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# Line 1  Line 1 
1    #
2    # Copyright (c) 2003-2006 University of Chicago and Fellowship
3    # for Interpretations of Genomes. All Rights Reserved.
4    #
5    # This file is part of the SEED Toolkit.
6    #
7    # The SEED Toolkit is free software. You can redistribute
8    # it and/or modify it under the terms of the SEED Toolkit
9    # Public License.
10    #
11    # You should have received a copy of the SEED Toolkit Public License
12    # along with this program; if not write to the University of Chicago
13    # at info@ci.uchicago.edu or the Fellowship for Interpretation of
14    # Genomes at veronika@thefig.info or download a copy from
15    # http://www.theseed.org/LICENSE.TXT.
16    #
17    
18  package Tracer;  package Tracer;
19    
20      require Exporter;      require Exporter;
21      @ISA = ('Exporter');      @ISA = ('Exporter');
22      @EXPORT = qw(Trace T TSetup QTrace Confess Cluck Min Max Assert Open OpenDir TICK);      @EXPORT = qw(Trace T TSetup QTrace Confess Cluck Min Max Assert Open OpenDir TICK StandardSetup EmergencyKey ETracing ScriptSetup ScriptFinish Insure ChDir Emergency);
23      @EXPORT_OK = qw(GetFile GetOptions Merge MergeOptions ParseCommand ParseRecord UnEscape Escape);      @EXPORT_OK = qw(GetFile GetOptions Merge MergeOptions ParseCommand ParseRecord UnEscape Escape);
24      use strict;      use strict;
25      use Carp qw(longmess croak);      use Carp qw(longmess croak);
26      use CGI;      use CGI;
27        use Cwd;
28      use FIG_Config;      use FIG_Config;
29      use PageBuilder;      use PageBuilder;
30      use Digest::MD5;      use Digest::MD5;
31        use File::Basename;
32        use File::Path;
33        use File::stat;
34        use LWP::UserAgent;
35        use Time::HiRes 'gettimeofday';
36        use URI::Escape;
37        use Time::Local;
38    
39  =head1 Tracing and Debugging Helpers  =head1 Tracing and Debugging Helpers
40    
41  =head2 Introduction  =head2 Tracing
42    
43  This package provides simple tracing for debugging and reporting purposes. To use it simply call the  This package provides simple tracing for debugging and reporting purposes. To use it simply call the
44  L</TSetup> method to set the options and call L</Trace> to write out trace messages. Each trace  L</TSetup> or L</ETracing> method to set the options and call L</Trace> to write out trace messages.
45  message has a I<trace level> and I<category> associated with it. In addition, the tracing package itself  L</TSetup> and L</ETracing> both establish a I<trace level> and a list of I<categories>. Similarly,
46  has a list of categories and a single trace level set by the B<TSetup> method. Only messages whose trace  each trace message has a I<trace level> and I<category> associated with it. Only messages whose trace
47  level is less than or equal to this package's trace level and whose category is activated will  level is less than or equal to the setup trace level and whose category is activated will
48  be written. Thus, a higher trace level on a message indicates that the message  be written. Thus, a higher trace level on a message indicates that the message
49  is less likely to be seen. A higher trace level passed to B<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
50  appear. To generate a trace message, use the following syntax.  appear.
51    
52    =head3 Putting Trace Messages in Your Code
53    
54  C<< Trace($message) if T(errors => 4); >>  To generate a trace message, use the following syntax.
55    
56        Trace($message) if T(errors => 4);
57    
58  This statement will produce a trace message if the trace level is 4 or more and the C<errors>  This statement will produce a trace message if the trace level is 4 or more and the C<errors>
59  category is active. Note that the special category C<main> is always active, so  category is active. There is a special category C<main> that is always active, so
60    
61  C<< Trace($message) if T(main => 4); >>      Trace($message) if T(main => 4);
62    
63  will trace if the trace level is 4 or more.  will trace if the trace level is 4 or more.
64    
# Line 37  Line 66 
66  following call is made in the B<Sprout> package, it will appear if the C<Sprout> category is  following call is made in the B<Sprout> package, it will appear if the C<Sprout> category is
67  active and the trace level is 2 or more.  active and the trace level is 2 or more.
68    
69  C<< Trace($message) if T(2); >>      Trace($message) if T(2);
70    
71    In scripts, where no package name is available, the category defaults to C<main>.
72    
73  To set up tracing, you call the L</TSetup> method. The method takes as input a trace level, a list  =head3 Custom Tracing
74  of category names, and a set of options. The trace level and list of category names are  
75    Many programs have customized tracing configured using the L</TSetup> method. This is no longer
76    the preferred method, but a knowledge of how custom tracing works can make the more modern
77    L</Emergency Tracing> easier to understand.
78    
79    To set up custom tracing, you call the L</TSetup> method. The method takes as input a trace level,
80    a list of category names, and a destination. The trace level and list of category names are
81  specified as a space-delimited string. Thus  specified as a space-delimited string. Thus
82    
83  C<< TSetup('3 errors Sprout ERDB', 'HTML'); >>      TSetup('3 errors Sprout ERDB', 'TEXT');
84    
85  sets the trace level to 3, activates the C<errors>, C<Sprout>, and C<ERDB> categories, and  sets the trace level to 3, activates the C<errors>, C<Sprout>, and C<ERDB> categories, and
86  specifies that messages should be output as HTML paragraphs.  specifies that messages should be sent to the standard output.
87    
88  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
89  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
90  useful in a CGI environment.  useful in a CGI environment.
91    
92  C<< TSetup('3 *', 'WARN'); >>      TSetup('3 *', 'WARN');
93    
94  In addition to HTML and file output for trace messages, you can specify that the trace messages  In addition standard error and file output for trace messages, you can specify that the trace messages
95  be queued. The messages can then be retrieved by calling the L</QTrace> method. This approach  be queued. The messages can then be retrieved by calling the L</QTrace> method. This approach
96  is useful if you are building a web page. Instead of having the trace messages interspersed with  is useful if you are building a web page. Instead of having the trace messages interspersed with
97  the page output, they can be gathered together and displayed at the end of the page. This makes  the page output, they can be gathered together and displayed at the end of the page. This makes
98  it easier to debug page formatting problems.  it easier to debug page formatting problems.
99    
100  Finally, you can specify that all trace messages be emitted as warnings.  Finally, you can specify that all trace messages be emitted to a file, or the standard output and
101    a file at the same time. To trace to a file, specify the filename with an output character in front
102    of it.
103    
104        TSetup('4 SQL', ">$fileName");
105    
106    To trace to the standard output and a file at the same time, put a C<+> in front of the angle
107    bracket.
108    
109        TSetup('3 *', "+>$fileName");
110    
111  The flexibility of tracing makes it superior to simple use of directives like C<die> and C<warn>.  The flexibility of tracing makes it superior to simple use of directives like C<die> and C<warn>.
112  Tracer calls can be left in the code with minimal overhead and then turned on only when needed.  Tracer calls can be left in the code with minimal overhead and then turned on only when needed.
113  Thus, debugging information is available and easily retrieved even when the application is  Thus, debugging information is available and easily retrieved even when the application is
114  being used out in the field.  being used out in the field.
115    
116    =head3 Trace Levels
117    
118  There is no hard and fast rule on how to use trace levels. The following is therefore only  There is no hard and fast rule on how to use trace levels. The following is therefore only
119  a suggestion.  a suggestion.
120    
121  =over 4  =over 4
122    
123  =item 0 Error  =item Error 0
124    
125  Message indicates an error that may lead to incorrect results or that has stopped the  Message indicates an error that may lead to incorrect results or that has stopped the
126  application entirely.  application entirely.
127    
128  =item 1 Warning  =item Warning 1
129    
130  Message indicates something that is unexpected but that probably did not interfere  Message indicates something that is unexpected but that probably did not interfere
131  with program execution.  with program execution.
132    
133  =item 2 Notice  =item Notice 2
134    
135  Message indicates the beginning or end of a major task.  Message indicates the beginning or end of a major task.
136    
137  =item 3 Information  =item Information 3
138    
139  Message indicates a subtask. In the FIG system, a subtask generally relates to a single  Message indicates a subtask. In the FIG system, a subtask generally relates to a single
140  genome. This would be a big loop that is not expected to execute more than 500 times or so.  genome. This would be a big loop that is not expected to execute more than 500 times or so.
141    
142  =item 4 Detail  =item Detail 4
143    
144  Message indicates a low-level loop iteration.  Message indicates a low-level loop iteration.
145    
146  =back  =back
147    
148    The format of trace messages is important because some utilities analyze trace files.
149    There are three fields-- the time stamp, the category name, and the text.
150    The time stamp is between square brackets and the category name between angle brackets.
151    After the category name there is a colon (C<:>) followed by the message text.
152    If the square brackets or angle brackets are missing, then the trace management
153    utilities assume that they are encountering a set of pre-formatted lines.
154    
155    Note, however, that this formatting is done automatically by the tracing functions. You
156    only need to know about it if you want to parse a trace file.
157    
158    =head3 Emergency Tracing
159    
160    Sometimes, you need a way for tracing to happen automatically without putting parameters
161    in a form or on the command line. Emergency tracing does this. You invoke emergency tracing
162    from the debug form, which is accessed from I<MySeedInstance>C</FIG/Html/SetPassword.html>.
163    Emergency tracing requires you specify a tracing key. For command-line tools, the key is
164    taken from the C<TRACING> environment variable. For web services, the key is taken from
165    a cookie. Either way, the key tells the tracing facility who you are, so that you control
166    the tracing in your environment without stepping on other users.
167    
168    The key can be anything you want. If you don't have a key, the C<SetPassword> page will
169    generate one for you.
170    
171    You can activate and de-activate emergency tracing from the debugging control panel, as
172    well as display the trace file itself.
173    
174    To enable emergency tracing in your code, call
175    
176        ETracing($cgi)
177    
178    from a web script and
179    
180        ETracing()
181    
182    from a command-line script.
183    
184    The web script will look for the tracing key in the cookies, and the command-line
185    script will look for it in the C<TRACING> environment variable. If you are
186    using the L</StandardScript> or L</StandardSetup> methods, emergency tracing
187    will be configured automatically.
188    
189    =head3 Debugging Control Panel
190    
191    The debugging control panel provides several tools to assist in development of
192    SEED and Sprout software. You access the debugging control panel from the URL
193    C</FIG/Html/SetPassword.html> in whichever seed instance you're using. (So,
194    for example, the panel access point for the development NMPDR system is
195    C<http://web-1.nmpdr.org/next/FIG/Html/SetPassword.html>. Contact Bruce to
196    find out what the password is. From this page, you can also specify a tracing
197    key. If you don't specify a key, one will be generated for you.
198    
199    =head4 Emergency Tracing Form
200    
201    At the bottom of the debugging control panel is a form that allows you to
202    specify a trace level and tracing categories. Special and common categories
203    are listed with check boxes. You can hold your mouse over a check box to see
204    what its category does. In general, however, a category name is the same as
205    the name of the package in which the trace message occurs.
206    
207    Additional categories can be entered in an input box, delimited by spaces or commas.
208    
209    The B<Activate> button turns on Emergency tracing at the level you specify with the
210    specified categories active. The B<Terminate> button turns tracing off. The
211    B<Show File> button displays the current contents of the trace file. The tracing
212    form at the bottom of the control panel is designed for emergency tracing, so it
213    will only affect programs that call L</ETracing>, L</StandardScript>,
214    or L</StandardSetup>.
215    
216    =head4 Script Form
217    
218    The top form of the debugging control panel allows you to enter a tiny script and
219    have the output generated in a formatted table. Certain object variables are
220    predefined in the script, including a FIG object (C<$fig>), a CGI object (C<$cgi>),
221    and-- if Sprout is active-- Sprout (C<$sprout>) and SFXlate (C<$sfx>) objects.
222    
223    The last line of the script must be a scalar, but it can be a reference to a hash,
224    a list, a list of lists, and various other combinations. If you select the appropriate
225    data type in the dropdown box, the output will be formatted accordingly. The form
226    also has controls for specifying tracing. These controls override any emergency
227    tracing in effect.
228    
229    =head4 Database Query Forms
230    
231    The forms between the script form and the emergency tracing form allow you to
232    make queries against the database. The FIG query form allows simple queries against
233    a single FIG table. The Sprout query form uses the B<GetAll> method to do a
234    multi-table query against the Sprout database. B<GetAll> is located in the B<ERDB>
235    package, and it takes five parameters.
236    
237        GetAll(\@objectNames, $filterClause, \@parameters, \@fields, $count);
238    
239    Each of the five parameters corresponds to a text box on the query form:
240    
241    =over 4
242    
243    =item Objects
244    
245    Comma-separated list containing the names of the entity and relationship objects to be retrieved.
246    
247    =item Filter
248    
249    WHERE/ORDER BY clause (without the WHERE) to be used to filter and sort the query. The WHERE clause can
250    be parameterized with parameter markers (C<?>). Each field used must be specified in the standard form
251    B<I<objectName>(I<fieldName>)> or B<$I<number>(I<fieldName>)> where I<fieldName> is the name of a
252    field, I<objectName> is the name of the entity or relationship object containing the field, and
253    I<number> is the 1-based position of the object in the object list. Any parameters
254    specified in the filter clause should be specified in the B<Params> field.
255    The fields in a filter clause can come from primary entity relations,
256    relationship relations, or secondary entity relations; however, all of the
257    entities and relationships involved must be included in the list of object names.
258    
259    =item Params
260    
261    List of the parameters to be substituted in for the parameters marks in the filter clause. This
262    is a comma-separated list without any quoting or escaping.
263    
264    =item fields
265    
266    Comma-separated list of the fields to be returned in each element of the list returned. Fields
267    are specified in the same manner as in the filter clause.
268    
269    =item count
270    
271    Maximum number of records to return. If omitted or 0, all available records will be returned.
272    
273    =back
274    
275    B<GetAll> automatically joins together the entities and relationships listed in the object
276    names. This simplifies the coding of the filter clause, but it means that some queries are
277    not possible, since they cannot be expressed in a linear sequence of joins. This is a limitation
278    that has yet to be addressed.
279    
280  =cut  =cut
281    
282  # Declare the configuration variables.  # Declare the configuration variables.
# Line 157  Line 337 
337      # Presume category-based tracing until we learn otherwise.      # Presume category-based tracing until we learn otherwise.
338      $AllTrace = 0;      $AllTrace = 0;
339      # Build the category hash. Note that if we find a "*", we turn on non-category      # Build the category hash. Note that if we find a "*", we turn on non-category
340      # tracing.      # tracing. We must also clear away any pre-existing data.
341        %Categories = ( main => 1 );
342      for my $category (@categoryData) {      for my $category (@categoryData) {
343          if ($category eq '*') {          if ($category eq '*') {
344              $AllTrace = 1;              $AllTrace = 1;
# Line 175  Line 356 
356          }          }
357          if ($target =~ m/^>[^>]/) {          if ($target =~ m/^>[^>]/) {
358              open TRACEFILE, $target;              open TRACEFILE, $target;
359              print TRACEFILE Now() . " Tracing initialized.\n";              print TRACEFILE "[" . Now() . "] <Tracer>: Tracing initialized.\n";
360              close TRACEFILE;              close TRACEFILE;
361              $Destination = ">$target";              $Destination = ">$target";
362          } else {          } else {
# Line 188  Line 369 
369      $SetupCount++;      $SetupCount++;
370  }  }
371    
372    =head3 StandardSetup
373    
374    C<< my ($options, @parameters) = StandardSetup(\@categories, \%options, $parmHelp, @ARGV); >>
375    
376    This method performs standard command-line parsing and tracing setup. The return
377    values are a hash of the command-line options and a list of the positional
378    parameters. Tracing is automatically set up and the command-line options are
379    validated.
380    
381    This is a complex method that does a lot of grunt work. The parameters can
382    be more easily understood, however, once they are examined individually.
383    
384    The I<categories> parameter is the most obtuse. It is a reference to a list of
385    special-purpose tracing categories. Most tracing categories are PERL package
386    names. So, for example, if you wanted to turn on tracing inside the B<Sprout>,
387    B<ERDB>, and B<SproutLoad> packages, you would specify the categories
388    
389        ["Sprout", "SproutLoad", "ERDB"]
390    
391    This would cause trace messages in the specified three packages to appear in
392    the output. There are two special tracing categories that are automatically
393    handled by this method. In other words, if you used L</TSetup> you would need
394    to include these categories manually, but if you use this method they are turned
395    on automatically.
396    
397    =over 4
398    
399    =item SQL
400    
401    Traces SQL commands and activity.
402    
403    =item Tracer
404    
405    Traces error messages and call stacks.
406    
407    =back
408    
409    C<SQL> is only turned on if the C<-sql> option is specified in the command line.
410    The trace level is specified using the C<-trace> command-line option. For example,
411    the following command line for C<TransactFeatures> turns on SQL tracing and runs
412    all tracing at level 3.
413    
414        TransactFeatures -trace=3 -sql register ../xacts IDs.tbl
415    
416    Standard tracing is output to the standard output and echoed to the file
417    C<trace>I<$$>C<.log> in the FIG temporary directory, where I<$$> is the
418    process ID. You can also specify the C<user> parameter to put a user ID
419    instead of a process ID in the trace file name. So, for example
420    
421    The default trace level is 2. To get all messages, specify a trace level of 4.
422    For a genome-by-genome update, use 3.
423    
424        TransactFeatures -trace=3 -sql -user=Bruce register ../xacts IDs.tbl
425    
426    would send the trace output to C<traceBruce.log> in the temporary directory.
427    
428    The I<options> parameter is a reference to a hash containing the command-line
429    options, their default values, and an explanation of what they mean. Command-line
430    options may be in the form of switches or keywords. In the case of a switch, the
431    option value is 1 if it is specified and 0 if it is not specified. In the case
432    of a keyword, the value is separated from the option name by an equal sign. You
433    can see this last in the command-line example above.
434    
435    You can specify a different default trace level by setting C<$options->{trace}>
436    prior to calling this method.
437    
438    An example at this point would help. Consider, for example, the command-line utility
439    C<TransactFeatures>. It accepts a list of positional parameters plus the options
440    C<safe>, C<noAlias>, C<start>, and C<tblFiles>. To start up this command, we execute
441    the following code.
442    
443        my ($options, @parameters) = Tracer::StandardSetup(["DocUtils"],
444                            { safe => [0, "use database transactions"],
445                              noAlias => [0, "do not expect aliases in CHANGE transactions"],
446                              start => [' ', "start with this genome"],
447                              tblFiles => [0, "output TBL files containing the corrected IDs"] },
448                            "command transactionDirectory IDfile",
449                          @ARGV);
450    
451    
452    The call to C<ParseCommand> specifies the default values for the options and
453    stores the actual options in a hash that is returned as C<$options>. The
454    positional parameters are returned in C<@parameters>.
455    
456    The following is a sample command line for C<TransactFeatures>.
457    
458        TransactFeatures -trace=2 -noAlias register ../xacts IDs.tbl
459    
460    In this case, C<register>, C<../xacts>, and C<IDs.tbl> are the positional
461    parameters, and would find themselves in I<@parameters> after executing the
462    above code fragment. The tracing would be set to level 2, and the categories
463    would be C<Tracer>, and <DocUtils>. C<Tracer> is standard,
464    and C<DocUtils> was included because it came in within the first parameter
465    to this method. The I<$options> hash would be
466    
467        { trace => 2, sql => 0, safe => 0,
468          noAlias => 1, start => ' ', tblFiles => 0 }
469    
470    Use of C<StandardSetup> in this way provides a simple way of performing
471    standard tracing setup and command-line parsing. Note that the caller is
472    not even aware of the command-line switches C<-trace> and C<-sql>, which
473    are used by this method to control the tracing. If additional tracing features
474    need to be added in the future, they can be processed by this method without
475    upsetting the command-line utilities.
476    
477    If the C<background> option is specified on the command line, then the
478    standard and error outputs will be directed to files in the temporary
479    directory, using the same suffix as the trace file. So, if the command
480    line specified
481    
482        -user=Bruce -background
483    
484    then the trace output would go to C<traceBruce.log>, the standard output to
485    C<outBruce.log>, and the error output to C<errBruce.log>. This is designed to
486    simplify starting a command in the background.
487    
488    The user name is also used as the tracing key for L</Emergency Tracing>.
489    Specifying a value of C<E> for the trace level causes emergency tracing to
490    be used instead of custom tracing. If the user name is not specified,
491    the tracing key is taken from the C<Tracing> environment variable. If there
492    is no value for that variable, the tracing key will be computed from the PID.
493    
494    Finally, if the special option C<-h> is specified, the option names will
495    be traced at level 0 and the program will exit without processing.
496    This provides a limited help capability. For example, if the user enters
497    
498        TransactFeatures -h
499    
500    he would see the following output.
501    
502        TransactFeatures [options] command transactionDirectory IDfile
503            -trace    tracing level (default E)
504            -sql      trace SQL commands
505            -safe     use database transactions
506            -noAlias  do not expect aliases in CHANGE transactions
507            -start    start with this genome
508            -tblFiles output TBL files containing the corrected IDs
509    
510    The caller has the option of modifying the tracing scheme by placing a value
511    for C<trace> in the incoming options hash. The default value can be overridden,
512    or the tracing to the standard output can be turned off by suffixing a minus
513    sign to the trace level. So, for example,
514    
515        { trace => [0, "tracing level (default 0)"],
516           ...
517    
518    would set the default trace level to 0 instead of E, while
519    
520        { trace => ["2-", "tracing level (default 2)"],
521           ...
522    
523    would set the default to 2, but trace only to the log file, not to the
524    standard output.
525    
526    The parameters to this method are as follows.
527    
528    =over 4
529    
530    =item categories
531    
532    Reference to a list of tracing category names. These should be names of
533    packages whose internal workings will need to be debugged to get the
534    command working.
535    
536    =item options
537    
538    Reference to a hash containing the legal options for the current command mapped
539    to their default values and descriptions. The user can override the defaults
540    by specifying the options as command-line switches prefixed by a hyphen.
541    Tracing-related options may be added to this hash. If the C<-h> option is
542    specified on the command line, the option descriptions will be used to
543    explain the options. To turn off tracing to the standard output, add a
544    minus sign to the value for C<trace> (see above).
545    
546    =item parmHelp
547    
548    A string that vaguely describes the positional parameters. This is used
549    if the user specifies the C<-h> option.
550    
551    =item argv
552    
553    List of command line parameters, including the option switches, which must
554    precede the positional parameters and be prefixed by a hyphen.
555    
556    =item RETURN
557    
558    Returns a list. The first element of the list is the reference to a hash that
559    maps the command-line option switches to their values. These will either be the
560    default values or overrides specified on the command line. The remaining
561    elements of the list are the position parameters, in order.
562    
563    =back
564    
565    =cut
566    
567    sub StandardSetup {
568        # Get the parameters.
569        my ($categories, $options, $parmHelp, @argv) = @_;
570        # Get the default tracing key.
571        my $tkey = EmergencyKey();
572        # Add the tracing options.
573        if (! exists $options->{trace}) {
574            $options->{trace} = ['E', "tracing level (E for emergency tracing)"];
575        }
576        $options->{sql} = [0, "turn on SQL tracing"];
577        $options->{h} = [0, "display command-line options"];
578        $options->{user} = [$tkey, "tracing key"];
579        $options->{background} = [0, "spool standard and error output"];
580        # Create a parsing hash from the options hash. The parsing hash
581        # contains the default values rather than the default value
582        # and the description. While we're at it, we'll memorize the
583        # length of the longest option name.
584        my $longestName = 0;
585        my %parseOptions = ();
586        for my $key (keys %{$options}) {
587            if (length $key > $longestName) {
588                $longestName = length $key;
589            }
590            $parseOptions{$key} = $options->{$key}->[0];
591        }
592        # Parse the command line.
593        my ($retOptions, @retParameters) = ParseCommand(\%parseOptions, @argv);
594        # Get the logfile suffix.
595        my $suffix = $retOptions->{user};
596        # Check for background mode.
597        if ($retOptions->{background}) {
598            my $outFileName = "$FIG_Config::temp/out$suffix.log";
599            my $errFileName = "$FIG_Config::temp/err$suffix.log";
600            open STDOUT, ">$outFileName";
601            open STDERR, ">$errFileName";
602        }
603        # Now we want to set up tracing. First, we need to know if the user
604        # wants emergency tracing.
605        if ($retOptions->{trace} eq 'E') {
606            ETracing($retOptions->{user});
607        } else {
608            # Here the tracing is controlled from the command line.
609            my @cats = @{$categories};
610            if ($retOptions->{sql}) {
611                push @cats, "SQL";
612            }
613            # Add the default categories.
614            push @cats, "Tracer";
615            # Next, we create the category string by joining the categories.
616            my $cats = join(" ", @cats);
617            # Check to determine whether or not the caller wants to turn off tracing
618            # to the standard output.
619            my $traceLevel = $retOptions->{trace};
620            my $textOKFlag = 1;
621            if ($traceLevel =~ /^(.)-/) {
622                $traceLevel = $1;
623                $textOKFlag = 0;
624            }
625            # Now we set up the trace mode.
626            my $traceMode;
627            # Verify that we can open a file in the FIG temporary directory.
628            my $traceFileName = "$FIG_Config::temp/trace$suffix.log";
629            if (open TESTTRACE, ">$traceFileName") {
630                # Here we can trace to a file.
631                $traceMode = ">$traceFileName";
632                if ($textOKFlag) {
633                    # Echo to standard output if the text-OK flag is set.
634                    $traceMode = "+$traceMode";
635                }
636                # Close the test file.
637                close TESTTRACE;
638            } else {
639                # Here we can't trace to a file. We trace to the standard output if it's
640                # okay, and the error log otherwise.
641                if ($textOKFlag) {
642                    $traceMode = "TEXT";
643                } else {
644                    $traceMode = "WARN";
645                }
646            }
647            # Now set up the tracing.
648            TSetup("$traceLevel $cats", $traceMode);
649        }
650        # Check for the "h" option. If it is specified, dump the command-line
651        # options and exit the program.
652        if ($retOptions->{h}) {
653            $0 =~ m#[/\\](\w+)(\.pl)?$#i;
654            print "$1 [options] $parmHelp\n";
655            for my $key (sort keys %{$options}) {
656                my $name = Pad($key, $longestName, 0, ' ');
657                my $desc = $options->{$key}->[1];
658                if ($options->{$key}->[0]) {
659                    $desc .= " (default " . $options->{$key}->[0] . ")";
660                }
661                print "  $name $desc\n";
662            }
663            exit(0);
664        }
665        # Trace the options, if applicable.
666        if (T(3)) {
667            my @parms = grep { $retOptions->{$_} } keys %{$retOptions};
668            Trace("Selected options: " . join(", ", sort @parms) . ".");
669        }
670        # Return the parsed parameters.
671        return ($retOptions, @retParameters);
672    }
673    
674  =head3 Setups  =head3 Setups
675    
676  C<< my $count = Tracer::Setups(); >>  C<< my $count = Tracer::Setups(); >>
# Line 348  Line 831 
831    
832  =head3 OpenDir  =head3 OpenDir
833    
834  C<< my @files = OpenDir($dirName, $filtered); >>  C<< my @files = OpenDir($dirName, $filtered, $flag); >>
835    
836  Open a directory and return all the file names. This function essentially performs  Open a directory and return all the file names. This function essentially performs
837  the functions of an C<opendir> and C<readdir>. If the I<$filtered> parameter is  the functions of an C<opendir> and C<readdir>. If the I<$filtered> parameter is
838  set to TRUE, all filenames beginning with a period (C<.>) will be filtered out of  set to TRUE, all filenames beginning with a period (C<.>), dollar sign (C<$>),
839  the return list. If the directory does not open, an exception is thrown. So,  or pound sign (C<#>) and all filenames ending with a tilde C<~>) will be
840  for example,  filtered out of the return list. If the directory does not open and I<$flag> is not
841    set, an exception is thrown. So, for example,
842    
843      my @files = OpenDir("/Volumes/fig/contigs", 1);      my @files = OpenDir("/Volumes/fig/contigs", 1);
844    
845  is effectively the same as  is effectively the same as
846    
847      opendir(TMP, "/Volumes/fig/contigs") || Confess("Could not open /Volumes/fig/contigs.");      opendir(TMP, "/Volumes/fig/contigs") || Confess("Could not open /Volumes/fig/contigs.");
848      my @files = grep { $_ !~ /^\./ } readdir(TMP);      my @files = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir(TMP);
849    
850  Similarly, the following code  Similarly, the following code
851    
852      my @files = grep { $_ =~ /^\d/ } OpenDir("/Volumes/fig/orgs");      my @files = grep { $_ =~ /^\d/ } OpenDir("/Volumes/fig/orgs", 0, 1);
853    
854  Returns the names of all files in C</Volumes/fig/orgs> that begin with digits and  Returns the names of all files in C</Volumes/fig/orgs> that begin with digits and
855  automatically throws an error if the directory fails to open.  automatically returns an empty list if the directory fails to open.
856    
857  =over 4  =over 4
858    
# Line 381  Line 865 
865  TRUE if files whose names begin with a period (C<.>) should be automatically removed  TRUE if files whose names begin with a period (C<.>) should be automatically removed
866  from the list, else FALSE.  from the list, else FALSE.
867    
868    =item flag
869    
870    TRUE if a failure to open is okay, else FALSE
871    
872  =back  =back
873    
874  =cut  =cut
875  #: Return Type @;  #: Return Type @;
876  sub OpenDir {  sub OpenDir {
877      # Get the parameters.      # Get the parameters.
878      my ($dirName, $filtered) = @_;      my ($dirName, $filtered, $flag) = @_;
879      # Declare the return variable.      # Declare the return variable.
880      my @retVal;      my @retVal = ();
881      # Open the directory.      # Open the directory.
882      if (opendir(my $dirHandle, $dirName)) {      if (opendir(my $dirHandle, $dirName)) {
883          # The directory opened successfully. Get the appropriate list according to the          # The directory opened successfully. Get the appropriate list according to the
884          # strictures of the filter parameter.          # strictures of the filter parameter.
885          if ($filtered) {          if ($filtered) {
886              @retVal = grep { $_ !~ /^\./ } readdir $dirHandle;              @retVal = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir $dirHandle;
887          } else {          } else {
888              @retVal = readdir $dirHandle;              @retVal = readdir $dirHandle;
889          }          }
890      } else {      } elsif (! $flag) {
891          # Here the directory would not open.          # Here the directory would not open and it's considered an error.
892          Confess("Could not open directory $dirName.");          Confess("Could not open directory $dirName.");
893      }      }
894      # Return the result.      # Return the result.
# Line 449  Line 937 
937      return $value;      return $value;
938  }  }
939    
940    =head3 ParseTraceDate
941    
942    C<< my $time = Tracer::ParseTraceDate($dateString); >>
943    
944    Convert a date from the trace file into a PERL timestamp.
945    
946    =over 4
947    
948    =item dateString
949    
950    The date string from the trace file. The format of the string is determined by the
951    L</Now> method.
952    
953    =item RETURN
954    
955    Returns a PERL time, that is, a number of seconds since the epoch, or C<undef> if
956    the time string is invalid.
957    
958    =back
959    
960    =cut
961    
962    sub ParseTraceDate {
963        # Get the parameters.
964        my ($dateString) = @_;
965        # Declare the return variable.
966        my $retVal;
967        # Parse the date.
968        if ($dateString =~ m#(\d+)/(\d+)/(\d+)\s+(\d+):(\d+):(\d+)#) {
969            # Create a time object. Note we need to convert the day, month,
970            # and year to a different base. Years count from 1900, and
971            # the internal month value is relocated to January = 0.
972            $retVal = timelocal($6, $5, $4, $2, $1 - 1, $3 - 1900);
973        }
974        # Return the result.
975        return $retVal;
976    }
977    
978  =head3 LogErrors  =head3 LogErrors
979    
980  C<< Tracer::LogErrors($fileName); >>  C<< Tracer::LogErrors($fileName); >>
# Line 651  Line 1177 
1177      # Get the timestamp.      # Get the timestamp.
1178      my $timeStamp = Now();      my $timeStamp = Now();
1179      # Format the message. Note we strip off any line terminators at the end.      # Format the message. Note we strip off any line terminators at the end.
1180      my $formatted = "$timeStamp <$LastCategory>: " . Strip($message);      my $formatted = "[$timeStamp] <$LastCategory>: " . Strip($message);
1181      # Process according to the destination.      # Process according to the destination.
1182      if ($Destination eq "TEXT") {      if ($Destination eq "TEXT") {
1183          # Write the message to the standard output.          # Write the message to the standard output.
# Line 738  Line 1264 
1264          # Convert it to lower case before we hash it.          # Convert it to lower case before we hash it.
1265          $category = lc $category;          $category = lc $category;
1266          # Use the category and tracelevel to compute the result.          # Use the category and tracelevel to compute the result.
1267            if (ref $traceLevel) {
1268                Confess("Bad trace level.");
1269            } elsif (ref $TraceLevel) {
1270                Confess("Bad trace config.");
1271            }
1272          $retVal = ($traceLevel <= $TraceLevel && ($AllTrace || exists $Categories{$category}));          $retVal = ($traceLevel <= $TraceLevel && ($AllTrace || exists $Categories{$category}));
1273      }      }
1274      # Return the computed result.      # Return the computed result.
# Line 825  Line 1356 
1356  C<< my $codedString = Tracer::Escape($realString); >>  C<< my $codedString = Tracer::Escape($realString); >>
1357    
1358  Escape a string for use in a command length. Tabs will be replaced by C<\t>, new-lines  Escape a string for use in a command length. Tabs will be replaced by C<\t>, new-lines
1359  replaced by C<\n>, and backslashes will be doubled. The effect is to exactly reverse the  replaced by C<\n>, carriage returns will be deleted, and backslashes will be doubled. The
1360  effect of L</UnEscape>.  result is to reverse the effect of L</UnEscape>.
1361    
1362  =over 4  =over 4
1363    
# Line 850  Line 1381 
1381      # Loop through the parameter string, looking for sequences to escape.      # Loop through the parameter string, looking for sequences to escape.
1382      while (length $realString > 0) {      while (length $realString > 0) {
1383          # Look for the first sequence to escape.          # Look for the first sequence to escape.
1384          if ($realString =~ /^(.*?)([\n\t\\])/) {          if ($realString =~ /^(.*?)([\n\t\r\\])/) {
1385              # Here we found it. The text preceding the sequence is in $1. The sequence              # Here we found it. The text preceding the sequence is in $1. The sequence
1386              # itself is in $2. First, move the clear text to the return variable.              # itself is in $2. First, move the clear text to the return variable.
1387              $retVal .= $1;              $retVal .= $1;
1388              # Strip the processed section off the real string.              # Strip the processed section off the real string.
1389              $realString = substr $realString, (length $2) + (length $1);              $realString = substr $realString, (length $2) + (length $1);
1390              # Encode the escape sequence.              # Get the matched character.
1391              my $char = $2;              my $char = $2;
1392                # If we have a CR, we are done.
1393                if ($char ne "\r") {
1394                    # It's not a CR, so encode the escape sequence.
1395              $char =~ tr/\t\n/tn/;              $char =~ tr/\t\n/tn/;
1396              $retVal .= "\\" . $char;              $retVal .= "\\" . $char;
1397                }
1398          } else {          } else {
1399              # Here there are no more escape sequences. The rest of the string is              # Here there are no more escape sequences. The rest of the string is
1400              # transferred unmodified.              # transferred unmodified.
# Line 876  Line 1411 
1411  C<< my $realString = Tracer::UnEscape($codedString); >>  C<< my $realString = Tracer::UnEscape($codedString); >>
1412    
1413  Replace escape sequences with their actual equivalents. C<\t> will be replaced by  Replace escape sequences with their actual equivalents. C<\t> will be replaced by
1414  a tab, C<\n> by a new-line character, and C<\\> by a back-slash.  a tab, C<\n> by a new-line character, and C<\\> by a backslash. C<\r> codes will
1415    be deleted.
1416    
1417  =over 4  =over 4
1418    
# Line 905  Line 1441 
1441          # "\<tab>" no matter what we do.)          # "\<tab>" no matter what we do.)
1442          while (length $codedString > 0) {          while (length $codedString > 0) {
1443              # Look for the first escape sequence.              # Look for the first escape sequence.
1444              if ($codedString =~ /^(.*?)\\(\\|n|t)/) {              if ($codedString =~ /^(.*?)\\(\\|n|t|r)/) {
1445                  # Here we found it. The text preceding the sequence is in $1. The sequence                  # Here we found it. The text preceding the sequence is in $1. The sequence
1446                  # itself is in $2. First, move the clear text to the return variable.                  # itself is in $2. First, move the clear text to the return variable.
1447                  $retVal .= $1;                  $retVal .= $1;
1448                  $codedString = substr $codedString, (2 + length $1);                  $codedString = substr $codedString, (2 + length $1);
1449                  # Decode the escape sequence.                  # Get the escape value.
1450                  my $char = $2;                  my $char = $2;
1451                    # If we have a "\r", we are done.
1452                    if ($char ne 'r') {
1453                        # Here it's not an 'r', so we convert it.
1454                  $char =~ tr/\\tn/\\\t\n/;                  $char =~ tr/\\tn/\\\t\n/;
1455                  $retVal .= $char;                  $retVal .= $char;
1456                    }
1457              } else {              } else {
1458                  # Here there are no more escape sequences. The rest of the string is                  # Here there are no more escape sequences. The rest of the string is
1459                  # transferred unmodified.                  # transferred unmodified.
# Line 1019  Line 1559 
1559      return @inputList;      return @inputList;
1560  }  }
1561    
1562    =head3 Percent
1563    
1564    C<< my $percent = Tracer::Percent($number, $base); >>
1565    
1566    Returns the percent of the base represented by the given number. If the base
1567    is zero, returns zero.
1568    
1569    =over 4
1570    
1571    =item number
1572    
1573    Percent numerator.
1574    
1575    =item base
1576    
1577    Percent base.
1578    
1579    =item RETURN
1580    
1581    Returns the percentage of the base represented by the numerator.
1582    
1583    =back
1584    
1585    =cut
1586    
1587    sub Percent {
1588        # Get the parameters.
1589        my ($number, $base) = @_;
1590        # Declare the return variable.
1591        my $retVal = 0;
1592        # Compute the percent.
1593        if ($base != 0) {
1594            $retVal = $number * 100 / $base;
1595        }
1596        # Return the result.
1597        return $retVal;
1598    }
1599    
1600  =head3 GetFile  =head3 GetFile
1601    
1602  C<< my @fileContents = Tracer::GetFile($fileName); >>  C<< my @fileContents = Tracer::GetFile($fileName); >>
1603    
1604  Return the entire contents of a file.      or
1605    
1606    C<< my $fileContents = Tracer::GetFile($fileName); >>
1607    
1608    Return the entire contents of a file. In list context, line-ends are removed and
1609    each line is a list element. In scalar context, line-ends are replaced by C<\n>.
1610    
1611  =over 4  =over 4
1612    
# Line 1034  Line 1617 
1617  =item RETURN  =item RETURN
1618    
1619  In a list context, returns the entire file as a list with the line terminators removed.  In a list context, returns the entire file as a list with the line terminators removed.
1620  In a scalar context, returns the entire file as a string.  In a scalar context, returns the entire file as a string. If an error occurs opening
1621    the file, an empty list will be returned.
1622    
1623  =back  =back
1624    
# Line 1046  Line 1630 
1630      # Declare the return variable.      # Declare the return variable.
1631      my @retVal = ();      my @retVal = ();
1632      # Open the file for input.      # Open the file for input.
1633      my $ok = open INPUTFILE, "<$fileName";      my $handle = Open(undef, "<$fileName");
     if (!$ok) {  
         # If we had an error, trace it. We will automatically return a null value.  
         Trace("Could not open \"$fileName\" for input: $!") if T(0);  
     } else {  
1634          # Read the whole file into the return variable, stripping off any terminator          # Read the whole file into the return variable, stripping off any terminator
1635          # characters.          # characters.
1636          my $lineCount = 0;          my $lineCount = 0;
1637          while (my $line = <INPUTFILE>) {      while (my $line = <$handle>) {
1638              $lineCount++;              $lineCount++;
1639              $line = Strip($line);              $line = Strip($line);
1640              push @retVal, $line;              push @retVal, $line;
1641          }          }
1642          # Close it.          # Close it.
1643          close INPUTFILE;      close $handle;
1644          my $actualLines = @retVal;          my $actualLines = @retVal;
1645      }      Trace("$actualLines lines read from file $fileName.") if T(File => 2);
1646      # Return the file's contents in the desired format.      # Return the file's contents in the desired format.
1647      if (wantarray) {      if (wantarray) {
1648          return @retVal;          return @retVal;
# Line 1071  Line 1651 
1651      }      }
1652  }  }
1653    
1654    =head3 PutFile
1655    
1656    C<< Tracer::PutFile($fileName, \@lines); >>
1657    
1658    Write out a file from a list of lines of text.
1659    
1660    =over 4
1661    
1662    =item fileName
1663    
1664    Name of the output file.
1665    
1666    =item lines
1667    
1668    Reference to a list of text lines. The lines will be written to the file in order, with trailing
1669    new-line characters. Alternatively, may be a string, in which case the string will be written without
1670    modification.
1671    
1672    =back
1673    
1674    =cut
1675    
1676    sub PutFile {
1677        # Get the parameters.
1678        my ($fileName, $lines) = @_;
1679        # Open the output file.
1680        my $handle = Open(undef, ">$fileName");
1681        # Count the lines written.
1682        if (ref $lines ne 'ARRAY') {
1683            # Here we have a scalar, so we write it raw.
1684            print $handle $lines;
1685            Trace("Scalar put to file $fileName.") if T(File => 3);
1686        } else {
1687            # Write the lines one at a time.
1688            my $count = 0;
1689            for my $line (@{$lines}) {
1690                print $handle "$line\n";
1691                $count++;
1692            }
1693            Trace("$count lines put to file $fileName.") if T(File => 3);
1694        }
1695        # Close the output file.
1696        close $handle;
1697    }
1698    
1699  =head3 QTrace  =head3 QTrace
1700    
1701  C<< my $data = QTrace($format); >>  C<< my $data = QTrace($format); >>
# Line 1150  Line 1775 
1775  C<< Assert($condition1, $condition2, ... $conditionN); >>  C<< Assert($condition1, $condition2, ... $conditionN); >>
1776    
1777  Return TRUE if all the conditions are true. This method can be used in conjunction with  Return TRUE if all the conditions are true. This method can be used in conjunction with
1778  the OR operator and the L</Confess> method, B<Assert> can function as a debugging assert.  the OR operator and the L</Confess> method as a debugging assert.
1779  So, for example  So, for example
1780    
1781  C<< Assert($recNum >= 0) || Confess("Invalid record number $recNum."); >>  C<< Assert($recNum >= 0) || Confess("Invalid record number $recNum."); >>
# Line 1271  Line 1896 
1896    
1897  =head3 AddToListMap  =head3 AddToListMap
1898    
1899  C<< Tracer::AddToListMap(\%hash, $key, $value); >>  C<< Tracer::AddToListMap(\%hash, $key, $value1, $value2, ... valueN); >>
1900    
1901  Add a key-value pair to a hash of lists. If no value exists for the key, a singleton list  Add a key-value pair to a hash of lists. If no value exists for the key, a singleton list
1902  is created for the key. Otherwise, the new value is pushed onto the list.  is created for the key. Otherwise, the new value is pushed onto the list.
# Line 1286  Line 1911 
1911    
1912  Key for which the value is to be added.  Key for which the value is to be added.
1913    
1914  =item value  =item value1, value2, ... valueN
1915    
1916  Value to add to the key's value list.  List of values to add to the key's value list.
1917    
1918  =back  =back
1919    
# Line 1296  Line 1921 
1921    
1922  sub AddToListMap {  sub AddToListMap {
1923      # Get the parameters.      # Get the parameters.
1924      my ($hash, $key, $value) = @_;      my ($hash, $key, @values) = @_;
1925      # Process according to whether or not the key already has a value.      # Process according to whether or not the key already has a value.
1926      if (! exists $hash->{$key}) {      if (! exists $hash->{$key}) {
1927          $hash->{$key} = [$value];          $hash->{$key} = [@values];
1928      } else {      } else {
1929          push @{$hash->{$key}}, $value;          push @{$hash->{$key}}, @values;
1930      }      }
1931  }  }
1932    
# Line 1309  Line 1934 
1934    
1935  C<< if (Tracer::DebugMode) { ...code... } >>  C<< if (Tracer::DebugMode) { ...code... } >>
1936    
1937  Return TRUE if debug mode has been turned on, else output an error  Return TRUE if debug mode has been turned on, else abort.
 page and return FALSE.  
1938    
1939  Certain CGI scripts are too dangerous to exist in the production  Certain CGI scripts are too dangerous to exist in the production
1940  environment. This method provides a simple way to prevent them  environment. This method provides a simple way to prevent them
1941  from working unless they are explicitly turned on by creating a password  from working unless they are explicitly turned on by creating a password
1942  cookie via the B<SetPassword> script.  If debugging mode  cookie via the B<SetPassword> script.  If debugging mode
1943  is not turned on, an error web page will be output directing the  is not turned on, an error will occur.
 user to enter in the correct password.  
1944    
1945  =cut  =cut
1946    
# Line 1330  Line 1953 
1953      if ($encrypted eq "252dec43280e0c0d6a75ffcec486e61d") {      if ($encrypted eq "252dec43280e0c0d6a75ffcec486e61d") {
1954          $retVal = 1;          $retVal = 1;
1955      } else {      } else {
1956          # Here debug mode is off, so we generate an error page.          # Here debug mode is off, so we generate an error.
1957          my $pageString = PageBuilder::Build("<Html/ErrorPage.html", {}, "Html");          Confess("Cannot use this facility without logging in.");
         print $pageString;  
1958      }      }
1959      # Return the determination indicator.      # Return the determination indicator.
1960      return $retVal;      return $retVal;
# Line 1363  Line 1985 
1985  sub Strip {  sub Strip {
1986      # Get a copy of the parameter string.      # Get a copy of the parameter string.
1987      my ($string) = @_;      my ($string) = @_;
1988      my $retVal = $string;      my $retVal = (defined $string ? $string : "");
1989      # Strip the line terminator characters.      # Strip the line terminator characters.
1990      $retVal =~ s/(\r|\n)+$//g;      $retVal =~ s/(\r|\n)+$//g;
1991      # Return the result.      # Return the result.
# Line 1431  Line 2053 
2053      return $retVal;      return $retVal;
2054  }  }
2055    
2056    =head3 EOF
2057    
2058    This is a constant that is lexically greater than any useful string.
2059    
2060    =cut
2061    
2062    sub EOF {
2063        return "\xFF\xFF\xFF\xFF\xFF";
2064    }
2065    
2066  =head3 TICK  =head3 TICK
2067    
2068  C<< my @results = TICK($commandString); >>  C<< my @results = TICK($commandString); >>
# Line 1472  Line 2104 
2104      return `$commandString`;      return `$commandString`;
2105  }  }
2106    
2107    =head3 ScriptSetup
2108    
2109    C<< my ($cgi, $varHash) = ScriptSetup($noTrace); >>
2110    
2111    Perform standard tracing and debugging setup for scripts. The value returned is
2112    the CGI object followed by a pre-built variable hash. At the end of the script,
2113    the client should call L</ScriptFinish> to output the web page.
2114    
2115    This method calls L</ETracing> to configure tracing, which allows the tracing
2116    to be configured via the emergency tracing form on the debugging control panel.
2117    Tracing will then be turned on automatically for all programs that use the L</ETracing>
2118    method, which includes every program that uses this method or L</StandardSetup>.
2119    
2120    =over 4
2121    
2122    =item noTrace (optional)
2123    
2124    If specified, tracing will be suppressed. This is useful if the script wants to set up
2125    tracing manually.
2126    
2127    =item RETURN
2128    
2129    Returns a two-element list consisting of a CGI query object and a variable hash for
2130    the output page.
2131    
2132    =back
2133    
2134    =cut
2135    
2136    sub ScriptSetup {
2137        # Get the parameters.
2138        my ($noTrace) = @_;
2139        # Get the CGI query object.
2140        my $cgi = CGI->new();
2141        # Set up tracing if it's not suppressed.
2142        ETracing($cgi) unless $noTrace;
2143        # Create the variable hash.
2144        my $varHash = { results => '' };
2145        # Return the query object and variable hash.
2146        return ($cgi, $varHash);
2147    }
2148    
2149    =head3 ETracing
2150    
2151    C<< ETracing($parameter); >>
2152    
2153    Set up emergency tracing. Emergency tracing is tracing that is turned
2154    on automatically for any program that calls this method. The emergency
2155    tracing parameters are stored in a a file identified by a tracing key.
2156    If this method is called with a CGI object, then the tracing key is
2157    taken from a cookie. If it is called with no parameters, then the tracing
2158    key is taken from an environment variable. If it is called with a string,
2159    the tracing key is that string.
2160    
2161    =over 4
2162    
2163    =item parameter
2164    
2165    A parameter from which the tracing key is computed. If it is a scalar,
2166    that scalar is used as the tracing key. If it is a CGI object, the
2167    tracing key is taken from the C<IP> cookie. If it is omitted, the
2168    tracing key is taken from the C<TRACING> environment variable. If it
2169    is a CGI object and emergency tracing is not on, the C<Trace> and
2170    C<TF> parameters will be used to determine the type of tracing.
2171    
2172    =back
2173    
2174    =cut
2175    
2176    sub ETracing {
2177        # Get the parameter.
2178        my ($parameter) = @_;
2179        # Check for CGI mode.
2180        my $cgi = (ref $parameter eq 'CGI' ? $parameter : undef);
2181        # Default to no tracing except errors.
2182        my ($tracing, $dest) = ("0", "WARN");
2183        # Check for emergency tracing.
2184        my $tkey = EmergencyKey($parameter);
2185        my $emergencyFile = EmergencyFileName($tkey);
2186        if (-e $emergencyFile) {
2187            # We have the file. Read in the data.
2188            my @tracing = GetFile($emergencyFile);
2189            # Pull off the time limit.
2190            my $expire = shift @tracing;
2191            # Convert it to seconds.
2192            $expire *= 3600;
2193            # Check the file data.
2194            my $stat = stat($emergencyFile);
2195            my ($now) = gettimeofday;
2196            if ($now - $stat->mtime > $expire) {
2197                # Delete the expired file.
2198                unlink $emergencyFile;
2199            } else {
2200                # Emergency tracing is on. Pull off the destination and
2201                # the trace level;
2202                $dest = shift @tracing;
2203                my $level = shift @tracing;
2204                # Convert the destination to a real tracing destination.
2205                # temp directory.
2206                $dest = EmergencyTracingDest($tkey, $dest);
2207                # Insure Tracer is specified.
2208                my %moduleHash = map { $_ => 1 } @tracing;
2209                $moduleHash{Tracer} = 1;
2210                # Set the trace parameter.
2211                $tracing = join(" ", $level, sort keys %moduleHash);
2212            }
2213        } elsif (defined $cgi) {
2214            # There's no emergency tracing, but we have a CGI object, so check
2215            # for tracing from the form parameters.
2216            if ($cgi->param('Trace')) {
2217                # Here the user has requested tracing via a form.
2218                $dest = ($cgi->param('TF') ? ">$FIG_Config::temp/Trace$$.log" : "QUEUE");
2219                $tracing = $cgi->param('Trace') . " Tracer";
2220            }
2221        }
2222        # Setup the tracing we've determined from all the stuff above.
2223        TSetup($tracing, $dest);
2224        # If we're a web script, trace the parameter and environment data.
2225        if (defined $cgi) {
2226            TraceParms($cgi);
2227        }
2228    }
2229    
2230    =head3 EmergencyFileName
2231    
2232    C<< my $fileName = Tracer::EmergencyFileName($tkey); >>
2233    
2234    Return the emergency tracing file name. This is the file that specifies
2235    the tracing information.
2236    
2237    =over 4
2238    
2239    =item tkey
2240    
2241    Tracing key for the current program.
2242    
2243    =item RETURN
2244    
2245    Returns the name of the file to contain the emergency tracing information.
2246    
2247    =back
2248    
2249    =cut
2250    
2251    sub EmergencyFileName {
2252        # Get the parameters.
2253        my ($tkey) = @_;
2254        # Compute the emergency tracing file name.
2255        return "$FIG_Config::temp/Emergency$tkey.txt";
2256    }
2257    
2258    =head3 EmergencyFileTarget
2259    
2260    C<< my $fileName = Tracer::EmergencyFileTarget($tkey); >>
2261    
2262    Return the emergency tracing target file name. This is the file that receives
2263    the tracing output for file-based tracing.
2264    
2265    =over 4
2266    
2267    =item tkey
2268    
2269    Tracing key for the current program.
2270    
2271    =item RETURN
2272    
2273    Returns the name of the file to contain the trace output.
2274    
2275    =back
2276    
2277    =cut
2278    
2279    sub EmergencyFileTarget {
2280        # Get the parameters.
2281        my ($tkey) = @_;
2282        # Compute the emergency tracing file name.
2283        return "$FIG_Config::temp/trace$tkey.log";
2284    }
2285    
2286    =head3 EmergencyTracingDest
2287    
2288    C<< my $dest = Tracer::EmergencyTracingDest($tkey, $myDest); >>
2289    
2290    This method converts an emergency tracing destination to a real
2291    tracing destination. The main difference is that if the
2292    destination is C<FILE> or C<APPEND>, we convert it to file
2293    output.
2294    
2295    =over 4
2296    
2297    =item tkey
2298    
2299    Tracing key for this environment.
2300    
2301    =item myDest
2302    
2303    Destination from the emergency tracing file.
2304    
2305    =item RETURN
2306    
2307    Returns a destination that can be passed into L</TSetup>.
2308    
2309    =back
2310    
2311    =cut
2312    
2313    sub EmergencyTracingDest {
2314        # Get the parameters.
2315        my ($tkey, $myDest) = @_;
2316        # Declare the return variable.
2317        my $retVal;
2318        # Process according to the destination value.
2319        if ($myDest eq 'FILE') {
2320            $retVal = ">" . EmergencyFileTarget($tkey);
2321        } elsif ($myDest eq 'APPEND') {
2322            $retVal = ">>" . EmergencyFileTarget($tkey);
2323        } else {
2324            $retVal = $myDest;
2325        }
2326        # Return the result.
2327        return $retVal;
2328    }
2329    
2330    =head3 Emergency
2331    
2332    C<< Emergency($key, $hours, $dest, $level, @modules); >>
2333    
2334    Turn on emergency tracing. This method can only be invoked over the web and is
2335    should not be called if debug mode is off. The caller specifies the duration of the
2336    emergency in hours, the desired tracing destination, the trace level,
2337    and a list of the trace modules to activate. For the length of the duration, when a
2338    program in an environment with the specified tracing key active invokes a Sprout
2339    CGI script, tracing will be turned on automatically. See L</TSetup> for more
2340    about tracing setup and L</ETracing> for more about emergency tracing.
2341    
2342    =over 4
2343    
2344    =item tkey
2345    
2346    The tracing key. This is used to identify the control file and the trace file.
2347    
2348    =item hours
2349    
2350    Number of hours to keep emergency tracing alive.
2351    
2352    =item dest
2353    
2354    Tracing destination. If no path information is specified for a file
2355    destination, it is put in the FIG temporary directory.
2356    
2357    =item level
2358    
2359    Tracing level. A higher level means more trace messages.
2360    
2361    =item modules
2362    
2363    A list of the tracing modules to activate.
2364    
2365    =back
2366    
2367    =cut
2368    
2369    sub Emergency {
2370        # Get the parameters.
2371        my ($tkey, $hours, $dest, $level, @modules) = @_;
2372        # Create the emergency file.
2373        my $specFile = EmergencyFileName($tkey);
2374        my $outHandle = Open(undef, ">$specFile");
2375        print $outHandle join("\n", $hours, $dest, $level, @modules, "");
2376    }
2377    
2378    =head3 EmergencyKey
2379    
2380    C<< my $tkey = EmergencyKey($parameter); >>
2381    
2382    Return the Key to be used for emergency tracing. This could be an IP address,
2383     a session ID, or a user name, depending on the environment.
2384    
2385    =over 4
2386    
2387    =item parameter
2388    
2389    Parameter defining the method for finding the tracing key. If it is a scalar,
2390    then it is presumed to be the tracing key itself. If it is a CGI object, then
2391    the tracing key is taken from the C<IP> cookie. Otherwise, the tracing key is
2392    taken from the C<TRACING> environment variable.
2393    
2394    =item RETURN
2395    
2396    Returns the key to be used for labels in emergency tracing.
2397    
2398    =back
2399    
2400    =cut
2401    
2402    sub EmergencyKey {
2403        # Get the parameters.
2404        my ($parameter) = @_;
2405        # Declare the return variable.
2406        my $retVal;
2407        # Determine the parameter type.
2408        if (! defined $parameter) {
2409            # Here we're supposed to check the environment.
2410            $retVal = $ENV{TRACING};
2411        } else {
2412            my $ptype = ref $parameter;
2413            if ($ptype eq 'CGI') {
2414                # Here we were invoked from a web page. Look for a cookie.
2415                $retVal = $parameter->cookie('IP');
2416            } elsif (! $ptype) {
2417                # Here the key was passed in.
2418                $retVal = $parameter;
2419            }
2420        }
2421        # If no luck finding a key, use the PID.
2422        if (! defined $retVal) {
2423            $retVal = $$;
2424        }
2425        # Return the result.
2426        return $retVal;
2427    }
2428    
2429    
2430    =head3 TraceParms
2431    
2432    C<< Tracer::TraceParms($cgi); >>
2433    
2434    Trace the CGI parameters at trace level CGI => 3 and the environment variables
2435    at level CGI => 4.
2436    
2437    =over 4
2438    
2439    =item cgi
2440    
2441    CGI query object containing the parameters to trace.
2442    
2443    =back
2444    
2445    =cut
2446    
2447    sub TraceParms {
2448        # Get the parameters.
2449        my ($cgi) = @_;
2450        if (T(CGI => 3)) {
2451            # Here we want to trace the parameter data.
2452            my @names = $cgi->param;
2453            for my $parmName (sort @names) {
2454                # Note we skip the Trace parameters, which are for our use only.
2455                if ($parmName ne 'Trace' && $parmName ne 'TF') {
2456                    my @values = $cgi->param($parmName);
2457                    Trace("CGI: $parmName = " . join(", ", @values));
2458                }
2459            }
2460            # Display the request method.
2461            my $method = $cgi->request_method();
2462            Trace("Method: $method");
2463        }
2464        if (T(CGI => 4)) {
2465            # Here we want the environment data too.
2466            for my $envName (sort keys %ENV) {
2467                Trace("ENV: $envName = $ENV{$envName}");
2468            }
2469        }
2470    }
2471    
2472    =head3 ScriptFinish
2473    
2474    C<< ScriptFinish($webData, $varHash); >>
2475    
2476    Output a web page at the end of a script. Either the string to be output or the
2477    name of a template file can be specified. If the second parameter is omitted,
2478    it is assumed we have a string to be output; otherwise, it is assumed we have the
2479    name of a template file. The template should have the variable C<DebugData>
2480    specified in any form that invokes a standard script. If debugging mode is turned
2481    on, a form field will be put in that allows the user to enter tracing data.
2482    Trace messages will be placed immediately before the terminal C<BODY> tag in
2483    the output, formatted as a list.
2484    
2485    A typical standard script would loook like the following.
2486    
2487        BEGIN {
2488            # Print the HTML header.
2489            print "CONTENT-TYPE: text/html\n\n";
2490        }
2491        use Tracer;
2492        use CGI;
2493        use FIG;
2494        # ... more uses ...
2495    
2496        my ($cgi, $varHash) = ScriptSetup();
2497        eval {
2498            # ... get data from $cgi, put it in $varHash ...
2499        };
2500        if ($@) {
2501            Trace("Script Error: $@") if T(0);
2502        }
2503        ScriptFinish("Html/MyTemplate.html", $varHash);
2504    
2505    The idea here is that even if the script fails, you'll see trace messages and
2506    useful output.
2507    
2508    =over 4
2509    
2510    =item webData
2511    
2512    A string containing either the full web page to be written to the output or the
2513    name of a template file from which the page is to be constructed. If the name
2514    of a template file is specified, then the second parameter must be present;
2515    otherwise, it must be absent.
2516    
2517    =item varHash (optional)
2518    
2519    If specified, then a reference to a hash mapping variable names for a template
2520    to their values. The template file will be read into memory, and variable markers
2521    will be replaced by data in this hash reference.
2522    
2523    =back
2524    
2525    =cut
2526    
2527    sub ScriptFinish {
2528        # Get the parameters.
2529        my ($webData, $varHash) = @_;
2530        # Check for a template file situation.
2531        my $outputString;
2532        if (defined $varHash) {
2533            # Here we have a template file. We need to determine the template type.
2534            my $template;
2535            if ($FIG_Config::template_url && $webData =~ /\.php$/) {
2536                $template = "$FIG_Config::template_url/$webData";
2537            } else {
2538                $template = "<<$webData";
2539            }
2540            $outputString = PageBuilder::Build($template, $varHash, "Html");
2541        } else {
2542            # Here the user gave us a raw string.
2543            $outputString = $webData;
2544        }
2545        # Check for trace messages.
2546        if ($Destination ne "NONE" && $TraceLevel > 0) {
2547            # We have trace messages, so we want to put them at the end of the body. This
2548            # is either at the end of the whole string or at the beginning of the BODY
2549            # end-tag.
2550            my $pos = length $outputString;
2551            if ($outputString =~ m#</body>#gi) {
2552                $pos = (pos $outputString) - 7;
2553            }
2554            # If the trace messages were queued, we unroll them. Otherwise, we display the
2555            # destination.
2556            my $traceHtml;
2557            if ($Destination eq "QUEUE") {
2558                $traceHtml = QTrace('Html');
2559            } elsif ($Destination =~ /^>>(.+)$/) {
2560                # Here the tracing output it to a file. We code it as a hyperlink so the user
2561                # can copy the file name into the clipboard easily.
2562                my $actualDest = $1;
2563                $traceHtml = "<p>Tracing output to $actualDest.</p>\n";
2564            } else {
2565                # Here we have one of the special destinations.
2566                $traceHtml = "<P>Tracing output type is $Destination.</p>\n";
2567            }
2568            substr $outputString, $pos, 0, $traceHtml;
2569        }
2570        # Write the output string.
2571        print $outputString;
2572    }
2573    
2574    =head3 Insure
2575    
2576    C<< Insure($dirName); >>
2577    
2578    Insure a directory is present.
2579    
2580    =over 4
2581    
2582    =item dirName
2583    
2584    Name of the directory to check. If it does not exist, it will be created.
2585    
2586    =back
2587    
2588    =cut
2589    
2590    sub Insure {
2591        my ($dirName) = @_;
2592        if (! -d $dirName) {
2593            Trace("Creating $dirName directory.") if T(File => 2);
2594            eval { mkpath $dirName; };
2595            if ($@) {
2596                Confess("Error creating $dirName: $@");
2597            }
2598        }
2599    }
2600    
2601    =head3 ChDir
2602    
2603    C<< ChDir($dirName); >>
2604    
2605    Change to the specified directory.
2606    
2607    =over 4
2608    
2609    =item dirName
2610    
2611    Name of the directory to which we want to change.
2612    
2613    =back
2614    
2615    =cut
2616    
2617    sub ChDir {
2618        my ($dirName) = @_;
2619        if (! -d $dirName) {
2620            Confess("Cannot change to directory $dirName: no such directory.");
2621        } else {
2622            Trace("Changing to directory $dirName.") if T(File => 4);
2623            my $okFlag = chdir $dirName;
2624            if (! $okFlag) {
2625                Confess("Error switching to directory $dirName.");
2626            }
2627        }
2628    }
2629    
2630    =head3 SendSMS
2631    
2632    C<< my $msgID = Tracer::SendSMS($phoneNumber, $msg); >>
2633    
2634    Send a text message to a phone number using Clickatell. The FIG_Config file must contain the
2635    user name, password, and API ID for the relevant account in the hash reference variable
2636    I<$FIG_Config::phone>, using the keys C<user>, C<password>, and C<api_id>. For
2637    example, if the user name is C<BruceTheHumanPet>, the password is C<silly>, and the API ID
2638    is C<2561022>, then the FIG_Config file must contain
2639    
2640        $phone =  { user => 'BruceTheHumanPet',
2641                    password => 'silly',
2642                    api_id => '2561022' };
2643    
2644    The original purpose of this method was to insure Bruce would be notified immediately when the
2645    Sprout Load terminates. Care should be taken if you do not wish Bruce to be notified immediately
2646    when you call this method.
2647    
2648    The message ID will be returned if successful, and C<undef> if an error occurs.
2649    
2650    =over 4
2651    
2652    =item phoneNumber
2653    
2654    Phone number to receive the message, in international format. A United States phone number
2655    would be prefixed by "1". A British phone number would be prefixed by "44".
2656    
2657    =item msg
2658    
2659    Message to send to the specified phone.
2660    
2661    =item RETURN
2662    
2663    Returns the message ID if successful, and C<undef> if the message could not be sent.
2664    
2665    =back
2666    
2667    =cut
2668    
2669    sub SendSMS {
2670        # Get the parameters.
2671        my ($phoneNumber, $msg) = @_;
2672        # Declare the return variable. If we do not change it, C<undef> will be returned.
2673        my $retVal;
2674        # Only proceed if we have phone support.
2675        if (! defined $FIG_Config::phone) {
2676            Trace("Phone support not present in FIG_Config.") if T(1);
2677        } else {
2678            # Get the phone data.
2679            my $parms = $FIG_Config::phone;
2680            # Get the Clickatell URL.
2681            my $url = "http://api.clickatell.com/http/";
2682            # Create the user agent.
2683            my $ua = LWP::UserAgent->new;
2684            # Request a Clickatell session.
2685            my $resp = $ua->post("$url/sendmsg", { user => $parms->{user},
2686                                         password => $parms->{password},
2687                                         api_id => $parms->{api_id},
2688                                         to => $phoneNumber,
2689                                         text => $msg});
2690            # Check for an error.
2691            if (! $resp->is_success) {
2692                Trace("Alert failed.") if T(1);
2693            } else {
2694                # Get the message ID.
2695                my $rstring = $resp->content;
2696                if ($rstring =~ /^ID:\s+(.*)$/) {
2697                    $retVal = $1;
2698                } else {
2699                    Trace("Phone attempt failed with $rstring") if T(1);
2700                }
2701            }
2702        }
2703        # Return the result.
2704        return $retVal;
2705    }
2706    
2707    =head3 CommaFormat
2708    
2709    C<< my $formatted = Tracer::CommaFormat($number); >>
2710    
2711    Insert commas into a number.
2712    
2713    =over 4
2714    
2715    =item number
2716    
2717    A sequence of digits.
2718    
2719    =item RETURN
2720    
2721    Returns the same digits with commas strategically inserted.
2722    
2723    =back
2724    
2725    =cut
2726    
2727    sub CommaFormat {
2728        # Get the parameters.
2729        my ($number) = @_;
2730        # Pad the length up to a multiple of three.
2731        my $padded = "$number";
2732        $padded = " " . $padded while length($padded) % 3 != 0;
2733        # This is a fancy PERL trick. The parentheses in the SPLIT pattern
2734        # cause the delimiters to be included in the output stream. The
2735        # GREP removes the empty strings in between the delimiters.
2736        my $retVal = join(",", grep { $_ ne '' } split(/(...)/, $padded));
2737        # Clean out the spaces.
2738        $retVal =~ s/ //g;
2739        # Return the result.
2740        return $retVal;
2741    }
2742    =head3 SetPermissions
2743    
2744    C<< Tracer::SetPermissions($dirName, $group, $mask, %otherMasks); >>
2745    
2746    Set the permissions for a directory and all the files and folders inside it.
2747    In addition, the group ownership will be changed to the specified value.
2748    
2749    This method is more vulnerable than most to permission and compatability
2750    problems, so it does internal error recovery.
2751    
2752    =over 4
2753    
2754    =item dirName
2755    
2756    Name of the directory to process.
2757    
2758    =item group
2759    
2760    Name of the group to be assigned.
2761    
2762    =item mask
2763    
2764    Permission mask. Bits that are C<1> in this mask will be ORed into the
2765    permission bits of any file or directory that does not already have them
2766    set to 1.
2767    
2768    =item otherMasks
2769    
2770    Map of search patterns to permission masks. If a directory name matches
2771    one of the patterns, that directory and all its members and subdirectories
2772    will be assigned the new pattern. For example, the following would
2773    assign 01664 to most files, but would use 01777 for directories named C<tmp>.
2774    
2775        Tracer::SetPermissions($dirName, 'fig', 01664, '^tmp$' => 01777);
2776    
2777    The list is ordered, so the following would use 0777 for C<tmp1> and
2778    0666 for C<tmp>, C<tmp2>, or C<tmp3>.
2779    
2780        Tracer::SetPermissions($dirName, 'fig', 01664, '^tmp1' => 0777,
2781                                                       '^tmp' => 0666);
2782    
2783    Note that the pattern matches are all case-insensitive, and only directory
2784    names are matched, not file names.
2785    
2786    =back
2787    
2788    =cut
2789    
2790    sub SetPermissions {
2791        # Get the parameters.
2792        my ($dirName, $group, $mask, @otherMasks) = @_;
2793        # Set up for error recovery.
2794        eval {
2795            # Switch to the specified directory.
2796            ChDir($dirName);
2797            # Get the group ID.
2798            my $gid = getgrnam($group);
2799            # Get the mask for tracing.
2800            my $traceMask = sprintf("%04o", $mask) . "($mask)";
2801            Trace("Fixing permissions for directory $dirName using group $group($gid) and mask $traceMask.") if T(File => 2);
2802            my $fixCount = 0;
2803            my $lookCount = 0;
2804            # @dirs will be a stack of directories to be processed.
2805            my @dirs = (getcwd());
2806            while (scalar(@dirs) > 0) {
2807                # Get the current directory.
2808                my $dir = pop @dirs;
2809                # Check for a match to one of the specified directory names. To do
2810                # that, we need to pull the individual part of the name off of the
2811                # whole path.
2812                my $simpleName = $dir;
2813                if ($dir =~ m!/([^/]+)$!) {
2814                    $simpleName = $1;
2815                }
2816                Trace("Simple directory name for $dir is $simpleName.") if T(File => 4);
2817                # Search for a match.
2818                my $match = 0;
2819                my $i;
2820                for ($i = 0; $i < $#otherMasks && ! $match; $i += 2) {
2821                    my $pattern = $otherMasks[$i];
2822                    if ($simpleName =~ /$pattern/i) {
2823                        $match = 1;
2824                    }
2825                }
2826                # Check for a match. Note we use $i-1 because the loop added 2
2827                # before terminating due to the match.
2828                if ($match && $otherMasks[$i-1] != $mask) {
2829                    # This directory matches one of the incoming patterns, and it's
2830                    # a different mask, so we process it recursively with that mask.
2831                    SetPermissions($dir, $group, $otherMasks[$i-1], @otherMasks);
2832                } else {
2833                    # Here we can process normally. Get all of the non-hidden members.
2834                    my @submems = OpenDir($dir, 1);
2835                    for my $submem (@submems) {
2836                        # Get the full name.
2837                        my $thisMem = "$dir/$submem";
2838                        Trace("Checking member $thisMem.") if T(4);
2839                        $lookCount++;
2840                        if ($lookCount % 1000 == 0) {
2841                            Trace("$lookCount members examined. Current is $thisMem. Mask is $traceMask") if T(File => 3);
2842                        }
2843                        # Fix the group.
2844                        chown -1, $gid, $thisMem;
2845                        # Insure this member is not a symlink.
2846                        if (! -l $thisMem) {
2847                            # Get its info.
2848                            my $fileInfo = stat $thisMem;
2849                            # Only proceed if we got the info. Otherwise, it's a hard link
2850                            # and we want to skip it anyway.
2851                            if ($fileInfo) {
2852                                my $fileMode = $fileInfo->mode;
2853                                if (($fileMode & $mask) != $mask) {
2854                                    # Fix this member.
2855                                    $fileMode |= $mask;
2856                                    chmod $fileMode, $thisMem;
2857                                    $fixCount++;
2858                                }
2859                                # If it's a subdirectory, stack it.
2860                                if (-d $thisMem) {
2861                                    push @dirs, $thisMem;
2862                                }
2863                            }
2864                        }
2865                    }
2866                }
2867            }
2868            Trace("$lookCount files and directories processed, $fixCount fixed.") if T(File => 2);
2869        };
2870        # Check for an error.
2871        if ($@) {
2872            Confess("SetPermissions error: $@");
2873        }
2874    }
2875    
2876    =head3 CompareLists
2877    
2878    C<< my ($inserted, $deleted) = Tracer::CompareLists(\@newList, \@oldList, $keyIndex); >>
2879    
2880    Compare two lists of tuples, and return a hash analyzing the differences. The lists
2881    are presumed to be sorted alphabetically by the value in the $keyIndex column.
2882    The return value contains a list of items that are only in the new list
2883    (inserted) and only in the old list (deleted).
2884    
2885    =over 4
2886    
2887    =item newList
2888    
2889    Reference to a list of new tuples.
2890    
2891    =item oldList
2892    
2893    Reference to a list of old tuples.
2894    
2895    =item keyIndex (optional)
2896    
2897    Index into each tuple of its key field. The default is 0.
2898    
2899    =item RETURN
2900    
2901    Returns a 2-tuple consisting of a reference to the list of items that are only in the new
2902    list (inserted) followed by a reference to the list of items that are only in the old
2903    list (deleted).
2904    
2905    =back
2906    
2907    =cut
2908    
2909    sub CompareLists {
2910        # Get the parameters.
2911        my ($newList, $oldList, $keyIndex) = @_;
2912        if (! defined $keyIndex) {
2913            $keyIndex = 0;
2914        }
2915        # Declare the return variables.
2916        my ($inserted, $deleted) = ([], []);
2917        # Loop through the two lists simultaneously.
2918        my ($newI, $oldI) = (0, 0);
2919        my ($newN, $oldN) = (scalar @{$newList}, scalar @{$oldList});
2920        while ($newI < $newN || $oldI < $oldN) {
2921            # Get the current object in each list. Note that if one
2922            # of the lists is past the end, we'll get undef.
2923            my $newItem = $newList->[$newI];
2924            my $oldItem = $oldList->[$oldI];
2925            if (! defined($newItem) || defined($oldItem) && $newItem->[$keyIndex] gt $oldItem->[$keyIndex]) {
2926                # The old item is not in the new list, so mark it deleted.
2927                push @{$deleted}, $oldItem;
2928                $oldI++;
2929            } elsif (! defined($oldItem) || $oldItem->[$keyIndex] gt $newItem->[$keyIndex]) {
2930                # The new item is not in the old list, so mark it inserted.
2931                push @{$inserted}, $newItem;
2932                $newI++;
2933            } else {
2934                # The item is in both lists, so push forward.
2935                $oldI++;
2936                $newI++;
2937            }
2938        }
2939        # Return the result.
2940        return ($inserted, $deleted);
2941    }
2942    
2943    =head3 GetLine
2944    
2945    C<< my @data = Tracer::GetLine($handle); >>
2946    
2947    Read a line of data from a tab-delimited file.
2948    
2949    =over 4
2950    
2951    =item handle
2952    
2953    Open file handle from which to read.
2954    
2955    =item RETURN
2956    
2957    Returns a list of the fields in the record read. The fields are presumed to be
2958    tab-delimited. If we are at the end of the file, then an empty list will be
2959    returned. If an empty line is read, a single list item consisting of a null
2960    string will be returned.
2961    
2962    =back
2963    
2964    =cut
2965    
2966    sub GetLine {
2967        # Get the parameters.
2968        my ($handle) = @_;
2969        # Declare the return variable.
2970        my @retVal = ();
2971        Trace("File position is " . tell($handle) . ". EOF flag is " . eof($handle) . ".") if T(File => 4);
2972        # Read from the file.
2973        my $line = <$handle>;
2974        # Only proceed if we found something.
2975        if (defined $line) {
2976            # Remove the new-line. We are a bit over-cautious here because the file may be coming in via an
2977            # upload control and have a nonstandard EOL combination.
2978            $line =~ s/(\r|\n)+$//;
2979            # Here we do some fancy tracing to help in debugging complicated EOL marks.
2980            if (T(File => 4)) {
2981                my $escapedLine = $line;
2982                $escapedLine =~ s/\n/\\n/g;
2983                $escapedLine =~ s/\r/\\r/g;
2984                $escapedLine =~ s/\t/\\t/g;
2985                Trace("Line read: -->$escapedLine<--");
2986            }
2987            # If the line is empty, return a single empty string; otherwise, parse
2988            # it into fields.
2989            if ($line eq "") {
2990                push @retVal, "";
2991            } else {
2992                push @retVal, split /\t/,$line;
2993            }
2994        } else {
2995            # Trace the reason the read failed.
2996            Trace("End of file: $!") if T(File => 3);
2997        }
2998        # Return the result.
2999        return @retVal;
3000    }
3001    
3002    =head3 PutLine
3003    
3004    C<< Tracer::PutLine($handle, \@fields, $eol); >>
3005    
3006    Write a line of data to a tab-delimited file. The specified field values will be
3007    output in tab-separated form, with a trailing new-line.
3008    
3009    =over 4
3010    
3011    =item handle
3012    
3013    Output file handle.
3014    
3015    =item fields
3016    
3017    List of field values.
3018    
3019    =item eol (optional)
3020    
3021    End-of-line character (default is "\n").
3022    
3023    =back
3024    
3025    =cut
3026    
3027    sub PutLine {
3028        # Get the parameters.
3029        my ($handle, $fields, $eol) = @_;
3030        # Write the data.
3031        print $handle join("\t", @{$fields}) . ($eol || "\n");
3032    }
3033    
3034    =head3 GenerateURL
3035    
3036    C<< my $queryUrl = Tracer::GenerateURL($page, %parameters); >>
3037    
3038    Generate a GET-style URL for the specified page with the specified parameter
3039    names and values. The values will be URL-escaped automatically. So, for
3040    example
3041    
3042        Tracer::GenerateURL("form.cgi", type => 1, string => "\"high pass\" or highway")
3043    
3044    would return
3045    
3046        form.cgi?type=1;string=%22high%20pass%22%20or%20highway
3047    
3048    =over 4
3049    
3050    =item page
3051    
3052    Page URL.
3053    
3054    =item parameters
3055    
3056    Hash mapping parameter names to parameter values.
3057    
3058    =item RETURN
3059    
3060    Returns a GET-style URL that goes to the specified page and passes in the
3061    specified parameters and values.
3062    
3063    =back
3064    
3065    =cut
3066    
3067    sub GenerateURL {
3068        # Get the parameters.
3069        my ($page, %parameters) = @_;
3070        # Prime the return variable with the page URL.
3071        my $retVal = $page;
3072        # Loop through the parameters, creating parameter elements in a list.
3073        my @parmList = map { "$_=" . uri_escape($parameters{$_}) } keys %parameters;
3074        # If the list is nonempty, tack it on.
3075        if (@parmList) {
3076            $retVal .= "?" . join(";", @parmList);
3077        }
3078        # Return the result.
3079        return $retVal;
3080    }
3081    
3082    =head3 ApplyURL
3083    
3084    C<< Tracer::ApplyURL($table, $target, $url); >>
3085    
3086    Run through a two-dimensional table (or more accurately, a list of lists), converting the
3087    I<$target> column to HTML text having a hyperlink to a URL in the I<$url> column. The
3088    URL column will be deleted by this process and the target column will be HTML-escaped.
3089    
3090    This provides a simple way to process the results of a database query into something
3091    displayable by combining a URL with text.
3092    
3093    =over 4
3094    
3095    =item table
3096    
3097    Reference to a list of lists. The elements in the containing list will be updated by
3098    this method.
3099    
3100    =item target
3101    
3102    The index of the column to be converted into HTML.
3103    
3104    =item url
3105    
3106    The index of the column containing the URL. Note that the URL must have a recognizable
3107    C<http:> at the beginning.
3108    
3109    =back
3110    
3111    =cut
3112    
3113    sub ApplyURL {
3114        # Get the parameters.
3115        my ($table, $target, $url) = @_;
3116        # Loop through the table.
3117        for my $row (@{$table}) {
3118            # Apply the URL to the target cell.
3119            $row->[$target] = CombineURL($row->[$target], $row->[$url]);
3120            # Delete the URL from the row.
3121            delete $row->[$url];
3122        }
3123    }
3124    
3125    =head3 CombineURL
3126    
3127    C<< my $combinedHtml = Tracer::CombineURL($text, $url); >>
3128    
3129    This method will convert the specified text into HTML hyperlinked to the specified
3130    URL. The hyperlinking will only take place if the URL looks legitimate: that is, it
3131    is defined and begins with an C<http:> header.
3132    
3133    =over 4
3134    
3135    =item text
3136    
3137    Text to return. This will be HTML-escaped automatically.
3138    
3139    =item url
3140    
3141    A URL to be hyperlinked to the text. If it does not look like a URL, then the text
3142    will be returned without any hyperlinking.
3143    
3144    =item RETURN
3145    
3146    Returns the original text, HTML-escaped, with the URL hyperlinked to it. If the URL
3147    doesn't look right, the HTML-escaped text will be returned without any further
3148    modification.
3149    
3150    =back
3151    
3152    =cut
3153    
3154    sub CombineURL {
3155        # Get the parameters.
3156        my ($text, $url) = @_;
3157        # Declare the return variable.
3158        my $retVal = CGI::escapeHTML($text);
3159        # Verify the URL.
3160        if (defined($url) && $url =~ m!http://!i) {
3161            # It's good, so we apply it to the text.
3162            $retVal = "<a href=\"$url\">$retVal</a>";
3163        }
3164        # Return the result.
3165        return $retVal;
3166    }
3167    
3168  1;  1;

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