeStamp] <$LastCategory>: ";
496        my $formatted = $prefix . Strip($message);
497        # Process according to the destination.
498        if ($Destination eq "TEXT") {
499            # Write the message to the standard output.
500            print "$formatted\n";
501        } elsif ($Destination eq "ERROR") {
502            # Write the message to the error output.
503            print STDERR "$formatted\n";
504        } elsif ($Destination eq "QUEUE") {
505            # Push the message into the queue.
506            push @Queue, "$formatted";
507        } elsif ($Destination eq "HTML") {
508            # Convert the message to HTML and write it to the standard output.
509            my $escapedMessage = CGI::escapeHTML($message);
510            print "<p>$timeStamp $LastCategory: $escapedMessage</p>\n";
511        } elsif ($Destination eq "WARN") {
512           # Emit the message as a warning.
513           carp $message;
514        } elsif ($Destination =~ m/^>>/) {
515            # Write the trace message to an output file.
516            (open TRACING, $Destination) || die "Tracing open for \"$Destination\" failed: $!";
517            print TRACING "$formatted\n";
518            close TRACING;
519            # If the Tee flag is on, echo it to the standard output.
520            if ($TeeFlag) {
521                print "$formatted\n";
522            }
523        }
524    }
525    
526      { trace => [0, "tracing level (default 0)"],  =head3 T
        ...  
527    
528  would set the default trace level to 0 instead of 2, while      my $switch = T($category, $traceLevel);
529    
530      { trace => ["2-", "tracing level (default 2)"],      or
        ...  
531    
532  would leave the default at 2, but trace only to the log file, not to the      my $switch = T($traceLevel);
 standard output.  
533    
534  The parameters to this method are as follows.  Return TRUE if the trace level is at or above a specified value and the specified category
535    is active, else FALSE. If no category is specified, the caller's package name is used.
536    
537  =over 4  =over 4
538    
539  =item categories  =item category
540    
541  Reference to a list of tracing category names. These should be names of  Category to which the message belongs. If not specified, the caller's package name is
542  packages whose internal workings will need to be debugged to get the  used.
 command working.  
543    
544  =item options  =item traceLevel
545    
546  Reference to a hash containing the legal options for the current command mapped  Relevant tracing level.
 to their default values and descriptions. The user can override the defaults  
 by specifying the options as command-line switches prefixed by a hyphen.  
 Tracing-related options may be added to this hash. If the C<-h> option is  
 specified on the command line, the option descriptions will be used to  
 explain the options. To turn off tracing to the standard output, add a  
 minus sign to the value for C<trace> (see above).  
   
 =item parmHelp  
   
 A string that vaguely describes the positional parameters. This is used  
 if the user specifies the C<-h> option.  
   
 =item argv  
   
 List of command line parameters, including the option switches, which must  
 precede the positional parameters and be prefixed by a hyphen.  
547    
548  =item RETURN  =item RETURN
549    
550  Returns a list. The first element of the list is the reference to a hash that  TRUE if a message at the specified trace level would appear in the trace, else FALSE.
 maps the command-line option switches to their values. These will either be the  
 default values or overrides specified on the command line. The remaining  
 elements of the list are the position parameters, in order.  
551    
552  =back  =back
553    
554  =cut  =cut
555    
556  sub StandardSetup {  sub T {
557        # Declare the return variable.
558        my $retVal = 0;
559        # Only proceed if tracing is turned on.
560        if ($Destination ne "NONE") {
561      # Get the parameters.      # Get the parameters.
562      my ($categories, $options, $parmHelp, @argv) = @_;          my ($category, $traceLevel) = @_;
563      # Add the tracing options.          if (!defined $traceLevel) {
564      if (! exists $options->{trace}) {              # Here we have no category, so we need to get the calling package.
565          $options->{trace} = [2, "tracing level"];              # The calling package is normally the first parameter. If it is
566      }              # omitted, the first parameter will be the tracelevel. So, the
567      $options->{sql} = [0, "turn on SQL tracing"];              # first thing we do is shift the so-called category into the
568      $options->{h} = [0, "display command-line options"];              # $traceLevel variable where it belongs.
569      $options->{user} = [$$, "trace log file name suffix"];              $traceLevel = $category;
570      $options->{background} = [0, "spool standard and error output"];              my ($package, $fileName, $line) = caller;
571      # Create a parsing hash from the options hash. The parsing hash              # If there is no calling package, we default to "main".
572      # contains the default values rather than the default value              if (!$package) {
573      # and the description. While we're at it, we'll memorize the                  $category = "main";
     # length of the longest option name.  
     my $longestName = 0;  
     my %parseOptions = ();  
     for my $key (keys %{$options}) {  
         if (length $key > $longestName) {  
             $longestName = length $key;  
         }  
         $parseOptions{$key} = $options->{$key}->[0];  
     }  
     # Parse the command line.  
     my ($retOptions, @retParameters) = ParseCommand(\%parseOptions, @argv);  
     # Get the logfile suffix.  
     my $suffix = $retOptions->{user};  
     # Check for background mode.  
     if ($retOptions->{background}) {  
         my $outFileName = "$FIG_Config::temp/out$suffix.log";  
         my $errFileName = "$FIG_Config::temp/err$suffix.log";  
         open STDOUT, ">$outFileName";  
         open STDERR, ">$errFileName";  
     }  
     # Now we want to set up tracing. First, we need to know if SQL is to  
     # be traced.  
     my @cats = @{$categories};  
     if ($retOptions->{sql}) {  
         push @cats, "SQL";  
     }  
     # Add the default categories.  
     push @cats, "Tracer";  
     # Next, we create the category string by joining the categories.  
     my $cats = join(" ", @cats);  
     # Check to determine whether or not the caller wants to turn off tracing  
     # to the standard output.  
     my $traceLevel = $retOptions->{trace};  
     my $textOKFlag = 1;  
     if ($traceLevel =~ /^(.)-/) {  
         $traceLevel = $1;  
         $textOKFlag = 0;  
     }  
     # Now we set up the trace mode.  
     my $traceMode;  
     # Verify that we can open a file in the FIG temporary directory.  
     my $traceFileName = "$FIG_Config::temp/trace$suffix.log";  
     if (open TESTTRACE, ">$traceFileName") {  
         # Here we can trace to a file.  
         $traceMode = ">$traceFileName";  
         if ($textOKFlag) {  
             # Echo to standard output if the text-OK flag is set.  
             $traceMode = "+$traceMode";  
         }  
         # Close the test file.  
         close TESTTRACE;  
     } else {  
         # Here we can't trace to a file. We trace to the standard output if it's  
         # okay, and the error log otherwise.  
         if ($textOKFlag) {  
             $traceMode = "TEXT";  
574          } else {          } else {
575              $traceMode = "WARN";                  my @cats = split /::/, $package;
576                    $category = $cats[$#cats];
577          }          }
578      }      }
579      # Now set up the tracing.          # Save the category name.
580      TSetup("$traceLevel $cats", $traceMode);          $LastCategory = $category;
581      # Check for the "h" option. If it is specified, dump the command-line          # Convert it to lower case before we hash it.
582      # options and exit the program.          $category = lc $category;
583      if ($retOptions->{h}) {          # Use the category and tracelevel to compute the result.
584          $0 =~ m#[/\\](\w+)(\.pl)?$#i;          if (ref $traceLevel) {
585          print "$1 [options] $parmHelp\n";              Confess("Bad trace level.");
586          for my $key (sort keys %{$options}) {          } elsif (ref $TraceLevel) {
587              my $name = Pad($key, $longestName, 0, ' ');              Confess("Bad trace config.");
             my $desc = $options->{$key}->[1];  
             if ($options->{$key}->[0]) {  
                 $desc .= " (default " . $options->{$key}->[0] . ")";  
             }  
             print "  $name $desc\n";  
588          }          }
589          exit(0);          $retVal = ($traceLevel <= $TraceLevel && ($AllTrace || exists $Categories{$category}));
590      }      }
591      # Return the parsed parameters.      # Return the computed result.
592      return ($retOptions, @retParameters);      return $retVal;
593  }  }
594    
595  =head3 Setups  =head3 QTrace
596    
597  C<< my $count = Tracer::Setups(); >>      my $data = QTrace($format);
598    
599  Return the number of times L</TSetup> has been called.  Return the queued trace data in the specified format.
600    
601  This method allows for the creation of conditional tracing setups where, for example, we  =over 4
602  may want to set up tracing if nobody else has done it before us.  
603    =item format
604    
605    C<html> to format the data as an HTML list, C<text> to format it as straight text.
606    
607    =back
608    
609  =cut  =cut
610    
611  sub Setups {  sub QTrace {
612      return $SetupCount;      # Get the parameter.
613        my ($format) = @_;
614        # Create the return variable.
615        my $retVal = "";
616        # Only proceed if there is an actual queue.
617        if (@Queue) {
618            # Process according to the format.
619            if ($format =~ m/^HTML$/i) {
620                # Convert the queue into an HTML list.
621                $retVal = "<ul>\n";
622                for my $line (@Queue) {
623                    my $escapedLine = CGI::escapeHTML($line);
624                    $retVal .= "<li>$escapedLine</li>\n";
625                }
626                $retVal .= "</ul>\n";
627            } elsif ($format =~ m/^TEXT$/i) {
628                # Convert the queue into a list of text lines.
629                $retVal = join("\n", @Queue) . "\n";
630            }
631            # Clear the queue.
632            @Queue = ();
633        }
634        # Return the formatted list.
635        return $retVal;
636  }  }
637    
638  =head3 Open  =head3 Confess
639    
640  C<< my $handle = Open($fileHandle, $fileSpec, $message); >>      Confess($message);
641    
642  Open a file.  Trace the call stack and abort the program with the specified message. When used with
643    the OR operator and the L</Assert> method, B<Confess> can function as a debugging assert.
644    So, for example
645    
646  The I<$fileSpec> is essentially the second argument of the PERL C<open>      Assert($recNum >= 0) || Confess("Invalid record number $recNum.");
 function. The mode is specified using Unix-like shell information. So, for  
 example,  
647    
648      Open(\*LOGFILE, '>>/usr/spool/news/twitlog', "Could not open twit log.");  Will abort the program with a stack trace if the value of C<$recNum> is negative.
649    
650  would open for output appended to the specified file, and  =over 4
651    
652      Open(\*DATASTREAM, "| sort -u >$outputFile", "Could not open $outputFile.");  =item message
653    
654  would open a pipe that sorts the records written and removes duplicates. Note  Message to include in the trace.
 the use of file handle syntax in the Open call. To use anonymous file handles,  
 code as follows.  
655    
656      my $logFile = Open(undef, '>>/usr/spool/news/twitlog', "Could not open twit log.");  =back
657    
658  The I<$message> parameter is used if the open fails. If it is set to C<0>, then  =cut
 the open returns TRUE if successful and FALSE if an error occurred. Otherwise, a  
 failed open will throw an exception and the third parameter will be used to construct  
 an error message. If the parameter is omitted, a standard message is constructed  
 using the file spec.  
659    
660      Could not open "/usr/spool/news/twitlog"  sub Confess {
661        # Get the parameters.
662        my ($message) = @_;
663        if (! defined($FIG_Config::no_tool_hdr)) {
664            # Here we have a tool header. Display its length so that the user can adjust the line numbers.
665            my $toolHeaderFile = "$FIG_Config::fig_disk/dist/releases/current/$FIG_Config::arch/tool_hdr";
666            # Only proceed if the tool header file is actually present.
667            if (-f $toolHeaderFile) {
668                my @lines = GetFile($toolHeaderFile);
669                Trace("Tool header has " . scalar(@lines) . " lines.");
670            }
671        }
672        # Trace the call stack.
673        Cluck($message);
674        # Abort the program.
675        croak(">>> $message");
676    }
677    
678  Note that the mode characters are automatically cleaned from the file name.  =head3 Assert
 The actual error message from the file system will be captured and appended to the  
 message in any case.  
679    
680      Could not open "/usr/spool/news/twitlog": file not found.      Assert($condition1, $condition2, ... $conditionN);
681    
682  In some versions of PERL the only error message we get is a number, which  Return TRUE if all the conditions are true. This method can be used in conjunction with
683  corresponds to the C++ C<errno> value.  the OR operator and the L</Confess> method as a debugging assert.
684    So, for example
685    
686      Could not open "/usr/spool/news/twitlog": 6.      Assert($recNum >= 0) || Confess("Invalid record number $recNum.");
687    
688  =over 4  Will abort the program with a stack trace if the value of C<$recNum> is negative.
689    
690  =item fileHandle  =cut
691    sub Assert {
692        my $retVal = 1;
693        LOOP: for my $condition (@_) {
694            if (! $condition) {
695                $retVal = 0;
696                last LOOP;
697            }
698        }
699        return $retVal;
700    }
701    
702  File handle. If this parameter is C<undef>, a file handle will be generated  =head3 Cluck
 and returned as the value of this method.  
703    
704  =item fileSpec      Cluck($message);
705    
706  File name and mode, as per the PERL C<open> function.  Trace the call stack. Note that for best results, you should qualify the call with a
707    trace condition. For example,
708    
709  =item message (optional)      Cluck("Starting record parse.") if T(3);
710    
711  Error message to use if the open fails. If omitted, a standard error message  will only trace the stack if the trace level for the package is 3 or more.
 will be generated. In either case, the error information from the file system  
 is appended to the message. To specify a conditional open that does not throw  
 an error if it fails, use C<0>.  
712    
713  =item RETURN  =over 4
714    
715  Returns the name of the file handle assigned to the file, or C<undef> if the  =item message
716  open failed.  
717    Message to include in the trace.
718    
719  =back  =back
720    
721  =cut  =cut
722    
723  sub Open {  sub Cluck {
724      # Get the parameters.      # Get the parameters.
725      my ($fileHandle, $fileSpec, $message) = @_;      my ($message) = @_;
726      # Attempt to open the file.      # Trace what's happening.
727      my $rv = open $fileHandle, $fileSpec;      Trace("Stack trace for event: $message");
728      # If the open failed, generate an error message.      my $confession = longmess($message);
729      if (! $rv) {      # Convert the confession to a series of trace messages. Note we skip any
730          # Save the system error message.      # messages relating to calls into Tracer.
731          my $sysMessage = $!;      for my $line (split /\s*\n/, $confession) {
732          # See if we need a default message.          Trace($line) if ($line !~ /Tracer\.pm/);
         if (!$message) {  
             # Clean any obvious mode characters and leading spaces from the  
             # filename.  
             my ($fileName) = FindNamePart($fileSpec);  
             $message = "Could not open \"$fileName\"";  
         }  
         # Terminate with an error using the supplied message and the  
         # error message from the file system.  
         Confess("$message: $!");  
733      }      }
     # Return the file handle.  
     return $fileHandle;  
734  }  }
735    
736  =head3 FindNamePart  =head3 ScriptSetup
   
 C<< my ($fileName, $start, $len) = Tracer::FindNamePart($fileSpec); >>  
   
 Extract the portion of a file specification that contains the file name.  
737    
738  A file specification is the string passed to an C<open> call. It specifies the file      my ($cgi, $varHash) = ScriptSetup($noTrace);
 mode and name. In a truly complex situation, it can specify a pipe sequence. This  
 method assumes that the file name is whatever follows the first angle bracket  
 sequence.  So, for example, in the following strings the file name is  
 C</usr/fig/myfile.txt>.  
739    
740      >>/usr/fig/myfile.txt  Perform standard tracing and debugging setup for scripts. The value returned is
741      </usr/fig/myfile.txt  the CGI object followed by a pre-built variable hash. At the end of the script,
742      | sort -u > /usr/fig/myfile.txt  the client should call L</ScriptFinish> to output the web page.
743    
744  If the method cannot find a file name using its normal methods, it will return the  This method calls L</ETracing> to configure tracing, which allows the tracing
745  whole incoming string.  to be configured via the emergency tracing form on the debugging control panel.
746    Tracing will then be turned on automatically for all programs that use the L</ETracing>
747    method, which includes every program that uses this method or L</StandardSetup>.
748    
749  =over 4  =over 4
750    
751  =item fileSpec  =item noTrace (optional)
752    
753  File specification string from which the file name is to be extracted.  If specified, tracing will be suppressed. This is useful if the script wants to set up
754    tracing manually.
755    
756  =item RETURN  =item RETURN
757    
758  Returns a three-element list. The first element contains the file name portion of  Returns a two-element list consisting of a CGI query object and a variable hash for
759  the specified string, or the whole string if a file name cannot be found via normal  the output page.
 methods. The second element contains the start position of the file name portion and  
 the third element contains the length.  
760    
761  =back  =back
762    
763  =cut  =cut
764  #: Return Type $;  
765  sub FindNamePart {  sub ScriptSetup {
766      # Get the parameters.      # Get the parameters.
767      my ($fileSpec) = @_;      my ($noTrace) = @_;
768      # Default to the whole input string.      # Get the CGI query object.
769      my ($retVal, $pos, $len) = ($fileSpec, 0, length $fileSpec);      my $cgi = CGI->new();
770      # Parse out the file name if we can.      # Set up tracing if it's not suppressed.
771      if ($fileSpec =~ m/(<|>>?)(.+?)(\s*)$/) {      ETracing($cgi) unless $noTrace;
772          $retVal = $2;      # Create the variable hash.
773          $len = length $retVal;      my $varHash = { results => '' };
774          $pos = (length $fileSpec) - (length $3) - $len;      # Return the query object and variable hash.
775      }      return ($cgi, $varHash);
     # Return the result.  
     return ($retVal, $pos, $len);  
776  }  }
777    
778  =head3 OpenDir  =head3 ETracing
779    
780  C<< my @files = OpenDir($dirName, $filtered, $flag); >>      ETracing($parameter);
781    
782  Open a directory and return all the file names. This function essentially performs  Set up emergency tracing. Emergency tracing is tracing that is turned
783  the functions of an C<opendir> and C<readdir>. If the I<$filtered> parameter is  on automatically for any program that calls this method. The emergency
784  set to TRUE, all filenames beginning with a period (C<.>), dollar sign (C<$>),  tracing parameters are stored in a a file identified by a tracing key.
785  or pound sign (C<#>) and all filenames ending with a tilde C<~>) will be  If this method is called with a CGI object, then the tracing key is
786  filtered out of the return list. If the directory does not open and I<$flag> is not  taken from a cookie. If it is called with no parameters, then the tracing
787  set, an exception is thrown. So, for example,  key is taken from an environment variable. If it is called with a string,
788    the tracing key is that string.
789    
790      my @files = OpenDir("/Volumes/fig/contigs", 1);  =over 4
791    
792  is effectively the same as  =item parameter
793    
794      opendir(TMP, "/Volumes/fig/contigs") || Confess("Could not open /Volumes/fig/contigs.");  A parameter from which the tracing key is computed. If it is a scalar,
795      my @files = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir(TMP);  that scalar is used as the tracing key. If it is a CGI object, the
796    tracing key is taken from the C<IP> cookie. If it is omitted, the
797    tracing key is taken from the C<TRACING> environment variable. If it
798    is a CGI object and emergency tracing is not on, the C<Trace> and
799    C<TF> parameters will be used to determine the type of tracing.
800    
801  Similarly, the following code  =back
802    
803      my @files = grep { $_ =~ /^\d/ } OpenDir("/Volumes/fig/orgs", 0, 1);  =cut
804    
805  Returns the names of all files in C</Volumes/fig/orgs> that begin with digits and  sub ETracing {
806  automatically returns an empty list if the directory fails to open.      # Get the parameter.
807        my ($parameter) = @_;
808        # Check for CGI mode.
809        my $cgi = (ref $parameter eq 'CGI' ? $parameter : undef);
810        # Default to no tracing except errors.
811        my ($tracing, $dest) = ("0", "WARN");
812        # Check for emergency tracing.
813        my $tkey = EmergencyKey($parameter);
814        my $emergencyFile = EmergencyFileName($tkey);
815        if (-e $emergencyFile) {
816            # We have the file. Read in the data.
817            my @tracing = GetFile($emergencyFile);
818            # Pull off the time limit.
819            my $expire = shift @tracing;
820            # Convert it to seconds.
821            $expire *= 3600;
822            # Check the file data.
823            my $stat = stat($emergencyFile);
824            my ($now) = gettimeofday;
825            if ($now - $stat->mtime > $expire) {
826                # Delete the expired file.
827                unlink $emergencyFile;
828            } else {
829                # Emergency tracing is on. Pull off the destination and
830                # the trace level;
831                $dest = shift @tracing;
832                my $level = shift @tracing;
833                # Convert the destination to a real tracing destination.
834                # temp directory.
835                $dest = EmergencyTracingDest($tkey, $dest);
836                # Insure Tracer is specified.
837                my %moduleHash = map { $_ => 1 } @tracing;
838                $moduleHash{Tracer} = 1;
839                # Set the trace parameter.
840                $tracing = join(" ", $level, sort keys %moduleHash);
841            }
842        } elsif (defined $cgi) {
843            # There's no emergency tracing, but we have a CGI object, so check
844            # for tracing from the form parameters.
845            if ($cgi->param('Trace')) {
846                # Here the user has requested tracing via a form.
847                $dest = ($cgi->param('TF') ? ">$FIG_Config::temp/Trace$$.log" : "QUEUE");
848                $tracing = $cgi->param('Trace') . " Tracer";
849            }
850        }
851        # Setup the tracing we've determined from all the stuff above.
852        TSetup($tracing, $dest);
853        # Check to see if we're a web script.
854        if (defined $cgi) {
855            # Yes we are. Trace the form and environment data.
856            TraceParms($cgi);
857            # Check for RAW mode. In raw mode, we print a fake header so that we see everything
858            # emitted by the script in its raw form.
859            if (T(Raw => 3)) {
860                print CGI::header(-type => 'text/plain', -tracing => 'Raw');
861            }
862        }
863    }
864    
865  =over 4  =head3 EmergencyFileName
866    
867  =item dirName      my $fileName = Tracer::EmergencyFileName($tkey);
868    
869  Name of the directory to open.  Return the emergency tracing file name. This is the file that specifies
870    the tracing information.
871    
872  =item filtered  =over 4
873    
874  TRUE if files whose names begin with a period (C<.>) should be automatically removed  =item tkey
 from the list, else FALSE.  
875    
876  =item flag  Tracing key for the current program.
877    
878  TRUE if a failure to open is okay, else FALSE  =item RETURN
879    
880    Returns the name of the file to contain the emergency tracing information.
881    
882  =back  =back
883    
884  =cut  =cut
885  #: Return Type @;  
886  sub OpenDir {  sub EmergencyFileName {
887      # Get the parameters.      # Get the parameters.
888      my ($dirName, $filtered, $flag) = @_;      my ($tkey) = @_;
889      # Declare the return variable.      # Compute the emergency tracing file name.
890      my @retVal = ();      return "$FIG_Config::temp/Emergency$tkey.txt";
     # Open the directory.  
     if (opendir(my $dirHandle, $dirName)) {  
         # The directory opened successfully. Get the appropriate list according to the  
         # strictures of the filter parameter.  
         if ($filtered) {  
             @retVal = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir $dirHandle;  
         } else {  
             @retVal = readdir $dirHandle;  
         }  
     } elsif (! $flag) {  
         # Here the directory would not open and it's considered an error.  
         Confess("Could not open directory $dirName.");  
     }  
     # Return the result.  
     return @retVal;  
891  }  }
892    
893  =head3 SetLevel  =head3 EmergencyFileTarget
894    
895  C<< Tracer::SetLevel($newLevel); >>      my $fileName = Tracer::EmergencyFileTarget($tkey);
896    
897  Modify the trace level. A higher trace level will cause more messages to appear.  Return the emergency tracing target file name. This is the file that receives
898    the tracing output for file-based tracing.
899    
900  =over 4  =over 4
901    
902  =item newLevel  =item tkey
903    
904  Proposed new trace level.  Tracing key for the current program.
905    
906    =item RETURN
907    
908    Returns the name of the file to contain the trace output.
909    
910  =back  =back
911    
912  =cut  =cut
913    
914  sub SetLevel {  sub EmergencyFileTarget {
915      $TraceLevel = $_[0];      # Get the parameters.
916        my ($tkey) = @_;
917        # Compute the emergency tracing file name.
918        return "$FIG_Config::temp/trace$tkey.log";
919  }  }
920    
921  =head3 Now  =head3 EmergencyTracingDest
   
 C<< my $string = Tracer::Now(); >>  
   
 Return a displayable time stamp containing the local time.  
922    
923  =cut      my $dest = Tracer::EmergencyTracingDest($tkey, $myDest);
924    
925  sub Now {  This method converts an emergency tracing destination to a real
926      my ($sec,$min,$hour,$mday,$mon,$year,$wday,$yday,$isdst) = localtime(time);  tracing destination. The main difference is that if the
927      my $retVal = _p2($mon+1) . "/" . _p2($mday) . "/" . ($year + 1900) . " " .  destination is C<FILE> or C<APPEND>, we convert it to file
928                   _p2($hour) . ":" . _p2($min) . ":" . _p2($sec);  output. If the destination is C<DUAL>, we convert it to file
929      return $retVal;  and standard output.
 }  
930    
931  # Pad a number to 2 digits.  =over 4
 sub _p2 {  
     my ($value) = @_;  
     $value = "0$value" if ($value < 10);  
     return $value;  
 }  
932    
933  =head3 LogErrors  =item tkey
934    
935  C<< Tracer::LogErrors($fileName); >>  Tracing key for this environment.
936    
937  Route the standard error output to a log file.  =item myDest
938    
939  =over 4  Destination from the emergency tracing file.
940    
941  =item fileName  =item RETURN
942    
943  Name of the file to receive the error output.  Returns a destination that can be passed into L</TSetup>.
944    
945  =back  =back
946    
947  =cut  =cut
948    
949  sub LogErrors {  sub EmergencyTracingDest {
950      # Get the file name.      # Get the parameters.
951      my ($fileName) = @_;      my ($tkey, $myDest) = @_;
952      # Open the file as the standard error output.      # Declare the return variable.
953      open STDERR, '>', $fileName;      my $retVal = $myDest;
954        # Process according to the destination value.
955        if ($myDest eq 'FILE') {
956            $retVal = ">" . EmergencyFileTarget($tkey);
957        } elsif ($myDest eq 'APPEND') {
958            $retVal = ">>" . EmergencyFileTarget($tkey);
959        } elsif ($myDest eq 'DUAL') {
960            $retVal = "+>" . EmergencyFileTarget($tkey);
961        }
962        # Return the result.
963        return $retVal;
964  }  }
965    
966  =head3 ReadOptions  =head3 Emergency
967    
968  C<< my %options = Tracer::ReadOptions($fileName); >>      Emergency($key, $hours, $dest, $level, @modules);
969    
970  Read a set of options from a file. Each option is encoded in a line of text that has the  Turn on emergency tracing. This method is normally invoked over the web from
971  format  a debugging console, but it can also be called by the C<trace.pl> script.
972    The caller specifies the duration of the emergency in hours, the desired tracing
973    destination, the trace level, and a list of the trace modules to activate.
974    For the length of the duration, when a program in an environment with the
975    specified tracing key active invokes a Sprout CGI script, tracing will be
976    turned on automatically. See L</TSetup> for more about tracing setup and
977    L</ETracing> for more about emergency tracing.
978    
979  I<optionName>C<=>I<optionValue>C<; >I<comment>  =over 4
980    
981  The option name must consist entirely of letters, digits, and the punctuation characters  =item tkey
 C<.> and C<_>, and is case sensitive. Blank lines and lines in which the first nonblank  
 character is a semi-colon will be ignored. The return hash will map each option name to  
 the corresponding option value.  
982    
983  =over 4  The tracing key. This is used to identify the control file and the trace file.
984    
985  =item fileName  =item hours
986    
987  Name of the file containing the option data.  Number of hours to keep emergency tracing alive.
988    
989  =item RETURN  =item dest
990    
991  Returns a hash mapping the option names specified in the file to their corresponding option  Tracing destination. If no path information is specified for a file
992  value.  destination, it is put in the FIG temporary directory.
993    
994  =back  =item level
995    
996  =cut  Tracing level. A higher level means more trace messages.
997    
998  sub ReadOptions {  =item modules
     # Get the parameters.  
     my ($fileName) = @_;  
     # 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;  
 }  
   
 =head3 GetOptions  
999    
1000  C<< Tracer::GetOptions(\%defaults, \%options); >>  A list of the tracing modules to activate.
1001    
1002  Merge a specified set of options into a table of defaults. This method takes two hash references  =back
 as input and uses the data from the second to update the first. If the second does not exist,  
 there will be no effect. An error will be thrown if one of the entries in the second hash does not  
 exist in the first.  
1003    
1004  Consider the following example.  =cut
1005    
1006  C<< my $optionTable = GetOptions({ dbType => 'mySQL', trace => 0 }, $options); >>  sub Emergency {
1007        # Get the parameters.
1008        my ($tkey, $hours, $dest, $level, @modules) = @_;
1009        # Create the emergency file.
1010        my $specFile = EmergencyFileName($tkey);
1011        my $outHandle = Open(undef, ">$specFile");
1012        print $outHandle join("\n", $hours, $dest, $level, @modules, "");
1013    }
1014    
1015  In this example, the variable B<$options> is expected to contain at most two options-- B<dbType> and  =head3 EmergencyKey
 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  
1016    
1017  C<< {databaseType => 'Oracle'} >>      my $tkey = EmergencyKey($parameter);
1018    
1019  an error will occur because the B<databaseType> option does not exist.  Return the Key to be used for emergency tracing. This could be an IP address,
1020     a session ID, or a user name, depending on the environment.
1021    
1022  =over 4  =over 4
1023    
1024  =item defaults  =item parameter
   
 Table of default option values.  
   
 =item options  
1025    
1026  Table of overrides, if any.  Parameter defining the method for finding the tracing key. If it is a scalar,
1027    then it is presumed to be the tracing key itself. If it is a CGI object, then
1028    the tracing key is taken from the C<IP> cookie. Otherwise, the tracing key is
1029    taken from the C<TRACING> environment variable.
1030    
1031  =item RETURN  =item RETURN
1032    
1033  Returns a reference to the default table passed in as the first parameter.  Returns the key to be used for labels in emergency tracing.
1034    
1035  =back  =back
1036    
1037  =cut  =cut
1038    
1039  sub GetOptions {  sub EmergencyKey {
1040      # Get the parameters.      # Get the parameters.
1041      my ($defaults, $options) = @_;      my ($parameter) = @_;
1042      # Check for overrides.      # Declare the return variable.
1043      if ($options) {      my $retVal;
1044          # Loop through the overrides.      # Determine the parameter type.
1045          while (my ($option, $setting) = each %{$options}) {      if (! defined $parameter) {
1046              # Insure this override exists.          # Here we're supposed to check the environment.
1047              if (!exists $defaults->{$option}) {          $retVal = $ENV{TRACING};
1048                  croak "Unrecognized option $option encountered.";      } else {
1049              } else {          my $ptype = ref $parameter;
1050                  # Apply the override.          if ($ptype eq 'CGI') {
1051                  $defaults->{$option} = $setting;              # Here we were invoked from a web page. Look for a cookie.
1052              }              $retVal = $parameter->cookie('IP');
1053          }          } elsif (! $ptype) {
1054                # Here the key was passed in.
1055                $retVal = $parameter;
1056            }
1057        }
1058        # If no luck finding a key, use the PID.
1059        if (! defined $retVal) {
1060            $retVal = $$;
1061      }      }
1062      # Return the merged table.      # Return the result.
1063      return $defaults;      return $retVal;
1064  }  }
1065    
 =head3 MergeOptions  
   
 C<< Tracer::MergeOptions(\%table, \%defaults); >>  
1066    
1067  Merge default values into a hash table. This method looks at the key-value pairs in the  =head3 TraceParms
 second (default) hash, and if a matching key is not found in the first hash, the default  
 pair is copied in. The process is similar to L</GetOptions>, but there is no error-  
 checking and no return value.  
1068    
1069  =over 4      Tracer::TraceParms($cgi);
1070    
1071  =item table  Trace the CGI parameters at trace level CGI => 3 and the environment variables
1072    at level CGI => 4. A self-referencing URL is traced at level CGI => 2.
1073    
1074  Hash table to be updated with the default values.  =over 4
1075    
1076  =item defaults  =item cgi
1077    
1078  Default values to be merged into the first hash table if they are not already present.  CGI query object containing the parameters to trace.
1079    
1080  =back  =back
1081    
1082  =cut  =cut
1083    
1084  sub MergeOptions {  sub TraceParms {
1085      # Get the parameters.      # Get the parameters.
1086      my ($table, $defaults) = @_;      my ($cgi) = @_;
1087      # Loop through the defaults.      if (T(CGI => 2)) {
1088      while (my ($key, $value) = each %{$defaults}) {          # Here we trace the GET-style URL for the script.
1089          if (!exists $table->{$key}) {          Trace("URL: " . $cgi->url(-relative => 1, -query => 1));
1090              $table->{$key} = $value;      }
1091        if (T(CGI => 3)) {
1092            # Here we want to trace the parameter data.
1093            my @names = $cgi->param;
1094            for my $parmName (sort @names) {
1095                # Note we skip the Trace parameters, which are for our use only.
1096                if ($parmName ne 'Trace' && $parmName ne 'TF') {
1097                    my @values = $cgi->param($parmName);
1098                    Trace("CGI: $parmName = " . join(", ", @values));
1099                }
1100            }
1101            # Display the request method.
1102            my $method = $cgi->request_method();
1103            Trace("Method: $method");
1104        }
1105        if (T(CGI => 4)) {
1106            # Here we want the environment data too.
1107            for my $envName (sort keys %ENV) {
1108                Trace("ENV: $envName = $ENV{$envName}");
1109          }          }
1110      }      }
1111  }  }
1112    
1113  =head3 Trace  =head3 TraceImages
1114    
1115  C<< Trace($message); >>      Tracer::TraceImages($htmlString);
1116    
1117  Write a trace message to the target location specified in L</TSetup>. If there has not been  Trace information about all of an html document's images. The tracing
1118  any prior call to B<TSetup>.  will be for type "IMG" at level 3. The image's source string
1119    will be displayed. This is generally either the URL of the image or
1120    raw data for the image itself. If the source is too long, only the first 300
1121    characters will be shown at trace level 3. The entire source will be shown,
1122    however, at trace level 4. This method is not very smart, and might catch
1123    Javascript code, but it is still useful when debugging the arcane
1124    behavior of images in multiple browser environments.
1125    
1126  =over 4  =over 4
1127    
1128  =item message  =item htmlString
1129    
1130  Message to write.  HTML text for an outgoing web page.
1131    
1132  =back  =back
1133    
1134  =cut  =cut
1135    
1136  sub Trace {  sub TraceImages {
1137      # Get the parameters.      # Only proceed if we're at the proper trace level.
1138      my ($message) = @_;      if (T(IMG => 3)) {
1139      # Get the timestamp.          # For performance reasons we're manipulating $_[0] instead of retrieving the string
1140      my $timeStamp = Now();          # into a variable called "$htmlString". This is because we expect html strings to be
1141      # Format the message. Note we strip off any line terminators at the end.          # long, and don't want to copy them any more than we have to.
1142      my $formatted = "[$timeStamp] <$LastCategory>: " . Strip($message);          Trace(length($_[0]) . " characters in web page.");
1143      # Process according to the destination.          # Loop through the HTML, culling image tags.
1144      if ($Destination eq "TEXT") {          while ($_[0] =~ /<img\s+[^>]+?src="([^"]+)"/sgi) {
1145          # Write the message to the standard output.              # Extract the source string and determine whether or not it's too long.
1146          print "$formatted\n";              my $srcString = $1;
1147      } elsif ($Destination eq "ERROR") {              my $pos = pos($_[0]) - length($srcString);
1148          # Write the message to the error output.              my $excess = length($srcString) - 300;
1149          print STDERR "$formatted\n";              # We'll put the display string in here.
1150      } elsif ($Destination eq "QUEUE") {              my $srcDisplay = $srcString;
1151          # Push the message into the queue.              # If it's a data string, split it at the comma.
1152          push @Queue, "$formatted";              $srcDisplay =~ s/^(data[^,]+,)/$1\n/;
1153      } elsif ($Destination eq "HTML") {              # If there's no excess or we're at trace level 4, we're done. At level 3 with
1154          # Convert the message to HTML and write it to the standard output.              # a long string, however, we only show the first 300 characters.
1155          my $escapedMessage = CGI::escapeHTML($message);              if ($excess > 0 && ! T(IMG => 4)) {
1156          print "<p>$formatted</p>\n";                  $srcDisplay = substr($srcDisplay,0,300) . "\nplus $excess characters.";
1157      } elsif ($Destination eq "WARN") {              }
1158         # Emit the message as a warning.              # Output the trace message.
1159         warn $message;              Trace("Image tag at position $pos:\n$srcDisplay");
     } elsif ($Destination =~ m/^>>/) {  
         # Write the trace message to an output file.  
         (open TRACING, $Destination) || die "Tracing open for \"$Destination\" failed: $!";  
         print TRACING "$formatted\n";  
         close TRACING;  
         # If the Tee flag is on, echo it to the standard output.  
         if ($TeeFlag) {  
             print "$formatted\n";  
1160          }          }
1161      }      }
1162  }  }
1163    
 =head3 T  
1164    
1165  C<< my $switch = T($category, $traceLevel); >>  =head3 ScriptFinish
1166    
1167      or      ScriptFinish($webData, $varHash);
1168    
1169  C<< my $switch = T($traceLevel); >>  Output a web page at the end of a script. Either the string to be output or the
1170    name of a template file can be specified. If the second parameter is omitted,
1171    it is assumed we have a string to be output; otherwise, it is assumed we have the
1172    name of a template file. The template should have the variable C<DebugData>
1173    specified in any form that invokes a standard script. If debugging mode is turned
1174    on, a form field will be put in that allows the user to enter tracing data.
1175    Trace messages will be placed immediately before the terminal C<BODY> tag in
1176    the output, formatted as a list.
1177    
1178  Return TRUE if the trace level is at or above a specified value and the specified category  A typical standard script would loook like the following.
 is active, else FALSE. If no category is specified, the caller's package name is used.  
1179    
1180  =over 4      BEGIN {
1181            # Print the HTML header.
1182            print "CONTENT-TYPE: text/html\n\n";
1183        }
1184        use Tracer;
1185        use CGI;
1186        use FIG;
1187        # ... more uses ...
1188    
1189  =item category      my ($cgi, $varHash) = ScriptSetup();
1190        eval {
1191            # ... get data from $cgi, put it in $varHash ...
1192        };
1193        if ($@) {
1194            Trace("Script Error: $@") if T(0);
1195        }
1196        ScriptFinish("Html/MyTemplate.html", $varHash);
1197    
1198  Category to which the message belongs. If not specified, the caller's package name is  The idea here is that even if the script fails, you'll see trace messages and
1199  used.  useful output.
1200    
1201  =item traceLevel  =over 4
1202    
1203  Relevant tracing level.  =item webData
1204    
1205  =item RETURN  A string containing either the full web page to be written to the output or the
1206    name of a template file from which the page is to be constructed. If the name
1207    of a template file is specified, then the second parameter must be present;
1208    otherwise, it must be absent.
1209    
1210  TRUE if a message at the specified trace level would appear in the trace, else FALSE.  =item varHash (optional)
1211    
1212    If specified, then a reference to a hash mapping variable names for a template
1213    to their values. The template file will be read into memory, and variable markers
1214    will be replaced by data in this hash reference.
1215    
1216  =back  =back
1217    
1218  =cut  =cut
1219    
1220  sub T {  sub ScriptFinish {
     # Declare the return variable.  
     my $retVal = 0;  
     # Only proceed if tracing is turned on.  
     if ($Destination ne "NONE") {  
1221          # Get the parameters.          # Get the parameters.
1222          my ($category, $traceLevel) = @_;      my ($webData, $varHash) = @_;
1223          if (!defined $traceLevel) {      # Check for a template file situation.
1224              # Here we have no category, so we need to get the calling package.      my $outputString;
1225              # The calling package is normally the first parameter. If it is      if (defined $varHash) {
1226              # omitted, the first parameter will be the tracelevel. So, the          # Here we have a template file. We need to determine the template type.
1227              # first thing we do is shift the so-called category into the          my $template;
1228              # $traceLevel variable where it belongs.          if ($FIG_Config::template_url && $webData =~ /\.php$/) {
1229              $traceLevel = $category;              $template = "$FIG_Config::template_url/$webData";
             my ($package, $fileName, $line) = caller;  
             # If there is no calling package, we default to "main".  
             if (!$package) {  
                 $category = "main";  
1230              } else {              } else {
1231                  $category = $package;              $template = "<<$webData";
             }  
         }  
         # Save the category name.  
         $LastCategory = $category;  
         # Convert it to lower case before we hash it.  
         $category = lc $category;  
         # Use the category and tracelevel to compute the result.  
         if (ref $traceLevel) {  
             Confess("Bad trace level.");  
         } elsif (ref $TraceLevel) {  
             Confess("Bad trace config.");  
1232          }          }
1233          $retVal = ($traceLevel <= $TraceLevel && ($AllTrace || exists $Categories{$category}));          $outputString = PageBuilder::Build($template, $varHash, "Html");
1234        } else {
1235            # Here the user gave us a raw string.
1236            $outputString = $webData;
1237      }      }
1238      # Return the computed result.      # Check for trace messages.
1239      return $retVal;      if ($Destination ne "NONE" && $TraceLevel > 0) {
1240            # We have trace messages, so we want to put them at the end of the body. This
1241            # is either at the end of the whole string or at the beginning of the BODY
1242            # end-tag.
1243            my $pos = length $outputString;
1244            if ($outputString =~ m#</body>#gi) {
1245                $pos = (pos $outputString) - 7;
1246            }
1247            # If the trace messages were queued, we unroll them. Otherwise, we display the
1248            # destination.
1249            my $traceHtml;
1250            if ($Destination eq "QUEUE") {
1251                $traceHtml = QTrace('Html');
1252            } elsif ($Destination =~ /^>>(.+)$/) {
1253                # Here the tracing output it to a file. We code it as a hyperlink so the user
1254                # can copy the file name into the clipboard easily.
1255                my $actualDest = $1;
1256                $traceHtml = "<p>Tracing output to $actualDest.</p>\n";
1257            } else {
1258                # Here we have one of the special destinations.
1259                $traceHtml = "<P>Tracing output type is $Destination.</p>\n";
1260            }
1261            substr $outputString, $pos, 0, $traceHtml;
1262        }
1263        # Write the output string.
1264        print $outputString;
1265    }
1266    
1267    =head2 Command-Line Utility Methods
1268    
1269    =head3 SendSMS
1270    
1271        my $msgID = Tracer::SendSMS($phoneNumber, $msg);
1272    
1273    Send a text message to a phone number using Clickatell. The FIG_Config file must contain the
1274    user name, password, and API ID for the relevant account in the hash reference variable
1275    I<$FIG_Config::phone>, using the keys C<user>, C<password>, and C<api_id>. For
1276    example, if the user name is C<BruceTheHumanPet>, the password is C<silly>, and the API ID
1277    is C<2561022>, then the FIG_Config file must contain
1278    
1279        $phone =  { user => 'BruceTheHumanPet',
1280                    password => 'silly',
1281                    api_id => '2561022' };
1282    
1283    The original purpose of this method was to insure Bruce would be notified immediately when the
1284    Sprout Load terminates. Care should be taken if you do not wish Bruce to be notified immediately
1285    when you call this method.
1286    
1287    The message ID will be returned if successful, and C<undef> if an error occurs.
1288    
1289    =over 4
1290    
1291    =item phoneNumber
1292    
1293    Phone number to receive the message, in international format. A United States phone number
1294    would be prefixed by "1". A British phone number would be prefixed by "44".
1295    
1296    =item msg
1297    
1298    Message to send to the specified phone.
1299    
1300    =item RETURN
1301    
1302    Returns the message ID if successful, and C<undef> if the message could not be sent.
1303    
1304    =back
1305    
1306    =cut
1307    
1308    sub SendSMS {
1309        # Get the parameters.
1310        my ($phoneNumber, $msg) = @_;
1311        # Declare the return variable. If we do not change it, C<undef> will be returned.
1312        my $retVal;
1313        # Only proceed if we have phone support.
1314        if (! defined $FIG_Config::phone) {
1315            Trace("Phone support not present in FIG_Config.") if T(1);
1316        } else {
1317            # Get the phone data.
1318            my $parms = $FIG_Config::phone;
1319            # Get the Clickatell URL.
1320            my $url = "http://api.clickatell.com/http/";
1321            # Create the user agent.
1322            my $ua = LWP::UserAgent->new;
1323            # Request a Clickatell session.
1324            my $resp = $ua->post("$url/sendmsg", { user => $parms->{user},
1325                                         password => $parms->{password},
1326                                         api_id => $parms->{api_id},
1327                                         to => $phoneNumber,
1328                                         text => $msg});
1329            # Check for an error.
1330            if (! $resp->is_success) {
1331                Trace("Alert failed.") if T(1);
1332            } else {
1333                # Get the message ID.
1334                my $rstring = $resp->content;
1335                if ($rstring =~ /^ID:\s+(.*)$/) {
1336                    $retVal = $1;
1337                } else {
1338                    Trace("Phone attempt failed with $rstring") if T(1);
1339                }
1340            }
1341        }
1342        # Return the result.
1343        return $retVal;
1344    }
1345    
1346    =head3 StandardSetup
1347    
1348        my ($options, @parameters) = StandardSetup(\@categories, \%options, $parmHelp, @ARGV);
1349    
1350    This method performs standard command-line parsing and tracing setup. The return
1351    values are a hash of the command-line options and a list of the positional
1352    parameters. Tracing is automatically set up and the command-line options are
1353    validated.
1354    
1355    This is a complex method that does a lot of grunt work. The parameters can
1356    be more easily understood, however, once they are examined individually.
1357    
1358    The I<categories> parameter is the most obtuse. It is a reference to a list of
1359    special-purpose tracing categories. Most tracing categories are PERL package
1360    names. So, for example, if you wanted to turn on tracing inside the B<Sprout>,
1361    B<ERDB>, and B<SproutLoad> packages, you would specify the categories
1362    
1363        ["Sprout", "SproutLoad", "ERDB"]
1364    
1365    This would cause trace messages in the specified three packages to appear in
1366    the output. There are two special tracing categories that are automatically
1367    handled by this method. In other words, if you used L</TSetup> you would need
1368    to include these categories manually, but if you use this method they are turned
1369    on automatically.
1370    
1371    =over 4
1372    
1373    =item SQL
1374    
1375    Traces SQL commands and activity.
1376    
1377    =item Tracer
1378    
1379    Traces error messages and call stacks.
1380    
1381    =back
1382    
1383    C<SQL> is only turned on if the C<-sql> option is specified in the command line.
1384    The trace level is specified using the C<-trace> command-line option. For example,
1385    the following command line for C<TransactFeatures> turns on SQL tracing and runs
1386    all tracing at level 3.
1387    
1388        TransactFeatures -trace=3 -sql register ../xacts IDs.tbl
1389    
1390    Standard tracing is output to the standard output and echoed to the file
1391    C<trace>I<$$>C<.log> in the FIG temporary directory, where I<$$> is the
1392    process ID. You can also specify the C<user> parameter to put a user ID
1393    instead of a process ID in the trace file name. So, for example
1394    
1395    The default trace level is 2. To get all messages, specify a trace level of 4.
1396    For a genome-by-genome update, use 3.
1397    
1398        TransactFeatures -trace=3 -sql -user=Bruce register ../xacts IDs.tbl
1399    
1400    would send the trace output to C<traceBruce.log> in the temporary directory.
1401    
1402    The I<options> parameter is a reference to a hash containing the command-line
1403    options, their default values, and an explanation of what they mean. Command-line
1404    options may be in the form of switches or keywords. In the case of a switch, the
1405    option value is 1 if it is specified and 0 if it is not specified. In the case
1406    of a keyword, the value is separated from the option name by an equal sign. You
1407    can see this last in the command-line example above.
1408    
1409    You can specify a different default trace level by setting C<$options->{trace}>
1410    prior to calling this method.
1411    
1412    An example at this point would help. Consider, for example, the command-line utility
1413    C<TransactFeatures>. It accepts a list of positional parameters plus the options
1414    C<safe>, C<noAlias>, C<start>, and C<tblFiles>. To start up this command, we execute
1415    the following code.
1416    
1417        my ($options, @parameters) = Tracer::StandardSetup(["DocUtils"],
1418                            { safe => [0, "use database transactions"],
1419                              noAlias => [0, "do not expect aliases in CHANGE transactions"],
1420                              start => [' ', "start with this genome"],
1421                              tblFiles => [0, "output TBL files containing the corrected IDs"] },
1422                            "<command> <transactionDirectory> <IDfile>",
1423                          @ARGV);
1424    
1425    
1426    The call to C<ParseCommand> specifies the default values for the options and
1427    stores the actual options in a hash that is returned as C<$options>. The
1428    positional parameters are returned in C<@parameters>.
1429    
1430    The following is a sample command line for C<TransactFeatures>.
1431    
1432        TransactFeatures -trace=2 -noAlias register ../xacts IDs.tbl
1433    
1434    Single and double hyphens are equivalent. So, you could also code the
1435    above command as
1436    
1437        TransactFeatures --trace=2 --noAlias register ../xacts IDs.tbl
1438    
1439    In this case, C<register>, C<../xacts>, and C<IDs.tbl> are the positional
1440    parameters, and would find themselves in I<@parameters> after executing the
1441    above code fragment. The tracing would be set to level 2, and the categories
1442    would be C<Tracer>, and <DocUtils>. C<Tracer> is standard,
1443    and C<DocUtils> was included because it came in within the first parameter
1444    to this method. The I<$options> hash would be
1445    
1446        { trace => 2, sql => 0, safe => 0,
1447          noAlias => 1, start => ' ', tblFiles => 0 }
1448    
1449    Use of C<StandardSetup> in this way provides a simple way of performing
1450    standard tracing setup and command-line parsing. Note that the caller is
1451    not even aware of the command-line switches C<-trace> and C<-sql>, which
1452    are used by this method to control the tracing. If additional tracing features
1453    need to be added in the future, they can be processed by this method without
1454    upsetting the command-line utilities.
1455    
1456    If the C<background> option is specified on the command line, then the
1457    standard and error outputs will be directed to files in the temporary
1458    directory, using the same suffix as the trace file. So, if the command
1459    line specified
1460    
1461        -user=Bruce -background
1462    
1463    then the trace output would go to C<traceBruce.log>, the standard output to
1464    C<outBruce.log>, and the error output to C<errBruce.log>. This is designed to
1465    simplify starting a command in the background.
1466    
1467    The user name is also used as the tracing key for L</Emergency Tracing>.
1468    Specifying a value of C<E> for the trace level causes emergency tracing to
1469    be used instead of custom tracing. If the user name is not specified,
1470    the tracing key is taken from the C<Tracing> environment variable. If there
1471    is no value for that variable, the tracing key will be computed from the PID.
1472    
1473    Finally, if the special option C<-help> is specified, the option
1474    names will be traced at level 0 and the program will exit without processing.
1475    This provides a limited help capability. For example, if the user enters
1476    
1477        TransactFeatures -help
1478    
1479    he would see the following output.
1480    
1481        TransactFeatures [options] <command> <transactionDirectory> <IDfile>
1482            -trace    tracing level (default E)
1483            -sql      trace SQL commands
1484            -safe     use database transactions
1485            -noAlias  do not expect aliases in CHANGE transactions
1486            -start    start with this genome
1487            -tblFiles output TBL files containing the corrected IDs
1488    
1489    The caller has the option of modifying the tracing scheme by placing a value
1490    for C<trace> in the incoming options hash. The default value can be overridden,
1491    or the tracing to the standard output can be turned off by suffixing a minus
1492    sign to the trace level. So, for example,
1493    
1494        { trace => [0, "tracing level (default 0)"],
1495           ...
1496    
1497    would set the default trace level to 0 instead of E, while
1498    
1499        { trace => ["2-", "tracing level (default 2)"],
1500           ...
1501    
1502    would set the default to 2, but trace only to the log file, not to the
1503    standard output.
1504    
1505    The parameters to this method are as follows.
1506    
1507    =over 4
1508    
1509    =item categories
1510    
1511    Reference to a list of tracing category names. These should be names of
1512    packages whose internal workings will need to be debugged to get the
1513    command working.
1514    
1515    =item options
1516    
1517    Reference to a hash containing the legal options for the current command mapped
1518    to their default values and descriptions. The user can override the defaults
1519    by specifying the options as command-line switches prefixed by a hyphen.
1520    Tracing-related options may be added to this hash. If the C<-h> option is
1521    specified on the command line, the option descriptions will be used to
1522    explain the options. To turn off tracing to the standard output, add a
1523    minus sign to the value for C<trace> (see above).
1524    
1525    =item parmHelp
1526    
1527    A string that vaguely describes the positional parameters. This is used
1528    if the user specifies the C<-h> option.
1529    
1530    =item argv
1531    
1532    List of command line parameters, including the option switches, which must
1533    precede the positional parameters and be prefixed by a hyphen.
1534    
1535    =item RETURN
1536    
1537    Returns a list. The first element of the list is the reference to a hash that
1538    maps the command-line option switches to their values. These will either be the
1539    default values or overrides specified on the command line. The remaining
1540    elements of the list are the position parameters, in order.
1541    
1542    =back
1543    
1544    =cut
1545    
1546    sub StandardSetup {
1547        # Get the parameters.
1548        my ($categories, $options, $parmHelp, @argv) = @_;
1549        # Get the default tracing key.
1550        my $tkey = EmergencyKey();
1551        # Add the tracing options.
1552        if (! exists $options->{trace}) {
1553            $options->{trace} = ['2', "tracing level (E for emergency tracing)"];
1554        }
1555        $options->{sql} = [0, "turn on SQL tracing"];
1556        $options->{help} = [0, "display command-line options"];
1557        $options->{user} = [$tkey, "tracing key"];
1558        $options->{background} = [0, "spool standard and error output"];
1559        # Create a parsing hash from the options hash. The parsing hash
1560        # contains the default values rather than the default value
1561        # and the description. While we're at it, we'll memorize the
1562        # length of the longest option name.
1563        my $longestName = 0;
1564        my %parseOptions = ();
1565        for my $key (keys %{$options}) {
1566            if (length $key > $longestName) {
1567                $longestName = length $key;
1568            }
1569            $parseOptions{$key} = $options->{$key}->[0];
1570        }
1571        # Parse the command line.
1572        my ($retOptions, @retParameters) = ParseCommand(\%parseOptions, @argv);
1573        # Get the logfile suffix.
1574        my $suffix = $retOptions->{user};
1575        # Check for background mode.
1576        if ($retOptions->{background}) {
1577            my $outFileName = "$FIG_Config::temp/out$suffix.log";
1578            my $errFileName = "$FIG_Config::temp/err$suffix.log";
1579            open STDOUT, ">$outFileName";
1580            open STDERR, ">$errFileName";
1581            # Check for phone support. If we have phone support and a phone number,
1582            # we want to turn it on.
1583            if ($ENV{PHONE} && defined($FIG_Config::phone)) {
1584                $retOptions->{phone} = $ENV{PHONE};
1585            }
1586        }
1587        # Now we want to set up tracing. First, we need to know if the user
1588        # wants emergency tracing.
1589        if ($retOptions->{trace} eq 'E') {
1590            ETracing($retOptions->{user});
1591        } else {
1592            # Here the tracing is controlled from the command line.
1593            my @cats = @{$categories};
1594            if ($retOptions->{sql}) {
1595                push @cats, "SQL";
1596            }
1597            # Add the default categories.
1598            push @cats, "Tracer";
1599            # Next, we create the category string by joining the categories.
1600            my $cats = join(" ", @cats);
1601            # Check to determine whether or not the caller wants to turn off tracing
1602            # to the standard output.
1603            my $traceLevel = $retOptions->{trace};
1604            my $textOKFlag = 1;
1605            if ($traceLevel =~ /^(.)-/) {
1606                $traceLevel = $1;
1607                $textOKFlag = 0;
1608            }
1609            # Now we set up the trace mode.
1610            my $traceMode;
1611            # Verify that we can open a file in the FIG temporary directory.
1612            my $traceFileName = "$FIG_Config::temp/trace$suffix.log";
1613            if (open TESTTRACE, ">$traceFileName") {
1614                # Here we can trace to a file.
1615                $traceMode = ">$traceFileName";
1616                if ($textOKFlag) {
1617                    # Echo to standard output if the text-OK flag is set.
1618                    $traceMode = "+$traceMode";
1619                }
1620                # Close the test file.
1621                close TESTTRACE;
1622            } else {
1623                # Here we can't trace to a file. We trace to the standard output if it's
1624                # okay, and the error log otherwise.
1625                if ($textOKFlag) {
1626                    $traceMode = "TEXT";
1627                } else {
1628                    $traceMode = "WARN";
1629                }
1630            }
1631            # Now set up the tracing.
1632            TSetup("$traceLevel $cats", $traceMode);
1633        }
1634        # Check for the "help" option. If it is specified, dump the command-line
1635        # options and exit the program.
1636        if ($retOptions->{help}) {
1637            $0 =~ m#[/\\](\w+)(\.pl)?$#i;
1638            print "$1 [options] $parmHelp\n";
1639            for my $key (sort keys %{$options}) {
1640                my $name = Pad($key, $longestName, 0, ' ');
1641                my $desc = $options->{$key}->[1];
1642                if ($options->{$key}->[0]) {
1643                    $desc .= " (default " . $options->{$key}->[0] . ")";
1644                }
1645                print "  $name $desc\n";
1646            }
1647            exit(0);
1648        }
1649        # Trace the options, if applicable.
1650        if (T(3)) {
1651            my @parms = grep { $retOptions->{$_} } keys %{$retOptions};
1652            Trace("Selected options: " . join(", ", sort @parms) . ".");
1653        }
1654        # Return the parsed parameters.
1655        return ($retOptions, @retParameters);
1656  }  }
1657    
1658  =head3 ParseCommand  =head3 ReadOptions
   
 C<< my ($options, @arguments) = Tracer::ParseCommand(\%optionTable, @inputList); >>  
   
 Parse a command line consisting of a list of parameters. The initial parameters may be option  
 specifiers of the form C<->I<option> or C<->I<option>C<=>I<value>. The options are stripped  
 off and merged into a table of default options. The remainder of the command line is  
 returned as a list of positional arguments. For example, consider the following invocation.  
   
 C<< my ($options, @arguments) = ParseCommand({ errors => 0, logFile => 'trace.log'}, @words); >>  
   
 In this case, the list @words will be treated as a command line. There are two options available,  
 B<errors> and B<logFile>. If @words has the following format  
   
 C<< -logFile=error.log apple orange rutabaga >>  
   
 then at the end of the invocation, C<$options> will be  
1659    
1660  C<< { errors => 0, logFile => 'error.log' } >>      my %options = Tracer::ReadOptions($fileName);
1661    
1662  and C<@arguments> will contain  Read a set of options from a file. Each option is encoded in a line of text that has the
1663    format
1664    
1665  C<< apple orange rutabaga >>  I<optionName>C<=>I<optionValue>C<; >I<comment>
1666    
1667  The parser allows for some escape sequences. See L</UnEscape> for a description. There is no  The option name must consist entirely of letters, digits, and the punctuation characters
1668  support for quote characters.  C<.> and C<_>, and is case sensitive. Blank lines and lines in which the first nonblank
1669    character is a semi-colon will be ignored. The return hash will map each option name to
1670    the corresponding option value.
1671    
1672  =over 4  =over 4
1673    
1674  =item optionTable  =item fileName
   
 Table of default options.  
   
 =item inputList  
1675    
1676  List of words on the command line.  Name of the file containing the option data.
1677    
1678  =item RETURN  =item RETURN
1679    
1680  Returns a reference to the option table and a list of the positional arguments.  Returns a hash mapping the option names specified in the file to their corresponding option
1681    value.
1682    
1683  =back  =back
1684    
1685  =cut  =cut
1686    
1687  sub ParseCommand {  sub ReadOptions {
1688      # Get the parameters.      # Get the parameters.
1689      my ($optionTable, @inputList) = @_;      my ($fileName) = @_;
1690      # Process any options in the input list.      # Open the file.
1691      my %overrides = ();      (open CONFIGFILE, "<$fileName") || Confess("Could not open option file $fileName.");
1692      while ((@inputList > 0) && ($inputList[0] =~ /^-/)) {      # Count the number of records read.
1693          # Get the current option.      my ($records, $comments) = 0;
1694          my $arg = shift @inputList;      # Create the return hash.
1695          # Pull out the option name.      my %retVal = ();
1696          $arg =~ /^-([^=]*)/g;      # Loop through the file, accumulating key-value pairs.
1697          my $name = $1;      while (my $line = <CONFIGFILE>) {
1698          # Check for an option value.          # Denote we've read a line.
1699          if ($arg =~ /\G=(.*)$/g) {          $records++;
1700              # Here we have a value for the option.          # Determine the line type.
1701              $overrides{$name} = UnEscape($1);          if ($line =~ /^\s*[\n\r]/) {
1702                # A blank line is a comment.
1703                $comments++;
1704            } elsif ($line =~ /^\s*([A-Za-z0-9_\.]+)=([^;]*);/) {
1705                # Here we have an option assignment.
1706                retVal{$1} = $2;
1707            } elsif ($line =~ /^\s*;/) {
1708                # Here we have a text comment.
1709                $comments++;
1710          } else {          } else {
1711              # Here there is no value, so we use 1.              # Here we have an invalid line.
1712              $overrides{$name} = 1;              Trace("Invalid option statement in record $records.") if T(0);
         }  
1713      }      }
     # Merge the options into the defaults.  
     GetOptions($optionTable, \%overrides);  
     # Translate the remaining parameters.  
     my @retVal = ();  
     for my $inputParm (@inputList) {  
         push @retVal, UnEscape($inputParm);  
1714      }      }
1715      # Return the results.      # Return the hash created.
1716      return ($optionTable, @retVal);      return %retVal;
1717  }  }
1718    
1719  =head3 Escape  =head3 GetOptions
   
 C<< my $codedString = Tracer::Escape($realString); >>  
   
 Escape a string for use in a command length. Tabs will be replaced by C<\t>, new-lines  
 replaced by C<\n>, carriage returns will be deleted, and backslashes will be doubled. The  
 result is to reverse the effect of L</UnEscape>.  
   
 =over 4  
   
 =item realString  
1720    
1721  String to escape.      Tracer::GetOptions(\%defaults, \%options);
1722    
1723  =item RETURN  Merge a specified set of options into a table of defaults. This method takes two hash references
1724    as input and uses the data from the second to update the first. If the second does not exist,
1725    there will be no effect. An error will be thrown if one of the entries in the second hash does not
1726    exist in the first.
1727    
1728  Escaped equivalent of the real string.  Consider the following example.
1729    
1730  =back      my $optionTable = GetOptions({ dbType => 'mySQL', trace => 0 }, $options);
1731    
1732  =cut  In this example, the variable B<$options> is expected to contain at most two options-- B<dbType> and
1733    B<trace>. The default database type is C<mySQL> and the default trace level is C<0>. If the value of
1734    B<$options> is C<< {dbType => 'Oracle'} >>, then the database type will be changed to C<Oracle> and
1735    the trace level will remain at 0. If B<$options> is undefined, then the database type and trace level
1736    will remain C<mySQL> and C<0>. If, on the other hand, B<$options> is defined as
1737    
1738  sub Escape {      {databaseType => 'Oracle'}
     # Get the parameter.  
     my ($realString) = @_;  
     # Initialize the return variable.  
     my $retVal = "";  
     # Loop through the parameter string, looking for sequences to escape.  
     while (length $realString > 0) {  
         # Look for the first sequence to escape.  
         if ($realString =~ /^(.*?)([\n\t\r\\])/) {  
             # 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;  
             # Strip the processed section off the real string.  
             $realString = substr $realString, (length $2) + (length $1);  
             # Get the matched character.  
             my $char = $2;  
             # If we have a CR, we are done.  
             if ($char ne "\r") {  
                 # It's not a CR, so encode the escape sequence.  
                 $char =~ tr/\t\n/tn/;  
                 $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;  
 }  
1739    
1740  =head3 UnEscape  an error will occur because the B<databaseType> option does not exist.
1741    
1742  C<< my $realString = Tracer::UnEscape($codedString); >>  =over 4
1743    
1744  Replace escape sequences with their actual equivalents. C<\t> will be replaced by  =item defaults
 a tab, C<\n> by a new-line character, and C<\\> by a backslash. C<\r> codes will  
 be deleted.  
1745    
1746  =over 4  Table of default option values.
1747    
1748  =item codedString  =item options
1749    
1750  String to un-escape.  Table of overrides, if any.
1751    
1752  =item RETURN  =item RETURN
1753    
1754  Returns a copy of the original string with the escape sequences converted to their actual  Returns a reference to the default table passed in as the first parameter.
 values.  
1755    
1756  =back  =back
1757    
1758  =cut  =cut
1759    
1760  sub UnEscape {  sub GetOptions {
1761      # Get the parameter.      # Get the parameters.
1762      my ($codedString) = @_;      my ($defaults, $options) = @_;
1763      # Initialize the return variable.      # Check for overrides.
1764      my $retVal = "";      if ($options) {
1765      # Only proceed if the incoming string is nonempty.          # Loop through the overrides.
1766      if (defined $codedString) {          while (my ($option, $setting) = each %{$options}) {
1767          # Loop through the parameter string, looking for escape sequences. We can't do              # Insure this override exists.
1768          # translating because it causes problems with the escaped slash. ("\\t" becomes              if (!exists $defaults->{$option}) {
1769          # "\<tab>" no matter what we do.)                  croak "Unrecognized option $option encountered.";
         while (length $codedString > 0) {  
             # Look for the first escape sequence.  
             if ($codedString =~ /^(.*?)\\(\\|n|t|r)/) {  
                 # 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);  
                 # Get the escape value.  
                 my $char = $2;  
                 # If we have a "\r", we are done.  
                 if ($char ne 'r') {  
                     # Here it's not an 'r', so we convert it.  
                     $char =~ tr/\\tn/\\\t\n/;  
                     $retVal .= $char;  
                 }  
1770              } else {              } else {
1771                  # Here there are no more escape sequences. The rest of the string is                  # Apply the override.
1772                  # transferred unmodified.                  $defaults->{$option} = $setting;
                 $retVal .= $codedString;  
                 $codedString = "";  
1773              }              }
1774          }          }
1775      }      }
1776      # Return the result.      # Return the merged table.
1777      return $retVal;      return $defaults;
1778  }  }
1779    
1780  =head3 ParseRecord  =head3 MergeOptions
1781    
1782  C<< my @fields = Tracer::ParseRecord($line); >>      Tracer::MergeOptions(\%table, \%defaults);
1783    
1784  Parse a tab-delimited data line. The data line is split into field values. Embedded tab  Merge default values into a hash table. This method looks at the key-value pairs in the
1785  and new-line characters in the data line must be represented as C<\t> and C<\n>, respectively.  second (default) hash, and if a matching key is not found in the first hash, the default
1786  These will automatically be converted.  pair is copied in. The process is similar to L</GetOptions>, but there is no error-
1787    checking and no return value.
1788    
1789  =over 4  =over 4
1790    
1791  =item line  =item table
1792    
1793  Line of data containing the tab-delimited fields.  Hash table to be updated with the default values.
1794    
1795  =item RETURN  =item defaults
1796    
1797  Returns a list of the fields found in the data line.  Default values to be merged into the first hash table if they are not already present.
1798    
1799  =back  =back
1800    
1801  =cut  =cut
1802    
1803  sub ParseRecord {  sub MergeOptions {
1804      # Get the parameter.      # Get the parameters.
1805      my ($line) = @_;      my ($table, $defaults) = @_;
1806      # Remove the trailing new-line, if any.      # Loop through the defaults.
1807      chomp $line;      while (my ($key, $value) = each %{$defaults}) {
1808      # Split the line read into pieces using the tab character.          if (!exists $table->{$key}) {
1809      my @retVal = split /\t/, $line;              $table->{$key} = $value;
1810      # Trim and fix the escapes in each piece.          }
     for my $value (@retVal) {  
         # Trim leading whitespace.  
         $value =~ s/^\s+//;  
         # Trim trailing whitespace.  
         $value =~ s/\s+$//;  
         # Delete the carriage returns.  
         $value =~ s/\r//g;  
         # Convert the escapes into their real values.  
         $value =~ s/\\t/"\t"/ge;  
         $value =~ s/\\n/"\n"/ge;  
1811      }      }
     # Return the result.  
     return @retVal;  
1812  }  }
1813    
1814  =head3 Merge  =head3 ParseCommand
   
 C<< my @mergedList = Tracer::Merge(@inputList); >>  
   
 Sort a list of strings and remove duplicates.  
   
 =over 4  
1815    
1816  =item inputList      my ($options, @arguments) = Tracer::ParseCommand(\%optionTable, @inputList);
1817    
1818  List of scalars to sort and merge.  Parse a command line consisting of a list of parameters. The initial parameters may be option
1819    specifiers of the form C<->I<option> or C<->I<option>C<=>I<value>. The options are stripped
1820    off and merged into a table of default options. The remainder of the command line is
1821    returned as a list of positional arguments. For example, consider the following invocation.
1822    
1823  =item RETURN      my ($options, @arguments) = ParseCommand({ errors => 0, logFile => 'trace.log'}, @words);
1824    
1825  Returns a list containing the same elements sorted in ascending order with duplicates  In this case, the list @words will be treated as a command line and there are two options available,
1826  removed.  B<errors> and B<logFile>. If @words has the following format
1827    
1828  =back      -logFile=error.log apple orange rutabaga
1829    
1830  =cut  then at the end of the invocation, C<$options> will be
1831    
1832  sub Merge {      { errors => 0, logFile => 'error.log' }
     # Get the input list in sort order.  
     my @inputList = sort @_;  
     # Only proceed if the list has at least two elements.  
     if (@inputList > 1) {  
         # Now we want to move through the list splicing out duplicates.  
         my $i = 0;  
         while ($i < @inputList) {  
             # Get the current entry.  
             my $thisEntry = $inputList[$i];  
             # Find out how many elements duplicate the current entry.  
             my $j = $i + 1;  
             my $dup1 = $i + 1;  
             while ($j < @inputList && $inputList[$j] eq $thisEntry) { $j++; };  
             # If the number is nonzero, splice out the duplicates found.  
             if ($j > $dup1) {  
                 splice @inputList, $dup1, $j - $dup1;  
             }  
             # Now the element at position $dup1 is different from the element before it  
             # at position $i. We push $i forward one position and start again.  
             $i++;  
         }  
     }  
     # Return the merged list.  
     return @inputList;  
 }  
1833    
1834  =head3 Percent  and C<@arguments> will contain
1835    
1836  C<< my $percent = Tracer::Percent($number, $base); >>      apple orange rutabaga
1837    
1838  Returns the percent of the base represented by the given number. If the base  The parser allows for some escape sequences. See L</UnEscape> for a description. There is no
1839  is zero, returns zero.  support for quote characters. Options can be specified with single or double hyphens.
1840    
1841  =over 4  =over 4
1842    
1843  =item number  =item optionTable
1844    
1845  Percent numerator.  Table of default options.
1846    
1847  =item base  =item inputList
1848    
1849  Percent base.  List of words on the command line.
1850    
1851  =item RETURN  =item RETURN
1852    
1853  Returns the percentage of the base represented by the numerator.  Returns a reference to the option table and a list of the positional arguments.
1854    
1855  =back  =back
1856    
1857  =cut  =cut
1858    
1859  sub Percent {  sub ParseCommand {
1860      # Get the parameters.      # Get the parameters.
1861      my ($number, $base) = @_;      my ($optionTable, @inputList) = @_;
1862      # Declare the return variable.      # Process any options in the input list.
1863      my $retVal = 0;      my %overrides = ();
1864      # Compute the percent.      while ((@inputList > 0) && ($inputList[0] =~ /^--?/)) {
1865      if ($base != 0) {          # Get the current option.
1866          $retVal = $number * 100 / $base;          my $arg = shift @inputList;
1867            # Pull out the option name.
1868            $arg =~ /^--?([^=]*)/g;
1869            my $name = $1;
1870            # Check for an option value.
1871            if ($arg =~ /\G=(.*)$/g) {
1872                # Here we have a value for the option.
1873                $overrides{$name} = UnEscape($1);
1874            } else {
1875                # Here there is no value, so we use 1.
1876                $overrides{$name} = 1;
1877      }      }
     # Return the result.  
     return $retVal;  
1878  }  }
1879        # Merge the options into the defaults.
1880        GetOptions($optionTable, \%overrides);
1881        # Translate the remaining parameters.
1882        my @retVal = ();
1883        for my $inputParm (@inputList) {
1884            push @retVal, UnEscape($inputParm);
1885        }
1886        # Return the results.
1887        return ($optionTable, @retVal);
1888    }
1889    
1890    
1891    =head2 File Utility Methods
1892    
1893  =head3 GetFile  =head3 GetFile
1894    
1895  C<< my @fileContents = Tracer::GetFile($fileName); >>      my @fileContents = Tracer::GetFile($fileName);
1896    
1897      or      or
1898    
1899  C<< my $fileContents = Tracer::GetFile($fileName); >>      my $fileContents = Tracer::GetFile($fileName);
1900    
1901  Return the entire contents of a file. In list context, line-ends are removed and  Return the entire contents of a file. In list context, line-ends are removed and
1902  each line is a list element. In scalar context, line-ends are replaced by C<\n>.  each line is a list element. In scalar context, line-ends are replaced by C<\n>.
# Line 1436  Line 1935 
1935      # Close it.      # Close it.
1936      close $handle;      close $handle;
1937      my $actualLines = @retVal;      my $actualLines = @retVal;
1938        Trace("$actualLines lines read from file $fileName.") if T(File => 2);
1939      # Return the file's contents in the desired format.      # Return the file's contents in the desired format.
1940      if (wantarray) {      if (wantarray) {
1941          return @retVal;          return @retVal;
# Line 1446  Line 1946 
1946    
1947  =head3 PutFile  =head3 PutFile
1948    
1949  C<< Tracer::PutFile($fileName, \@lines); >>      Tracer::PutFile($fileName, \@lines);
1950    
1951  Write out a file from a list of lines of text.  Write out a file from a list of lines of text.
1952    
# Line 1471  Line 1971 
1971      my ($fileName, $lines) = @_;      my ($fileName, $lines) = @_;
1972      # Open the output file.      # Open the output file.
1973      my $handle = Open(undef, ">$fileName");      my $handle = Open(undef, ">$fileName");
1974        # Count the lines written.
1975      if (ref $lines ne 'ARRAY') {      if (ref $lines ne 'ARRAY') {
1976          # Here we have a scalar, so we write it raw.          # Here we have a scalar, so we write it raw.
1977          print $handle $lines;          print $handle $lines;
1978            Trace("Scalar put to file $fileName.") if T(File => 3);
1979      } else {      } else {
1980          # Write the lines one at a time.          # Write the lines one at a time.
1981            my $count = 0;
1982          for my $line (@{$lines}) {          for my $line (@{$lines}) {
1983              print $handle "$line\n";              print $handle "$line\n";
1984                $count++;
1985          }          }
1986            Trace("$count lines put to file $fileName.") if T(File => 3);
1987      }      }
1988      # Close the output file.      # Close the output file.
1989      close $handle;      close $handle;
1990  }  }
1991    
1992  =head3 QTrace  =head3 ParseRecord
   
 C<< my $data = QTrace($format); >>  
   
 Return the queued trace data in the specified format.  
   
 =over 4  
   
 =item format  
   
 C<html> to format the data as an HTML list, C<text> to format it as straight text.  
   
 =back  
   
 =cut  
   
 sub QTrace {  
     # Get the parameter.  
     my ($format) = @_;  
     # Create the return variable.  
     my $retVal = "";  
     # Only proceed if there is an actual queue.  
     if (@Queue) {  
         # Process according to the format.  
         if ($format =~ m/^HTML$/i) {  
             # Convert the queue into an HTML list.  
             $retVal = "<ul>\n";  
             for my $line (@Queue) {  
                 my $escapedLine = CGI::escapeHTML($line);  
                 $retVal .= "<li>$escapedLine</li>\n";  
             }  
             $retVal .= "</ul>\n";  
         } elsif ($format =~ m/^TEXT$/i) {  
             # Convert the queue into a list of text lines.  
             $retVal = join("\n", @Queue) . "\n";  
         }  
         # Clear the queue.  
         @Queue = ();  
     }  
     # Return the formatted list.  
     return $retVal;  
 }  
   
 =head3 Confess  
   
 C<< Confess($message); >>  
   
 Trace the call stack and abort the program with the specified message. When used with  
 the OR operator and the L</Assert> method, B<Confess> can function as a debugging assert.  
 So, for example  
   
 C<< Assert($recNum >= 0) || Confess("Invalid record number $recNum."); >>  
   
 Will abort the program with a stack trace if the value of C<$recNum> is negative.  
   
 =over 4  
   
 =item message  
   
 Message to include in the trace.  
   
 =back  
   
 =cut  
   
 sub Confess {  
     # Get the parameters.  
     my ($message) = @_;  
     # Trace the call stack.  
     Cluck($message);  
     # Abort the program.  
     croak(">>> $message");  
 }  
   
 =head3 Assert  
   
 C<< Assert($condition1, $condition2, ... $conditionN); >>  
   
 Return TRUE if all the conditions are true. This method can be used in conjunction with  
 the OR operator and the L</Confess> method as a debugging assert.  
 So, for example  
   
 C<< Assert($recNum >= 0) || Confess("Invalid record number $recNum."); >>  
   
 Will abort the program with a stack trace if the value of C<$recNum> is negative.  
   
 =cut  
 sub Assert {  
     my $retVal = 1;  
     LOOP: for my $condition (@_) {  
         if (! $condition) {  
             $retVal = 0;  
             last LOOP;  
         }  
     }  
     return $retVal;  
 }  
   
 =head3 Cluck  
   
 C<< Cluck($message); >>  
   
 Trace the call stack. Note that for best results, you should qualify the call with a  
 trace condition. For example,  
   
 C<< Cluck("Starting record parse.") if T(3); >>  
   
 will only trace the stack if the trace level for the package is 3 or more.  
   
 =over 4  
   
 =item message  
   
 Message to include in the trace.  
   
 =back  
   
 =cut  
   
 sub Cluck {  
     # Get the parameters.  
     my ($message) = @_;  
     # Trace what's happening.  
     Trace("Stack trace for event: $message");  
     my $confession = longmess($message);  
     # Convert the confession to a series of trace messages. Note we skip any  
     # messages relating to calls into Tracer.  
     for my $line (split /\s*\n/, $confession) {  
         Trace($line) if ($line !~ /Tracer\.pm/);  
     }  
 }  
   
 =head3 Min  
1993    
1994  C<< my $min = Min($value1, $value2, ... $valueN); >>      my @fields = Tracer::ParseRecord($line);
1995    
1996  Return the minimum argument. The arguments are treated as numbers.  Parse a tab-delimited data line. The data line is split into field values. Embedded tab
1997    and new-line characters in the data line must be represented as C<\t> and C<\n>, respectively.
1998    These will automatically be converted.
1999    
2000  =over 4  =over 4
2001    
2002  =item $value1, $value2, ... $valueN  =item line
2003    
2004  List of numbers to compare.  Line of data containing the tab-delimited fields.
2005    
2006  =item RETURN  =item RETURN
2007    
2008  Returns the lowest number in the list.  Returns a list of the fields found in the data line.
2009    
2010  =back  =back
2011    
2012  =cut  =cut
2013    
2014  sub Min {  sub ParseRecord {
2015      # Get the parameters. Note that we prime the return value with the first parameter.      # Get the parameter.
2016      my ($retVal, @values) = @_;      my ($line) = @_;
2017      # Loop through the remaining parameters, looking for the lowest.      # Remove the trailing new-line, if any.
2018      for my $value (@values) {      chomp $line;
2019          if ($value < $retVal) {      # Split the line read into pieces using the tab character.
2020              $retVal = $value;      my @retVal = split /\t/, $line;
2021          }      # Trim and fix the escapes in each piece.
2022        for my $value (@retVal) {
2023            # Trim leading whitespace.
2024            $value =~ s/^\s+//;
2025            # Trim trailing whitespace.
2026            $value =~ s/\s+$//;
2027            # Delete the carriage returns.
2028            $value =~ s/\r//g;
2029            # Convert the escapes into their real values.
2030            $value =~ s/\\t/"\t"/ge;
2031            $value =~ s/\\n/"\n"/ge;
2032      }      }
2033      # Return the minimum found.      # Return the result.
2034      return $retVal;      return @retVal;
2035  }  }
2036    
2037  =head3 Max  =head3 Merge
2038    
2039  C<< my $max = Max($value1, $value2, ... $valueN); >>      my @mergedList = Tracer::Merge(@inputList);
2040    
2041  Return the maximum argument. The arguments are treated as numbers.  Sort a list of strings and remove duplicates.
2042    
2043  =over 4  =over 4
2044    
2045  =item $value1, $value2, ... $valueN  =item inputList
2046    
2047  List of numbers to compare.  List of scalars to sort and merge.
2048    
2049  =item RETURN  =item RETURN
2050    
2051  Returns the highest number in the list.  Returns a list containing the same elements sorted in ascending order with duplicates
2052    removed.
2053    
2054  =back  =back
2055    
2056  =cut  =cut
2057    
2058  sub Max {  sub Merge {
2059      # Get the parameters. Note that we prime the return value with the first parameter.      # Get the input list in sort order.
2060      my ($retVal, @values) = @_;      my @inputList = sort @_;
2061      # Loop through the remaining parameters, looking for the highest.      # Only proceed if the list has at least two elements.
2062      for my $value (@values) {      if (@inputList > 1) {
2063          if ($value > $retVal) {          # Now we want to move through the list splicing out duplicates.
2064              $retVal = $value;          my $i = 0;
2065            while ($i < @inputList) {
2066                # Get the current entry.
2067                my $thisEntry = $inputList[$i];
2068                # Find out how many elements duplicate the current entry.
2069                my $j = $i + 1;
2070                my $dup1 = $i + 1;
2071                while ($j < @inputList && $inputList[$j] eq $thisEntry) { $j++; };
2072                # If the number is nonzero, splice out the duplicates found.
2073                if ($j > $dup1) {
2074                    splice @inputList, $dup1, $j - $dup1;
2075                }
2076                # Now the element at position $dup1 is different from the element before it
2077                # at position $i. We push $i forward one position and start again.
2078                $i++;
2079          }          }
2080      }      }
2081      # Return the maximum found.      # Return the merged list.
2082      return $retVal;      return @inputList;
2083  }  }
2084    
2085  =head3 AddToListMap  =head3 Open
2086    
2087  C<< Tracer::AddToListMap(\%hash, $key, $value1, $value2, ... valueN); >>      my $handle = Open($fileHandle, $fileSpec, $message);
2088    
2089  Add a key-value pair to a hash of lists. If no value exists for the key, a singleton list  Open a file.
 is created for the key. Otherwise, the new value is pushed onto the list.  
2090    
2091  =over 4  The I<$fileSpec> is essentially the second argument of the PERL C<open>
2092    function. The mode is specified using Unix-like shell information. So, for
2093    example,
2094    
2095  =item hash      Open(\*LOGFILE, '>>/usr/spool/news/twitlog', "Could not open twit log.");
2096    
2097  Reference to the target hash.  would open for output appended to the specified file, and
2098    
2099  =item key      Open(\*DATASTREAM, "| sort -u >$outputFile", "Could not open $outputFile.");
2100    
2101  Key for which the value is to be added.  would open a pipe that sorts the records written and removes duplicates. Note
2102    the use of file handle syntax in the Open call. To use anonymous file handles,
2103    code as follows.
2104    
2105  =item value1, value2, ... valueN      my $logFile = Open(undef, '>>/usr/spool/news/twitlog', "Could not open twit log.");
2106    
2107  List of values to add to the key's value list.  The I<$message> parameter is used if the open fails. If it is set to C<0>, then
2108    the open returns TRUE if successful and FALSE if an error occurred. Otherwise, a
2109    failed open will throw an exception and the third parameter will be used to construct
2110    an error message. If the parameter is omitted, a standard message is constructed
2111    using the file spec.
2112    
2113  =back      Could not open "/usr/spool/news/twitlog"
2114    
2115  =cut  Note that the mode characters are automatically cleaned from the file name.
2116    The actual error message from the file system will be captured and appended to the
2117    message in any case.
2118    
2119  sub AddToListMap {      Could not open "/usr/spool/news/twitlog": file not found.
     # Get the parameters.  
     my ($hash, $key, @values) = @_;  
     # Process according to whether or not the key already has a value.  
     if (! exists $hash->{$key}) {  
         $hash->{$key} = [@values];  
     } else {  
         push @{$hash->{$key}}, @values;  
     }  
 }  
2120    
2121  =head3 DebugMode  In some versions of PERL the only error message we get is a number, which
2122    corresponds to the C++ C<errno> value.
2123    
2124  C<< if (Tracer::DebugMode) { ...code... } >>      Could not open "/usr/spool/news/twitlog": 6.
2125    
2126  Return TRUE if debug mode has been turned on, else abort.  =over 4
2127    
2128  Certain CGI scripts are too dangerous to exist in the production  =item fileHandle
2129  environment. This method provides a simple way to prevent them  
2130  from working unless they are explicitly turned on by creating a password  File handle. If this parameter is C<undef>, a file handle will be generated
2131  cookie via the B<SetPassword> script.  If debugging mode  and returned as the value of this method.
2132  is not turned on, an error will occur.  
2133    =item fileSpec
2134    
2135    File name and mode, as per the PERL C<open> function.
2136    
2137    =item message (optional)
2138    
2139    Error message to use if the open fails. If omitted, a standard error message
2140    will be generated. In either case, the error information from the file system
2141    is appended to the message. To specify a conditional open that does not throw
2142    an error if it fails, use C<0>.
2143    
2144    =item RETURN
2145    
2146    Returns the name of the file handle assigned to the file, or C<undef> if the
2147    open failed.
2148    
2149    =back
2150    
2151  =cut  =cut
2152    
2153  sub DebugMode {  sub Open {
2154      # Declare the return variable.      # Get the parameters.
2155      my $retVal = 0;      my ($fileHandle, $fileSpec, $message) = @_;
2156      # Check the debug configuration.      # Attempt to open the file.
2157      my $password = CGI::cookie("DebugMode");      my $rv = open $fileHandle, $fileSpec;
2158      my $encrypted = Digest::MD5::md5_hex($password);      # If the open failed, generate an error message.
2159      if ($encrypted eq "252dec43280e0c0d6a75ffcec486e61d") {      if (! $rv) {
2160          $retVal = 1;          # Save the system error message.
2161      } else {          my $sysMessage = $!;
2162          # Here debug mode is off, so we generate an error.          # See if we need a default message.
2163          Confess("Cannot use this facility without logging in.");          if (!$message) {
2164                # Clean any obvious mode characters and leading spaces from the
2165                # filename.
2166                my ($fileName) = FindNamePart($fileSpec);
2167                $message = "Could not open \"$fileName\"";
2168      }      }
2169      # Return the determination indicator.          # Terminate with an error using the supplied message and the
2170      return $retVal;          # error message from the file system.
2171            Confess("$message: $!");
2172        }
2173        # Return the file handle.
2174        return $fileHandle;
2175  }  }
2176    
2177  =head3 Strip  =head3 FindNamePart
2178    
2179  C<< my $string = Tracer::Strip($line); >>      my ($fileName, $start, $len) = Tracer::FindNamePart($fileSpec);
2180    
2181  Strip all line terminators off a string. This is necessary when dealing with files  Extract the portion of a file specification that contains the file name.
2182  that may have been transferred back and forth several times among different  
2183  operating environments.  A file specification is the string passed to an C<open> call. It specifies the file
2184    mode and name. In a truly complex situation, it can specify a pipe sequence. This
2185    method assumes that the file name is whatever follows the first angle bracket
2186    sequence.  So, for example, in the following strings the file name is
2187    C</usr/fig/myfile.txt>.
2188    
2189        >>/usr/fig/myfile.txt
2190        </usr/fig/myfile.txt
2191        | sort -u > /usr/fig/myfile.txt
2192    
2193    If the method cannot find a file name using its normal methods, it will return the
2194    whole incoming string.
2195    
2196  =over 4  =over 4
2197    
2198  =item line  =item fileSpec
2199    
2200  Line of text to be stripped.  File specification string from which the file name is to be extracted.
2201    
2202  =item RETURN  =item RETURN
2203    
2204  The same line of text with all the line-ending characters chopped from the end.  Returns a three-element list. The first element contains the file name portion of
2205    the specified string, or the whole string if a file name cannot be found via normal
2206    methods. The second element contains the start position of the file name portion and
2207    the third element contains the length.
2208    
2209  =back  =back
2210    
2211  =cut  =cut
2212    #: Return Type $;
2213  sub Strip {  sub FindNamePart {
2214      # Get a copy of the parameter string.      # Get the parameters.
2215      my ($string) = @_;      my ($fileSpec) = @_;
2216      my $retVal = (defined $string ? $string : "");      # Default to the whole input string.
2217      # Strip the line terminator characters.      my ($retVal, $pos, $len) = ($fileSpec, 0, length $fileSpec);
2218      $retVal =~ s/(\r|\n)+$//g;      # Parse out the file name if we can.
2219        if ($fileSpec =~ m/(<|>>?)(.+?)(\s*)$/) {
2220            $retVal = $2;
2221            $len = length $retVal;
2222            $pos = (length $fileSpec) - (length $3) - $len;
2223        }
2224      # Return the result.      # Return the result.
2225      return $retVal;      return ($retVal, $pos, $len);
2226  }  }
2227    
2228  =head3 Pad  =head3 OpenDir
2229    
2230  C<< my $paddedString = Tracer::Pad($string, $len, $left, $padChar); >>      my @files = OpenDir($dirName, $filtered, $flag);
2231    
2232  Pad a string to a specified length. The pad character will be a  Open a directory and return all the file names. This function essentially performs
2233  space, and the padding will be on the right side unless specified  the functions of an C<opendir> and C<readdir>. If the I<$filtered> parameter is
2234  in the third parameter.  set to TRUE, all filenames beginning with a period (C<.>), dollar sign (C<$>),
2235    or pound sign (C<#>) and all filenames ending with a tilde C<~>) will be
2236    filtered out of the return list. If the directory does not open and I<$flag> is not
2237    set, an exception is thrown. So, for example,
2238    
2239  =over 4      my @files = OpenDir("/Volumes/fig/contigs", 1);
2240    
2241  =item string  is effectively the same as
2242    
2243  String to be padded.      opendir(TMP, "/Volumes/fig/contigs") || Confess("Could not open /Volumes/fig/contigs.");
2244        my @files = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir(TMP);
2245    
2246  =item len  Similarly, the following code
2247    
2248  Desired length of the padded string.      my @files = grep { $_ =~ /^\d/ } OpenDir("/Volumes/fig/orgs", 0, 1);
2249    
2250  =item left (optional)  Returns the names of all files in C</Volumes/fig/orgs> that begin with digits and
2251    automatically returns an empty list if the directory fails to open.
2252    
2253  TRUE if the string is to be left-padded; otherwise it will be padded on the right.  =over 4
2254    
2255  =item padChar (optional)  =item dirName
2256    
2257  Character to use for padding. The default is a space.  Name of the directory to open.
2258    
2259  =item RETURN  =item filtered
2260    
2261  Returns a copy of the original string with the pad character added to the  TRUE if files whose names begin with a period (C<.>) should be automatically removed
2262  specified end so that it achieves the desired length.  from the list, else FALSE.
2263    
2264    =item flag
2265    
2266    TRUE if a failure to open is okay, else FALSE
2267    
2268  =back  =back
2269    
2270  =cut  =cut
2271    #: Return Type @;
2272  sub Pad {  sub OpenDir {
2273      # Get the parameters.      # Get the parameters.
2274      my ($string, $len, $left, $padChar) = @_;      my ($dirName, $filtered, $flag) = @_;
2275      # Compute the padding character.      # Declare the return variable.
2276      if (! defined $padChar) {      my @retVal = ();
2277          $padChar = " ";      # Open the directory.
2278      }      if (opendir(my $dirHandle, $dirName)) {
2279      # Compute the number of spaces needed.          # The directory opened successfully. Get the appropriate list according to the
2280      my $needed = $len - length $string;          # strictures of the filter parameter.
2281      # Copy the string into the return variable.          if ($filtered) {
2282      my $retVal = $string;              @retVal = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir $dirHandle;
     # Only proceed if padding is needed.  
     if ($needed > 0) {  
         # Create the pad string.  
         my $pad = $padChar x $needed;  
         # Affix it to the return value.  
         if ($left) {  
             $retVal = $pad . $retVal;  
2283          } else {          } else {
2284              $retVal .= $pad;              @retVal = readdir $dirHandle;
2285          }          }
2286        } elsif (! $flag) {
2287            # Here the directory would not open and it's considered an error.
2288            Confess("Could not open directory $dirName.");
2289      }      }
2290      # Return the result.      # Return the result.
2291      return $retVal;      return @retVal;
2292  }  }
2293    
 =head3 EOF  
2294    
2295  This is a constant that is lexically greater than any useful string.  =head3 Insure
2296    
2297  =cut      Insure($dirName, $chmod);
2298    
2299  sub EOF {  Insure a directory is present.
     return "\xFF\xFF\xFF\xFF\xFF";  
 }  
2300    
2301  =head3 TICK  =over 4
2302    
2303  C<< my @results = TICK($commandString); >>  =item dirName
2304    
2305  Perform a back-tick operation on a command. If this is a Windows environment, any leading  Name of the directory to check. If it does not exist, it will be created.
 dot-slash (C<./> will be removed. So, for example, if you were doing  
2306    
2307      `./protein.cgi`  =item chmod (optional)
2308    
2309  from inside a CGI script, it would work fine in Unix, but would issue an error message  Security privileges to be given to the directory if it is created.
 in Windows complaining that C<'.'> is not a valid command. If instead you code  
2310    
2311      TICK("./protein.cgi")  =back
2312    
2313  it will work correctly in both environments.  =cut
2314    
2315  =over 4  sub Insure {
2316        my ($dirName, $chmod) = @_;
2317        if (! -d $dirName) {
2318            Trace("Creating $dirName directory.") if T(2);
2319            eval {
2320                mkpath $dirName;
2321                # If we have permissions specified, set them here.
2322                if (defined($chmod)) {
2323                    chmod $chmod, $dirName;
2324                }
2325            };
2326            if ($@) {
2327                Confess("Error creating $dirName: $@");
2328            }
2329        }
2330    }
2331    
2332  =item commandString  =head3 ChDir
2333    
2334  The command string to pass to the system.      ChDir($dirName);
2335    
2336  =item RETURN  Change to the specified directory.
2337    
2338  Returns the standard output from the specified command, as a list.  =over 4
2339    
2340    =item dirName
2341    
2342    Name of the directory to which we want to change.
2343    
2344  =back  =back
2345    
2346  =cut  =cut
2347  #: Return Type @;  
2348  sub TICK {  sub ChDir {
2349      # Get the parameters.      my ($dirName) = @_;
2350      my ($commandString) = @_;      if (! -d $dirName) {
2351      # Chop off the dot-slash if this is Windows.          Confess("Cannot change to directory $dirName: no such directory.");
2352      if ($FIG_Config::win_mode) {      } else {
2353          $commandString =~ s!^\./!!;          Trace("Changing to directory $dirName.") if T(File => 4);
2354            my $okFlag = chdir $dirName;
2355            if (! $okFlag) {
2356                Confess("Error switching to directory $dirName.");
2357            }
2358      }      }
     # Activate the command and return the result.  
     return `$commandString`;  
2359  }  }
2360    
2361  =head3 ScriptSetup  =head3 SetPermissions
2362    
2363  C<< my ($cgi, $varHash) = ScriptSetup($noTrace); >>      Tracer::SetPermissions($dirName, $group, $mask, %otherMasks);
2364    
2365  Perform standard tracing and debugging setup for scripts. The value returned is  Set the permissions for a directory and all the files and folders inside it.
2366  the CGI object followed by a pre-built variable hash.  In addition, the group ownership will be changed to the specified value.
2367    
2368  The C<Trace> query parameter is used to determine whether or not tracing is active and  This method is more vulnerable than most to permission and compatability
2369  which trace modules (other than C<Tracer> itself) should be turned on. Specifying  problems, so it does internal error recovery.
 the C<CGI> trace module will trace parameter and environment information. Parameters are  
 traced at level 3 and environment variables at level 4. To trace to a file instead of to  
 the web page, set C<TF> to 1. At the end of the script, the client should call  
 L</ScriptFinish> to output the web page.  
   
 In some situations, it is not practical to invoke tracing via form parameters. For this  
 situation, you can turn on emergency tracing by invoking the L</Emergency> method from  
 a web page. Emergency tracing is detected via a file with the name  
 C<Emergency>I<IPaddr>C<.txt> in the FIG temporary directory, where I<IPaddr> is the  
 IP address of the remote user who wants tracing turned on. The file contains a time  
 limit in hours on the first line, a tracing destination on the second line, a trace  
 level on the third line, and the tracing modules on subsequent lines.  
2370    
2371  =over 4  =over 4
2372    
2373  =item noTrace (optional)  =item dirName
   
 If specified, tracing will be suppressed. This is useful if the script wants to set up  
 tracing manually.  
2374    
2375  =item RETURN  Name of the directory to process.
2376    
2377  Returns a two-element list consisting of a CGI query object and a variable hash for  =item group
 the output page.  
2378    
2379  =back  Name of the group to be assigned.
2380    
2381  =cut  =item mask
2382    
2383  sub ScriptSetup {  Permission mask. Bits that are C<1> in this mask will be ORed into the
2384      # Get the parameters.  permission bits of any file or directory that does not already have them
2385      my ($noTrace) = @_;  set to 1.
     # Get the CGI query object.  
     my $cgi = CGI->new();  
     # Set up tracing if it's not suppressed.  
     CGITrace($cgi) unless $noTrace;  
     # Create the variable hash.  
     my $varHash = { results => '' };  
     # Return the query object and variable hash.  
     return ($cgi, $varHash);  
 }  
2386    
2387  =head3 CGITrace  =item otherMasks
2388    
2389  C<< Tracer::CGITrace($cgi); >>  Map of search patterns to permission masks. If a directory name matches
2390    one of the patterns, that directory and all its members and subdirectories
2391    will be assigned the new pattern. For example, the following would
2392    assign 01664 to most files, but would use 01777 for directories named C<tmp>.
2393    
2394  Set up tracing for a CGI script. See L</ScriptSetup> for more information.      Tracer::SetPermissions($dirName, 'fig', 01664, '^tmp$' => 01777);
2395    
2396  =over 4  The list is ordered, so the following would use 0777 for C<tmp1> and
2397    0666 for C<tmp>, C<tmp2>, or C<tmp3>.
2398    
2399  =item cgi      Tracer::SetPermissions($dirName, 'fig', 01664, '^tmp1' => 0777,
2400                                                       '^tmp' => 0666);
2401    
2402  Ths CGI query object for this script.  Note that the pattern matches are all case-insensitive, and only directory
2403    names are matched, not file names.
2404    
2405  =back  =back
2406    
2407  =cut  =cut
2408    
2409  sub CGITrace {  sub SetPermissions {
2410      # Get the parameters.      # Get the parameters.
2411      my ($cgi) = @_;      my ($dirName, $group, $mask, @otherMasks) = @_;
2412      # Default to no tracing except errors.      # Set up for error recovery.
2413      my ($tracing, $dest) = ("0", "WARN");      eval {
2414      # Check for emergency tracing.          # Switch to the specified directory.
2415      my $ip = EmergencyIP($cgi);          ChDir($dirName);
2416      my $emergencyFile = EmergencyFileName($ip);          # Get the group ID.
2417      if (-e $emergencyFile) {          my $gid = getgrnam($group);
2418          # We have the file. Read in the data.          # Get the mask for tracing.
2419          my @tracing = GetFile($emergencyFile);          my $traceMask = sprintf("%04o", $mask) . "($mask)";
2420          # Pull off the time limit.          Trace("Fixing permissions for directory $dirName using group $group($gid) and mask $traceMask.") if T(File => 2);
2421          my $expire = shift @tracing;          my $fixCount = 0;
2422          # Convert it to seconds.          my $lookCount = 0;
2423          $expire *= 3600;          # @dirs will be a stack of directories to be processed.
2424          # Check the file data.          my @dirs = (getcwd());
2425          my $stat = stat($emergencyFile);          while (scalar(@dirs) > 0) {
2426          my ($now) = gettimeofday;              # Get the current directory.
2427          if ($now - $stat->mtime > $expire) {              my $dir = pop @dirs;
2428              # Delete the expired file.              # Check for a match to one of the specified directory names. To do
2429              unlink $emergencyFile;              # that, we need to pull the individual part of the name off of the
2430                # whole path.
2431                my $simpleName = $dir;
2432                if ($dir =~ m!/([^/]+)$!) {
2433                    $simpleName = $1;
2434                }
2435                Trace("Simple directory name for $dir is $simpleName.") if T(File => 4);
2436                # Search for a match.
2437                my $match = 0;
2438                my $i;
2439                for ($i = 0; $i < $#otherMasks && ! $match; $i += 2) {
2440                    my $pattern = $otherMasks[$i];
2441                    if ($simpleName =~ /$pattern/i) {
2442                        $match = 1;
2443                    }
2444                }
2445                # Check for a match. Note we use $i-1 because the loop added 2
2446                # before terminating due to the match.
2447                if ($match && $otherMasks[$i-1] != $mask) {
2448                    # This directory matches one of the incoming patterns, and it's
2449                    # a different mask, so we process it recursively with that mask.
2450                    SetPermissions($dir, $group, $otherMasks[$i-1], @otherMasks);
2451          } else {          } else {
2452              # Emergency tracing is on. Pull off the destination and                  # Here we can process normally. Get all of the non-hidden members.
2453              # the trace level;                  my @submems = OpenDir($dir, 1);
2454              $dest = shift @tracing;                  for my $submem (@submems) {
2455              my $level = shift @tracing;                      # Get the full name.
2456              # Convert the destination to a real tracing destination.                      my $thisMem = "$dir/$submem";
2457              # temp directory.                      Trace("Checking member $thisMem.") if T(4);
2458              $dest = EmergencyTracingDest($ip, $dest);                      $lookCount++;
2459              # Insure Tracer is specified.                      if ($lookCount % 1000 == 0) {
2460              my %moduleHash = map { $_ => 1 } @tracing;                          Trace("$lookCount members examined. Current is $thisMem. Mask is $traceMask") if T(File => 3);
2461              $moduleHash{Tracer} = 1;                      }
2462              # Set the trace parameter.                      # Fix the group.
2463              $tracing = join(" ", $level, sort keys %moduleHash);                      chown -1, $gid, $thisMem;
2464              # Make sure the script knows tracing is on.                      # Insure this member is not a symlink.
2465              $cgi->param(-name => 'Trace', -value => $tracing);                      if (! -l $thisMem) {
2466              $cgi->param(-name => 'TF', -value => (($dest =~ /^>/) ? 1 : 0));                          # Get its info.
2467                            my $fileInfo = stat $thisMem;
2468                            # Only proceed if we got the info. Otherwise, it's a hard link
2469                            # and we want to skip it anyway.
2470                            if ($fileInfo) {
2471                                my $fileMode = $fileInfo->mode;
2472                                if (($fileMode & $mask) != $mask) {
2473                                    # Fix this member.
2474                                    $fileMode |= $mask;
2475                                    chmod $fileMode, $thisMem;
2476                                    $fixCount++;
2477                                }
2478                                # If it's a subdirectory, stack it.
2479                                if (-d $thisMem) {
2480                                    push @dirs, $thisMem;
2481                                }
2482                            }
2483                        }
2484          }          }
     } elsif ($cgi->param('Trace')) {  
         # Here the user has requested tracing via a form.  
         $dest = ($cgi->param('TF') ? ">$FIG_Config::temp/Trace$$.log" : "QUEUE");  
         $tracing = $cgi->param('Trace') . " Tracer";  
2485      }      }
2486      # Setup the tracing we've determined from all the stuff above.          }
2487      TSetup($tracing, $dest);          Trace("$lookCount files and directories processed, $fixCount fixed.") if T(File => 2);
2488      # Trace the parameter and environment data.      };
2489      TraceParms($cgi);      # Check for an error.
2490        if ($@) {
2491            Confess("SetPermissions error: $@");
2492        }
2493  }  }
2494    
2495  =head3 EmergencyFileName  =head3 GetLine
2496    
2497  C<< my $fileName = Tracer::EmergencyFileName($ip); >>      my @data = Tracer::GetLine($handle);
2498    
2499  Return the emergency tracing file name. This is the file that specifies  Read a line of data from a tab-delimited file.
 the tracing information.  
2500    
2501  =over 4  =over 4
2502    
2503  =item ip  =item handle
2504    
2505  IP address of the user who wants tracing, as taken from the C<< $cgi->remote_host() >>  Open file handle from which to read.
 method.  
2506    
2507  =item RETURN  =item RETURN
2508    
2509  Returns the name of the file to contain the emergency tracing information.  Returns a list of the fields in the record read. The fields are presumed to be
2510    tab-delimited. If we are at the end of the file, then an empty list will be
2511    returned. If an empty line is read, a single list item consisting of a null
2512    string will be returned.
2513    
2514  =back  =back
2515    
2516  =cut  =cut
2517    
2518  sub EmergencyFileName {  sub GetLine {
2519      # Get the parameters.      # Get the parameters.
2520      my ($ip) = @_;      my ($handle) = @_;
2521      # Compute the emergency tracing file name.      # Declare the return variable.
2522      return "$FIG_Config::temp/Emergency$ip.txt";      my @retVal = ();
2523        Trace("File position is " . tell($handle) . ". EOF flag is " . eof($handle) . ".") if T(File => 4);
2524        # Read from the file.
2525        my $line = <$handle>;
2526        # Only proceed if we found something.
2527        if (defined $line) {
2528            # Remove the new-line. We are a bit over-cautious here because the file may be coming in via an
2529            # upload control and have a nonstandard EOL combination.
2530            $line =~ s/(\r|\n)+$//;
2531            # Here we do some fancy tracing to help in debugging complicated EOL marks.
2532            if (T(File => 4)) {
2533                my $escapedLine = $line;
2534                $escapedLine =~ s/\n/\\n/g;
2535                $escapedLine =~ s/\r/\\r/g;
2536                $escapedLine =~ s/\t/\\t/g;
2537                Trace("Line read: -->$escapedLine<--");
2538            }
2539            # If the line is empty, return a single empty string; otherwise, parse
2540            # it into fields.
2541            if ($line eq "") {
2542                push @retVal, "";
2543            } else {
2544                push @retVal, split /\t/,$line;
2545            }
2546        } else {
2547            # Trace the reason the read failed.
2548            Trace("End of file: $!") if T(File => 3);
2549        }
2550        # Return the result.
2551        return @retVal;
2552  }  }
2553    
2554  =head3 EmergencyFileTarget  =head3 PutLine
2555    
2556  C<< my $fileName = Tracer::EmergencyFileTarget($ip); >>      Tracer::PutLine($handle, \@fields, $eol);
2557    
2558  Return the emergency tracing target file name. This is the file that receives  Write a line of data to a tab-delimited file. The specified field values will be
2559  the tracing output for file-based tracing.  output in tab-separated form, with a trailing new-line.
2560    
2561  =over 4  =over 4
2562    
2563  =item ip  =item handle
2564    
2565    Output file handle.
2566    
2567  IP address of the user who wants tracing, as taken from the C<< $cgi->remote_host() >>  =item fields
 method.  
2568    
2569  =item RETURN  List of field values.
2570    
2571  Returns the name of the file to contain the emergency tracing information.  =item eol (optional)
2572    
2573    End-of-line character (default is "\n").
2574    
2575  =back  =back
2576    
2577  =cut  =cut
2578    
2579  sub EmergencyFileTarget {  sub PutLine {
2580      # Get the parameters.      # Get the parameters.
2581      my ($ip) = @_;      my ($handle, $fields, $eol) = @_;
2582      # Compute the emergency tracing file name.      # Write the data.
2583      return "$FIG_Config::temp/Emergency$ip.log";      print $handle join("\t", @{$fields}) . ($eol || "\n");
2584  }  }
2585    
 =head3 EmergencyTracingDest  
2586    
 C<< my $dest = Tracer::EmergencyTracingDest($ip, $myDest); >>  
2587    
2588  This method converts an emergency tracing destination to a real  =head2 Other Useful Methods
 tracing destination. The main difference is that if the  
 destination is C<FILE> or C<APPEND>, we convert it to file  
 output.  
2589    
2590  =over 4  =head3 ParseParm
2591    
2592  =item ip      my $listValue = Tracer::ParseParm($string);
2593    
2594  IP address of the user who wants tracing, as taken from the C<< $cgi->remote_host() >>  Convert a parameter into a list reference. If the parameter is undefined,
2595  method.  an undefined value will be returned. Otherwise, it will be parsed as a
2596    comma-separated list of values.
2597    
2598  =item myDest  =over 4
2599    
2600  Destination from the emergency tracing file.  =item string
2601    
2602    Incoming string.
2603    
2604  =item RETURN  =item RETURN
2605    
2606  Returns a destination that can be passed into L</TSetup>.  Returns a reference to a list of values, or C<undef> if the incoming value
2607    was undefined.
2608    
2609  =back  =back
2610    
2611  =cut  =cut
2612    
2613  sub EmergencyTracingDest {  sub ParseParm {
2614      # Get the parameters.      # Get the parameters.
2615      my ($ip, $myDest) = @_;      my ($string) = @_;
2616      # Declare the return variable.      # Declare the return variable.
2617      my $retVal;      my $retVal;
2618      # Process according to the destination value.      # Check for data.
2619      if ($myDest eq 'FILE') {      if (defined $string) {
2620          $retVal = ">" . EmergencyFileTarget($ip);          # We have some, so split it into a list.
2621      } elsif ($myDest eq 'APPEND') {          $retVal = [ split /\s*,\s*/, $string];
         $retVal = ">>" . EmergencyFileTarget($ip);  
     } else {  
         $retVal = $myDest;  
2622      }      }
2623      # Return the result.      # Return the result.
2624      return $retVal;      return $retVal;
2625  }  }
2626    
 =head3 Emergency  
2627    
 C<< Emergency($cgi, $hours, $dest, $level, @modules); >>  
2628    
 Turn on emergency tracing. This method can only be invoked over the web and is  
 should not be called if debug mode is off. The caller specifies the duration of the  
 emergency in hours, the desired tracing destination, the trace level,  
 and a list of the trace modules to activate. For the duration, when a user  
 from the specified remote web location invokes a Sprout CGI script, tracing  
 will be turned on automatically. See L</TSetup> for more about tracing  
 setup and L</ScriptSetup> for more about emergency tracing.  
2629    
2630  =over 4  =head3 Now
2631    
2632  =item cgi      my $string = Tracer::Now();
2633    
2634  A CGI query object.  Return a displayable time stamp containing the local time.
2635    
2636  =item hours  =cut
2637    
2638  Number of hours to keep emergency tracing alive.  sub Now {
2639        my ($sec,$min,$hour,$mday,$mon,$year,$wday,$yday,$isdst) = localtime(time);
2640        my $retVal = _p2($mon+1) . "/" . _p2($mday) . "/" . ($year + 1900) . " " .
2641                     _p2($hour) . ":" . _p2($min) . ":" . _p2($sec);
2642        return $retVal;
2643    }
2644    
2645  =item dest  # Pad a number to 2 digits.
2646    sub _p2 {
2647        my ($value) = @_;
2648        $value = "0$value" if ($value < 10);
2649        return $value;
2650    }
2651    
2652  Tracing destination. If no path information is specified for a file  =head3 Escape
 destination, it is put in the FIG temporary directory.  
2653    
2654  =item level      my $codedString = Tracer::Escape($realString);
2655    
2656  Tracing level. A higher level means more trace messages.  Escape a string for use in a command. Tabs will be replaced by C<\t>, new-lines
2657    replaced by C<\n>, carriage returns will be deleted, and backslashes will be doubled. The
2658    result is to reverse the effect of L</UnEscape>.
2659    
2660  =item modules  =over 4
2661    
2662  A list of the tracing modules to activate.  =item realString
2663    
2664    String to escape.
2665    
2666    =item RETURN
2667    
2668    Escaped equivalent of the real string.
2669    
2670  =back  =back
2671    
2672  =cut  =cut
2673    
2674  sub Emergency {  sub Escape {
2675      # Get the parameters.      # Get the parameter.
2676      my ($cgi, $hours, $dest, $level, @modules) = @_;      my ($realString) = @_;
2677      # Get the IP address.      # Initialize the return variable.
2678      my $ip = EmergencyIP($cgi);      my $retVal = "";
2679      # Create the emergency file.      # Loop through the parameter string, looking for sequences to escape.
2680      my $specFile = EmergencyFileName($ip);      while (length $realString > 0) {
2681      my $outHandle = Open(undef, ">$specFile");          # Look for the first sequence to escape.
2682      print $outHandle join("\n",$hours, $dest, $level, @modules, "");          if ($realString =~ /^(.*?)([\n\t\r\\])/) {
2683                # Here we found it. The text preceding the sequence is in $1. The sequence
2684                # itself is in $2. First, move the clear text to the return variable.
2685                $retVal .= $1;
2686                # Strip the processed section off the real string.
2687                $realString = substr $realString, (length $2) + (length $1);
2688                # Get the matched character.
2689                my $char = $2;
2690                # If we have a CR, we are done.
2691                if ($char ne "\r") {
2692                    # It's not a CR, so encode the escape sequence.
2693                    $char =~ tr/\t\n/tn/;
2694                    $retVal .= "\\" . $char;
2695                }
2696            } else {
2697                # Here there are no more escape sequences. The rest of the string is
2698                # transferred unmodified.
2699                $retVal .= $realString;
2700                $realString = "";
2701            }
2702        }
2703        # Return the result.
2704        return $retVal;
2705  }  }
2706    
2707  =head3 EmergencyIP  =head3 UnEscape
2708    
2709  C<< my $ip = EmergencyIP($cgi); >>      my $realString = Tracer::UnEscape($codedString);
2710    
2711  Return the IP address to be used for emergency tracing. If at smoe point we need  Replace escape sequences with their actual equivalents. C<\t> will be replaced by
2712  to change the way we compute the IP address, or we decide to use something else,  a tab, C<\n> by a new-line character, and C<\\> by a backslash. C<\r> codes will
2713  all we need to do is change this method.  be deleted.
2714    
2715  =over 4  =over 4
2716    
2717  =item cgi  =item codedString
2718    
2719  CGI query object.  String to un-escape.
2720    
2721  =item RETURN  =item RETURN
2722    
2723  Returns the IP address to be used for labelling emergency tracing.  Returns a copy of the original string with the escape sequences converted to their actual
2724    values.
2725    
2726  =back  =back
2727    
2728  =cut  =cut
2729    
2730  sub EmergencyIP {  sub UnEscape {
2731      # Get the parameters.      # Get the parameter.
2732      my ($cgi) = @_;      my ($codedString) = @_;
2733        # Initialize the return variable.
2734        my $retVal = "";
2735        # Only proceed if the incoming string is nonempty.
2736        if (defined $codedString) {
2737            # Loop through the parameter string, looking for escape sequences. We can't do
2738            # translating because it causes problems with the escaped slash. ("\\t" becomes
2739            # "\<tab>" no matter what we do.)
2740            while (length $codedString > 0) {
2741                # Look for the first escape sequence.
2742                if ($codedString =~ /^(.*?)\\(\\|n|t|r)/) {
2743                    # Here we found it. The text preceding the sequence is in $1. The sequence
2744                    # itself is in $2. First, move the clear text to the return variable.
2745                    $retVal .= $1;
2746                    $codedString = substr $codedString, (2 + length $1);
2747                    # Get the escape value.
2748                    my $char = $2;
2749                    # If we have a "\r", we are done.
2750                    if ($char ne 'r') {
2751                        # Here it's not an 'r', so we convert it.
2752                        $char =~ tr/\\tn/\\\t\n/;
2753                        $retVal .= $char;
2754                    }
2755                } else {
2756                    # Here there are no more escape sequences. The rest of the string is
2757                    # transferred unmodified.
2758                    $retVal .= $codedString;
2759                    $codedString = "";
2760                }
2761            }
2762        }
2763      # Return the result.      # Return the result.
2764      return $cgi->remote_addr();      return $retVal;
2765  }  }
2766    
2767    =head3 Percent
2768    
2769  =head3 TraceParms      my $percent = Tracer::Percent($number, $base);
   
 C<< Tracer::TraceParms($cgi); >>  
2770    
2771  Trace the CGI parameters at trace level CGI => 3 and the environment variables  Returns the percent of the base represented by the given number. If the base
2772  at level CGI => 4.  is zero, returns zero.
2773    
2774  =over 4  =over 4
2775    
2776  =item cgi  =item number
2777    
2778  CGI query object containing the parameters to trace.  Percent numerator.
2779    
2780    =item base
2781    
2782    Percent base.
2783    
2784    =item RETURN
2785    
2786    Returns the percentage of the base represented by the numerator.
2787    
2788  =back  =back
2789    
2790  =cut  =cut
2791    
2792  sub TraceParms {  sub Percent {
2793      # Get the parameters.      # Get the parameters.
2794      my ($cgi) = @_;      my ($number, $base) = @_;
2795      if (T(CGI => 3)) {      # Declare the return variable.
2796          # Here we want to trace the parameter data.      my $retVal = 0;
2797          my @names = $cgi->param;      # Compute the percent.
2798          for my $parmName (sort @names) {      if ($base != 0) {
2799              # Note we skip the Trace parameters, which are for our use only.          $retVal = $number * 100 / $base;
             if ($parmName ne 'Trace' && $parmName ne 'TF') {  
                 my @values = $cgi->param($parmName);  
                 Trace("CGI: $parmName = " . join(", ", @values));  
             }  
         }  
         # Display the request method.  
         my $method = $cgi->request_method();  
         Trace("Method: $method");  
     }  
     if (T(CGI => 4)) {  
         # Here we want the environment data too.  
         for my $envName (sort keys %ENV) {  
             Trace("ENV: $envName = $ENV{$envName}");  
         }  
2800      }      }
2801        # Return the result.
2802        return $retVal;
2803  }  }
2804    
2805  =head3 ScriptFinish  =head3 Min
2806    
2807  C<< ScriptFinish($webData, $varHash); >>      my $min = Min($value1, $value2, ... $valueN);
2808    
2809  Output a web page at the end of a script. Either the string to be output or the  Return the minimum argument. The arguments are treated as numbers.
 name of a template file can be specified. If the second parameter is omitted,  
 it is assumed we have a string to be output; otherwise, it is assumed we have the  
 name of a template file. The template should have the variable C<DebugData>  
 specified in any form that invokes a standard script. If debugging mode is turned  
 on, a form field will be put in that allows the user to enter tracing data.  
 Trace messages will be placed immediately before the terminal C<BODY> tag in  
 the output, formatted as a list.  
2810    
2811  A typical standard script would loook like the following.  =over 4
2812    
2813      BEGIN {  =item $value1, $value2, ... $valueN
         # Print the HTML header.  
         print "CONTENT-TYPE: text/html\n\n";  
     }  
     use Tracer;  
     use CGI;  
     use FIG;  
     # ... more uses ...  
2814    
2815      my ($cgi, $varHash) = ScriptSetup();  List of numbers to compare.
2816      eval {  
2817          # ... get data from $cgi, put it in $varHash ...  =item RETURN
2818      };  
2819      if ($@) {  Returns the lowest number in the list.
2820          Trace("Script Error: $@") if T(0);  
2821    =back
2822    
2823    =cut
2824    
2825    sub Min {
2826        # Get the parameters. Note that we prime the return value with the first parameter.
2827        my ($retVal, @values) = @_;
2828        # Loop through the remaining parameters, looking for the lowest.
2829        for my $value (@values) {
2830            if ($value < $retVal) {
2831                $retVal = $value;
2832            }
2833        }
2834        # Return the minimum found.
2835        return $retVal;
2836      }      }
     ScriptFinish("Html/MyTemplate.html", $varHash);  
2837    
2838  The idea here is that even if the script fails, you'll see trace messages and  =head3 Max
2839  useful output.  
2840        my $max = Max($value1, $value2, ... $valueN);
2841    
2842    Return the maximum argument. The arguments are treated as numbers.
2843    
2844  =over 4  =over 4
2845    
2846  =item webData  =item $value1, $value2, ... $valueN
2847    
2848  A string containing either the full web page to be written to the output or the  List of numbers to compare.
 name of a template file from which the page is to be constructed. If the name  
 of a template file is specified, then the second parameter must be present;  
 otherwise, it must be absent.  
2849    
2850  =item varHash (optional)  =item RETURN
2851    
2852  If specified, then a reference to a hash mapping variable names for a template  Returns the highest number in the list.
 to their values. The template file will be read into memory, and variable markers  
 will be replaced by data in this hash reference.  
2853    
2854  =back  =back
2855    
2856  =cut  =cut
2857    
2858  sub ScriptFinish {  sub Max {
2859      # Get the parameters.      # Get the parameters. Note that we prime the return value with the first parameter.
2860      my ($webData, $varHash) = @_;      my ($retVal, @values) = @_;
2861      # Check for a template file situation.      # Loop through the remaining parameters, looking for the highest.
2862      my $outputString;      for my $value (@values) {
2863      if (defined $varHash) {          if ($value > $retVal) {
2864          # Here we have a template file. We need to determine the template type.              $retVal = $value;
         my $template;  
         if ($FIG_Config::template_url && $webData =~ /\.php$/) {  
             $template = "$FIG_Config::template_url/$webData";  
         } else {  
             $template = "<<$webData";  
2865          }          }
         $outputString = PageBuilder::Build($template, $varHash, "Html");  
     } else {  
         # Here the user gave us a raw string.  
         $outputString = $webData;  
2866      }      }
2867      # Check for trace messages.      # Return the maximum found.
2868      if ($Destination ne "NONE" && $TraceLevel > 0) {      return $retVal;
         # We have trace messages, so we want to put them at the end of the body. This  
         # is either at the end of the whole string or at the beginning of the BODY  
         # end-tag.  
         my $pos = length $outputString;  
         if ($outputString =~ m#</body>#gi) {  
             $pos = (pos $outputString) - 7;  
2869          }          }
2870          # If the trace messages were queued, we unroll them. Otherwise, we display the  
2871          # destination.  =head3 DebugMode
2872          my $traceHtml;  
2873          if ($Destination eq "QUEUE") {      if (Tracer::DebugMode) { ...code... }
2874              $traceHtml = QTrace('Html');  
2875          } elsif ($Destination =~ /^>>(.+)$/) {  Return TRUE if debug mode has been turned on, else abort.
2876              # Here the tracing output it to a file. We code it as a hyperlink so the user  
2877              # can copy the file name into the clipboard easily.  Certain CGI scripts are too dangerous to exist in the production
2878              my $actualDest = $1;  environment. This method provides a simple way to prevent them
2879              $traceHtml = "<p>Tracing output to <a href=\"$actualDest\">$actualDest</a>.</p>\n";  from working unless they are explicitly turned on by creating a password
2880    cookie via the B<SetPassword> script.  If debugging mode
2881    is not turned on, an error will occur.
2882    
2883    =cut
2884    
2885    sub DebugMode {
2886        # Declare the return variable.
2887        my $retVal = 0;
2888        # Check the debug configuration.
2889        my $password = CGI::cookie("DebugMode");
2890        my $encrypted = Digest::MD5::md5_hex($password);
2891        if ($encrypted eq "252dec43280e0c0d6a75ffcec486e61d") {
2892            $retVal = 1;
2893          } else {          } else {
2894              # Here we have one of the special destinations.          # Here debug mode is off, so we generate an error.
2895              $traceHtml = "<P>Tracing output type is $Destination.</p>\n";          Confess("Cannot use this facility without logging in.");
         }  
         substr $outputString, $pos, 0, $traceHtml;  
2896      }      }
2897      # Write the output string.      # Return the determination indicator.
2898      print $outputString;      return $retVal;
2899  }  }
2900    
2901  =head3 Insure  =head3 Strip
2902    
2903  C<< Insure($dirName); >>      my $string = Tracer::Strip($line);
2904    
2905  Insure a directory is present.  Strip all line terminators off a string. This is necessary when dealing with files
2906    that may have been transferred back and forth several times among different
2907    operating environments.
2908    
2909  =over 4  =over 4
2910    
2911  =item dirName  =item line
2912    
2913  Name of the directory to check. If it does not exist, it will be created.  Line of text to be stripped.
2914    
2915    =item RETURN
2916    
2917    The same line of text with all the line-ending characters chopped from the end.
2918    
2919  =back  =back
2920    
2921  =cut  =cut
2922    
2923  sub Insure {  sub Strip {
2924      my ($dirName) = @_;      # Get a copy of the parameter string.
2925      if (! -d $dirName) {      my ($string) = @_;
2926          Trace("Creating $dirName directory.") if T(2);      my $retVal = (defined $string ? $string : "");
2927          eval { mkpath $dirName; };      # Strip the line terminator characters.
2928          if ($@) {      $retVal =~ s/(\r|\n)+$//g;
2929              Confess("Error creating $dirName: $@");      # Return the result.
2930          }      return $retVal;
     }  
2931  }  }
2932    
2933  =head3 ChDir  =head3 Pad
2934    
2935  C<< ChDir($dirName); >>      my $paddedString = Tracer::Pad($string, $len, $left, $padChar);
2936    
2937  Change to the specified directory.  Pad a string to a specified length. The pad character will be a
2938    space, and the padding will be on the right side unless specified
2939    in the third parameter.
2940    
2941  =over 4  =over 4
2942    
2943  =item dirName  =item string
2944    
2945  Name of the directory to which we want to change.  String to be padded.
2946    
2947    =item len
2948    
2949    Desired length of the padded string.
2950    
2951    =item left (optional)
2952    
2953    TRUE if the string is to be left-padded; otherwise it will be padded on the right.
2954    
2955    =item padChar (optional)
2956    
2957    Character to use for padding. The default is a space.
2958    
2959    =item RETURN
2960    
2961    Returns a copy of the original string with the pad character added to the
2962    specified end so that it achieves the desired length.
2963    
2964  =back  =back
2965    
2966  =cut  =cut
2967    
2968  sub ChDir {  sub Pad {
2969      my ($dirName) = @_;      # Get the parameters.
2970      if (! -d $dirName) {      my ($string, $len, $left, $padChar) = @_;
2971          Confess("Cannot change to directory $dirName: no such directory.");      # Compute the padding character.
2972        if (! defined $padChar) {
2973            $padChar = " ";
2974        }
2975        # Compute the number of spaces needed.
2976        my $needed = $len - length $string;
2977        # Copy the string into the return variable.
2978        my $retVal = $string;
2979        # Only proceed if padding is needed.
2980        if ($needed > 0) {
2981            # Create the pad string.
2982            my $pad = $padChar x $needed;
2983            # Affix it to the return value.
2984            if ($left) {
2985                $retVal = $pad . $retVal;
2986      } else {      } else {
2987          Trace("Changing to directory $dirName.") if T(4);              $retVal .= $pad;
         my $okFlag = chdir $dirName;  
         if (! $okFlag) {  
             Confess("Error switching to directory $dirName.");  
2988          }          }
2989      }      }
2990        # Return the result.
2991        return $retVal;
2992  }  }
2993    
2994  =head3 SendSMS  =head3 EOF
2995    
2996  C<< my $msgID = Tracer::SendSMS($phoneNumber, $msg); >>  This is a constant that is lexically greater than any useful string.
2997    
2998  Send a text message to a phone number using Clickatell. The FIG_Config file must contain the  =cut
 user name, password, and API ID for the relevant account in the hash reference variable  
 I<$FIG_Config::phone>, using the keys C<user>, C<password>, and C<api_id>. For  
 example, if the user name is C<BruceTheHumanPet>, the password is C<silly>, and the API ID  
 is C<2561022>, then the FIG_Config file must contain  
2999    
3000      $phone =  { user => 'BruceTheHumanPet',  sub EOF {
3001                  password => 'silly',      return "\xFF\xFF\xFF\xFF\xFF";
3002                  api_id => '2561022' };  }
3003    
3004  The original purpose of this method was to insure Bruce would be notified immediately when the  =head3 TICK
 Sprout Load terminates. Care should be taken if you do not wish Bruce to be notified immediately  
 when you call this method.  
3005    
3006  The message ID will be returned if successful, and C<undef> if an error occurs.      my @results = TICK($commandString);
3007    
3008  =over 4  Perform a back-tick operation on a command. If this is a Windows environment, any leading
3009    dot-slash (C<./> will be removed. So, for example, if you were doing
3010    
3011  =item phoneNumber      `./protein.cgi`
3012    
3013  Phone number to receive the message, in international format. A United States phone number  from inside a CGI script, it would work fine in Unix, but would issue an error message
3014  would be prefixed by "1". A British phone number would be prefixed by "44".  in Windows complaining that C<'.'> is not a valid command. If instead you code
3015    
3016  =item msg      TICK("./protein.cgi")
3017    
3018  Message to send to the specified phone.  it will work correctly in both environments.
3019    
3020  =item RETURN  =over 4
3021    
3022  Returns the message ID if successful, and C<undef> if the message could not be sent.  =item commandString
3023    
3024  =back  The command string to pass to the system.
3025    
3026  =cut  =item RETURN
3027    
3028  sub SendSMS {  Returns the standard output from the specified command, as a list.
3029      # Get the parameters.  
3030      my ($phoneNumber, $msg) = @_;  =back
3031      # Declare the return variable. If we do not change it, C<undef> will be returned.  
3032      my $retVal;  =cut
3033      # Only proceed if we have phone support.  #: Return Type @;
3034      if (! defined $FIG_Config::phone) {  sub TICK {
3035          Trace("Phone support not present in FIG_Config.") if T(1);      # Get the parameters.
3036      } else {      my ($commandString) = @_;
3037          # Get the phone data.      # Chop off the dot-slash if this is Windows.
3038          my $parms = $FIG_Config::phone;      if ($FIG_Config::win_mode) {
3039          # Get the Clickatell URL.          $commandString =~ s!^\./!!;
         my $url = "http://api.clickatell.com/http/";  
         # Create the user agent.  
         my $ua = LWP::UserAgent->new;  
         # Request a Clickatell session.  
         my $resp = $ua->post("$url/sendmsg", { user => $parms->{user},  
                                      password => $parms->{password},  
                                      api_id => $parms->{api_id},  
                                      to => $phoneNumber,  
                                      text => $msg});  
         # Check for an error.  
         if (! $resp->is_success) {  
             Trace("Alert failed.") if T(1);  
         } else {  
             # Get the message ID.  
             my $rstring = $resp->content;  
             if ($rstring =~ /^ID:\s+(.*)$/) {  
                 $retVal = $1;  
             } else {  
                 Trace("Phone attempt failed with $rstring") if T(1);  
             }  
         }  
3040      }      }
3041      # Return the result.      # Activate the command and return the result.
3042      return $retVal;      return `$commandString`;
3043  }  }
3044    
3045    
3046  =head3 CommaFormat  =head3 CommaFormat
3047    
3048  C<< my $formatted = Tracer::CommaFormat($number); >>      my $formatted = Tracer::CommaFormat($number);
3049    
3050  Insert commas into a number.  Insert commas into a number.
3051    
# Line 2503  Line 3078 
3078      # Return the result.      # Return the result.
3079      return $retVal;      return $retVal;
3080  }  }
 =head3 SetPermissions  
   
 C<< Tracer::SetPermissions($dirName, $group, $mask, %otherMasks); >>  
   
 Set the permissions for a directory and all the files and folders inside it.  
 In addition, the group ownership will be changed to the specified value.  
   
 This method is more vulnerable than most to permission and compatability  
 problems, so it does internal error recovery.  
   
 =over 4  
   
 =item dirName  
   
 Name of the directory to process.  
   
 =item group  
   
 Name of the group to be assigned.  
   
 =item mask  
   
 Permission mask. Bits that are C<1> in this mask will be ORed into the  
 permission bits of any file or directory that does not already have them  
 set to 1.  
   
 =item otherMasks  
   
 Map of search patterns to permission masks. If a directory name matches  
 one of the patterns, that directory and all its members and subdirectories  
 will be assigned the new pattern. For example, the following would  
 assign 01664 to most files, but would use 01777 for directories named C<tmp>.  
3081    
     Tracer::SetPermissions($dirName, 'fig', 01664, '^tmp$' => 01777);  
   
 The list is ordered, so the following would use 0777 for C<tmp1> and  
 0666 for C<tmp>, C<tmp2>, or C<tmp3>.  
   
     Tracer::SetPermissions($dirName, 'fig', 01664, '^tmp1' => 0777,  
                                                    '^tmp' => 0666);  
   
 Note that the pattern matches are all case-insensitive, and only directory  
 names are matched, not file names.  
   
 =back  
   
 =cut  
   
 sub SetPermissions {  
     # Get the parameters.  
     my ($dirName, $group, $mask, @otherMasks) = @_;  
     # Set up for error recovery.  
     eval {  
         # Switch to the specified directory.  
         ChDir($dirName);  
         # Get the group ID.  
         my $gid = getgrnam($group);  
         # Get the mask for tracing.  
         my $traceMask = sprintf("%04o", $mask) . "($mask)";  
         Trace("Fixing permissions for directory $dirName using group $group($gid) and mask $traceMask.") if T(2);  
         my $fixCount = 0;  
         my $lookCount = 0;  
         # @dirs will be a stack of directories to be processed.  
         my @dirs = (getcwd());  
         while (scalar(@dirs) > 0) {  
             # Get the current directory.  
             my $dir = pop @dirs;  
             # Check for a match to one of the specified directory names. To do  
             # that, we need to pull the individual part of the name off of the  
             # whole path.  
             my $simpleName = $dir;  
             if ($dir =~ m!/([^/]+)$!) {  
                 $simpleName = $1;  
             }  
             Trace("Simple directory name for $dir is $simpleName.") if T(4);  
             # Search for a match.  
             my $match = 0;  
             my $i;  
             for ($i = 0; $i < $#otherMasks && ! $match; $i += 2) {  
                 my $pattern = $otherMasks[$i];  
                 if ($simpleName =~ /$pattern/i) {  
                     $match = 1;  
                 }  
             }  
             # Check for a match. Note we use $i-1 because the loop added 2  
             # before terminating due to the match.  
             if ($match && $otherMasks[$i-1] != $mask) {  
                 # This directory matches one of the incoming patterns, and it's  
                 # a different mask, so we process it recursively with that mask.  
                 SetPermissions($dir, $group, $otherMasks[$i-1], @otherMasks);  
             } else {  
                 # Here we can process normally. Get all of the non-hidden members.  
                 my @submems = OpenDir($dir, 1);  
                 for my $submem (@submems) {  
                     # Get the full name.  
                     my $thisMem = "$dir/$submem";  
                     Trace("Checking member $thisMem.") if T(4);  
                     $lookCount++;  
                     if ($lookCount % 1000 == 0) {  
                         Trace("$lookCount members examined. Current is $thisMem. Mask is $traceMask") if T(3);  
                     }  
                     # Fix the group.  
                     chown -1, $gid, $thisMem;  
                     # Insure this member is not a symlink.  
                     if (! -l $thisMem) {  
                         # Get its info.  
                         my $fileInfo = stat $thisMem;  
                         # Only proceed if we got the info. Otherwise, it's a hard link  
                         # and we want to skip it anyway.  
                         if ($fileInfo) {  
                             my $fileMode = $fileInfo->mode;  
                             if (($fileMode & $mask) != $mask) {  
                                 # Fix this member.  
                                 $fileMode |= $mask;  
                                 chmod $fileMode, $thisMem;  
                                 $fixCount++;  
                             }  
                             # If it's a subdirectory, stack it.  
                             if (-d $thisMem) {  
                                 push @dirs, $thisMem;  
                             }  
                         }  
                     }  
                 }  
             }  
         }  
         Trace("$lookCount files and directories processed, $fixCount fixed.") if T(2);  
     };  
     # Check for an error.  
     if ($@) {  
         Confess("SetPermissions error: $@");  
     }  
 }  
3082    
3083  =head3 CompareLists  =head3 CompareLists
3084    
3085  C<< my ($inserted, $deleted) = Tracer::CompareLists(\@newList, \@oldList, $keyIndex); >>      my ($inserted, $deleted) = Tracer::CompareLists(\@newList, \@oldList, $keyIndex);
3086    
3087  Compare two lists of tuples, and return a hash analyzing the differences. The lists  Compare two lists of tuples, and return a hash analyzing the differences. The lists
3088  are presumed to be sorted alphabetically by the value in the $keyIndex column.  are presumed to be sorted alphabetically by the value in the $keyIndex column.
# Line 2704  Line 3147 
3147      return ($inserted, $deleted);      return ($inserted, $deleted);
3148  }  }
3149    
3150  =head3 GetLine  =head3 GenerateURL
3151    
3152  C<< my @data = Tracer::GetLine($handle); >>      my $queryUrl = Tracer::GenerateURL($page, %parameters);
3153    
3154  Read a line of data from a tab-delimited file.  Generate a GET-style URL for the specified page with the specified parameter
3155    names and values. The values will be URL-escaped automatically. So, for
3156    example
3157    
3158        Tracer::GenerateURL("form.cgi", type => 1, string => "\"high pass\" or highway")
3159    
3160    would return
3161    
3162        form.cgi?type=1;string=%22high%20pass%22%20or%20highway
3163    
3164  =over 4  =over 4
3165    
3166  =item handle  =item page
3167    
3168  Open file handle from which to read.  Page URL.
3169    
3170    =item parameters
3171    
3172    Hash mapping parameter names to parameter values.
3173    
3174  =item RETURN  =item RETURN
3175    
3176  Returns a list of the fields in the record read. The fields are presumed to be  Returns a GET-style URL that goes to the specified page and passes in the
3177  tab-delimited. If we are at the end of the file, then an empty list will be  specified parameters and values.
 returned. If an empty line is read, a single list item consisting of a null  
 string will be returned.  
3178    
3179  =back  =back
3180    
3181  =cut  =cut
3182    
3183  sub GetLine {  sub GenerateURL {
3184      # Get the parameters.      # Get the parameters.
3185      my ($handle) = @_;      my ($page, %parameters) = @_;
3186      # Declare the return variable.      # Prime the return variable with the page URL.
3187      my @retVal = ();      my $retVal = $page;
3188      # Read from the file.      # Loop through the parameters, creating parameter elements in a list.
3189      my $line = <$handle>;      my @parmList = map { "$_=" . uri_escape($parameters{$_}) } keys %parameters;
3190      # Only proceed if we found something.      # If the list is nonempty, tack it on.
3191      if (defined $line) {      if (@parmList) {
3192          # Remove the new-line.          $retVal .= "?" . join(";", @parmList);
         chomp $line;  
         # If the line is empty, return a single empty string; otherwise, parse  
         # it into fields.  
         if ($line eq "") {  
             push @retVal, "";  
         } else {  
             push @retVal, split /\t/,$line;  
         }  
3193      }      }
3194      # Return the result.      # Return the result.
3195      return @retVal;      return $retVal;
3196  }  }
3197    
3198  =head3 PutLine  =head3 ApplyURL
3199    
3200  C<< Tracer::PutLine($handle, \@fields); >>      Tracer::ApplyURL($table, $target, $url);
3201    
3202  Write a line of data to a tab-delimited file. The specified field values will be  Run through a two-dimensional table (or more accurately, a list of lists), converting the
3203  output in tab-separated form, with a trailing new-line.  I<$target> column to HTML text having a hyperlink to a URL in the I<$url> column. The
3204    URL column will be deleted by this process and the target column will be HTML-escaped.
3205    
3206    This provides a simple way to process the results of a database query into something
3207    displayable by combining a URL with text.
3208    
3209  =over 4  =over 4
3210    
3211  =item handle  =item table
3212    
3213  Output file handle.  Reference to a list of lists. The elements in the containing list will be updated by
3214    this method.
3215    
3216  =item fields  =item target
3217    
3218  List of field values.  The index of the column to be converted into HTML.
3219    
3220    =item url
3221    
3222    The index of the column containing the URL. Note that the URL must have a recognizable
3223    C<http:> at the beginning.
3224    
3225  =back  =back
3226    
3227  =cut  =cut
3228    
3229  sub PutLine {  sub ApplyURL {
3230      # Get the parameters.      # Get the parameters.
3231      my ($handle, $fields) = @_;      my ($table, $target, $url) = @_;
3232      # Write the data.      # Loop through the table.
3233      print $handle join("\t", @{$fields}) . "\n";      for my $row (@{$table}) {
3234            # Apply the URL to the target cell.
3235            $row->[$target] = CombineURL($row->[$target], $row->[$url]);
3236            # Delete the URL from the row.
3237            delete $row->[$url];
3238        }
3239  }  }
3240    
3241  =head3 GenerateURL  =head3 CombineURL
3242    
3243  C<< my $queryUrl = Tracer::GenerateURL($page, %parameters); >>      my $combinedHtml = Tracer::CombineURL($text, $url);
3244    
3245  Generate a GET-style URL for the specified page with the specified parameter  This method will convert the specified text into HTML hyperlinked to the specified
3246  names and values. The values will be URL-escaped automatically. So, for  URL. The hyperlinking will only take place if the URL looks legitimate: that is, it
3247  example  is defined and begins with an C<http:> header.
3248    
3249      Tracer::GenerateURL("form.cgi", type => 1, string => "\"high pass\" or highway")  =over 4
3250    
3251  would return  =item text
3252    
3253    Text to return. This will be HTML-escaped automatically.
3254    
3255    =item url
3256    
3257    A URL to be hyperlinked to the text. If it does not look like a URL, then the text
3258    will be returned without any hyperlinking.
3259    
3260    =item RETURN
3261    
3262    Returns the original text, HTML-escaped, with the URL hyperlinked to it. If the URL
3263    doesn't look right, the HTML-escaped text will be returned without any further
3264    modification.
3265    
3266      form.cgi?type=1&string=%22high%20pass%22%20or%20highway  =back
3267    
3268    =cut
3269    
3270    sub CombineURL {
3271        # Get the parameters.
3272        my ($text, $url) = @_;
3273        # Declare the return variable.
3274        my $retVal = CGI::escapeHTML($text);
3275        # Verify the URL.
3276        if (defined($url) && $url =~ m!http://!i) {
3277            # It's good, so we apply it to the text.
3278            $retVal = "<a href=\"$url\">$retVal</a>";
3279        }
3280        # Return the result.
3281        return $retVal;
3282    }
3283    
3284    =head3 Cmp
3285    
3286        my $cmp = Tracer::Cmp($a, $b);
3287    
3288    This method performs a universal sort comparison. Each value coming in is
3289    separated into a leading text part and a trailing number part. The text
3290    part is string compared, and if both parts are equal, then the number
3291    parts are compared numerically. A stream of just numbers or a stream of
3292    just strings will sort correctly, and a mixed stream will sort with the
3293    numbers first. Strings with a label and a number will sort in the
3294    expected manner instead of lexically.
3295    
3296  =over 4  =over 4
3297    
3298  =item page  =item a
3299    
3300  Page URL.  First item to compare.
3301    
3302  =item parameters  =item b
3303    
3304  Hash mapping parameter names to parameter values.  Second item to compare.
3305    
3306  =item RETURN  =item RETURN
3307    
3308  Returns a GET-style URL that goes to the specified page and passes in the  Returns a negative number if the first item should sort first (is less), a positive
3309  specified parameters and values.  number if the first item should sort second (is greater), and a zero if the items are
3310    equal.
3311    
3312  =back  =back
3313    
3314  =cut  =cut
3315    
3316  sub GenerateURL {  sub Cmp {
3317      # Get the parameters.      # Get the parameters.
3318      my ($page, %parameters) = @_;      my ($a, $b) = @_;
3319      # Prime the return variable with the page URL.      # Declare the return value.
3320      my $retVal = $page;      my $retVal;
3321      # Loop through the parameters, creating parameter elements in a list.      # Check for nulls.
3322