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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 $desc\n";
662            }
663            exit(0);
664        }
665        # Return the parsed parameters.
666        return ($retOptions, @retParameters);
667    }
668    
669  =head3 Setups  =head3 Setups
670    
671  C<< my $count = Tracer::Setups(); >>  C<< my $count = Tracer::Setups(); >>
# Line 348  Line 826 
826    
827  =head3 OpenDir  =head3 OpenDir
828    
829  C<< my @files = OpenDir($dirName, $filtered); >>  C<< my @files = OpenDir($dirName, $filtered, $flag); >>
830    
831  Open a directory and return all the file names. This function essentially performs  Open a directory and return all the file names. This function essentially performs
832  the functions of an C<opendir> and C<readdir>. If the I<$filtered> parameter is  the functions of an C<opendir> and C<readdir>. If the I<$filtered> parameter is
833  set to TRUE, all filenames beginning with a period (C<.>) will be filtered out of  set to TRUE, all filenames beginning with a period (C<.>), dollar sign (C<$>),
834  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
835  for example,  filtered out of the return list. If the directory does not open and I<$flag> is not
836    set, an exception is thrown. So, for example,
837    
838      my @files = OpenDir("/Volumes/fig/contigs", 1);      my @files = OpenDir("/Volumes/fig/contigs", 1);
839    
840  is effectively the same as  is effectively the same as
841    
842      opendir(TMP, "/Volumes/fig/contigs") || Confess("Could not open /Volumes/fig/contigs.");      opendir(TMP, "/Volumes/fig/contigs") || Confess("Could not open /Volumes/fig/contigs.");
843      my @files = grep { $_ !~ /^\./ } readdir(TMP);      my @files = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir(TMP);
844    
845  Similarly, the following code  Similarly, the following code
846    
847      my @files = grep { $_ =~ /^\d/ } OpenDir("/Volumes/fig/orgs");      my @files = grep { $_ =~ /^\d/ } OpenDir("/Volumes/fig/orgs", 0, 1);
848    
849  Returns the names of all files in C</Volumes/fig/orgs> that begin with digits and  Returns the names of all files in C</Volumes/fig/orgs> that begin with digits and
850  automatically throws an error if the directory fails to open.  automatically returns an empty list if the directory fails to open.
851    
852  =over 4  =over 4
853    
# Line 381  Line 860 
860  TRUE if files whose names begin with a period (C<.>) should be automatically removed  TRUE if files whose names begin with a period (C<.>) should be automatically removed
861  from the list, else FALSE.  from the list, else FALSE.
862    
863    =item flag
864    
865    TRUE if a failure to open is okay, else FALSE
866    
867  =back  =back
868    
869  =cut  =cut
870  #: Return Type @;  #: Return Type @;
871  sub OpenDir {  sub OpenDir {
872      # Get the parameters.      # Get the parameters.
873      my ($dirName, $filtered) = @_;      my ($dirName, $filtered, $flag) = @_;
874      # Declare the return variable.      # Declare the return variable.
875      my @retVal;      my @retVal = ();
876      # Open the directory.      # Open the directory.
877      if (opendir(my $dirHandle, $dirName)) {      if (opendir(my $dirHandle, $dirName)) {
878          # The directory opened successfully. Get the appropriate list according to the          # The directory opened successfully. Get the appropriate list according to the
879          # strictures of the filter parameter.          # strictures of the filter parameter.
880          if ($filtered) {          if ($filtered) {
881              @retVal = grep { $_ !~ /^\./ } readdir $dirHandle;              @retVal = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir $dirHandle;
882          } else {          } else {
883              @retVal = readdir $dirHandle;              @retVal = readdir $dirHandle;
884          }          }
885      } else {      } elsif (! $flag) {
886          # Here the directory would not open.          # Here the directory would not open and it's considered an error.
887          Confess("Could not open directory $dirName.");          Confess("Could not open directory $dirName.");
888      }      }
889      # Return the result.      # Return the result.
# Line 449  Line 932 
932      return $value;      return $value;
933  }  }
934    
935    =head3 ParseTraceDate
936    
937    C<< my $time = Tracer::ParseTraceDate($dateString); >>
938    
939    Convert a date from the trace file into a PERL timestamp.
940    
941    =over 4
942    
943    =item dateString
944    
945    The date string from the trace file. The format of the string is determined by the
946    L</Now> method.
947    
948    =item RETURN
949    
950    Returns a PERL time, that is, a number of seconds since the epoch, or C<undef> if
951    the time string is invalid.
952    
953    =cut
954    
955    sub ParseTraceDate {
956        # Get the parameters.
957        my ($dateString) = @_;
958        # Declare the return variable.
959        my $retVal;
960        # Parse the date.
961        if ($dateString =~ m#(\d+)/(\d+)/(\d+)\s+(\d+):(\d+):(\d+)#) {
962            # Create a time object. Note we need to convert the day, month,
963            # and year to a different base. Years count from 1900, and
964            # the internal month value is relocated to January = 0.
965            $retVal = timelocal($6, $5, $4, $2, $1 - 1, $3 - 1900);
966        }
967        # Return the result.
968        return $retVal;
969    }
970    
971  =head3 LogErrors  =head3 LogErrors
972    
973  C<< Tracer::LogErrors($fileName); >>  C<< Tracer::LogErrors($fileName); >>
# Line 651  Line 1170 
1170      # Get the timestamp.      # Get the timestamp.
1171      my $timeStamp = Now();      my $timeStamp = Now();
1172      # 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.
1173      my $formatted = "$timeStamp <$LastCategory>: " . Strip($message);      my $formatted = "[$timeStamp] <$LastCategory>: " . Strip($message);
1174      # Process according to the destination.      # Process according to the destination.
1175      if ($Destination eq "TEXT") {      if ($Destination eq "TEXT") {
1176          # Write the message to the standard output.          # Write the message to the standard output.
# Line 738  Line 1257 
1257          # Convert it to lower case before we hash it.          # Convert it to lower case before we hash it.
1258          $category = lc $category;          $category = lc $category;
1259          # Use the category and tracelevel to compute the result.          # Use the category and tracelevel to compute the result.
1260            if (ref $traceLevel) {
1261                Confess("Bad trace level.");
1262            } elsif (ref $TraceLevel) {
1263                Confess("Bad trace config.");
1264            }
1265          $retVal = ($traceLevel <= $TraceLevel && ($AllTrace || exists $Categories{$category}));          $retVal = ($traceLevel <= $TraceLevel && ($AllTrace || exists $Categories{$category}));
1266      }      }
1267      # Return the computed result.      # Return the computed result.
# Line 824  Line 1348 
1348    
1349  C<< my $codedString = Tracer::Escape($realString); >>  C<< my $codedString = Tracer::Escape($realString); >>
1350    
1351  Escape a string for use in a command length. Spaces will be replaced by C<\b>,  Escape a string for use in a command length. Tabs will be replaced by C<\t>, new-lines
1352  tabs replaced by C<\t>, new-lines replaced by C<\n>, and backslashes will be  replaced by C<\n>, carriage returns will be deleted, and backslashes will be doubled. The
1353  doubled. The effect is to exactly reverse the effect of L</UnEscape>.  result is to reverse the effect of L</UnEscape>.
1354    
1355  =over 4  =over 4
1356    
# Line 850  Line 1374 
1374      # Loop through the parameter string, looking for sequences to escape.      # Loop through the parameter string, looking for sequences to escape.
1375      while (length $realString > 0) {      while (length $realString > 0) {
1376          # Look for the first sequence to escape.          # Look for the first sequence to escape.
1377          if ($realString =~ /^(.*?)([ \n\t\\])/) {          if ($realString =~ /^(.*?)([\n\t\r\\])/) {
1378              # 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
1379              # 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.
1380              $retVal .= $1;              $retVal .= $1;
1381              # Strip the processed section off the real string.              # Strip the processed section off the real string.
1382              $realString = substr $realString, (length $2) + (length $1);              $realString = substr $realString, (length $2) + (length $1);
1383              # Encode the escape sequence.              # Get the matched character.
1384              my $char = $2;              my $char = $2;
1385              $char =~ tr/ \t\n/btn/;              # If we have a CR, we are done.
1386                if ($char ne "\r") {
1387                    # It's not a CR, so encode the escape sequence.
1388                    $char =~ tr/\t\n/tn/;
1389              $retVal .= "\\" . $char;              $retVal .= "\\" . $char;
1390                }
1391          } else {          } else {
1392              # 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
1393              # transferred unmodified.              # transferred unmodified.
# Line 875  Line 1403 
1403    
1404  C<< my $realString = Tracer::UnEscape($codedString); >>  C<< my $realString = Tracer::UnEscape($codedString); >>
1405    
1406  Replace escape sequences with their actual equivalents. C<\b> will be replaced by a space,  Replace escape sequences with their actual equivalents. C<\t> will be replaced by
1407  C<\t> by 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
1408    be deleted.
1409    
1410  =over 4  =over 4
1411    
# Line 896  Line 1425 
1425  sub UnEscape {  sub UnEscape {
1426      # Get the parameter.      # Get the parameter.
1427      my ($codedString) = @_;      my ($codedString) = @_;
     Tracer("Coded string is \"$codedString\".") if T(4);  
1428      # Initialize the return variable.      # Initialize the return variable.
1429      my $retVal = "";      my $retVal = "";
1430      # Only proceed if the incoming string is nonempty.      # Only proceed if the incoming string is nonempty.
1431      if (defined $codedString) {      if (defined $codedString) {
1432          # Loop through the parameter string, looking for escape sequences. We can't do          # Loop through the parameter string, looking for escape sequences. We can't do
1433          # translating because it causes problems with the escaped slash. ("\\b" becomes          # translating because it causes problems with the escaped slash. ("\\t" becomes
1434          # "\ " no matter what we do.)          # "\<tab>" no matter what we do.)
1435          while (length $codedString > 0) {          while (length $codedString > 0) {
1436              # Look for the first escape sequence.              # Look for the first escape sequence.
1437              if ($codedString =~ /^(.*?)\\(\\|b|n|t)/) {              if ($codedString =~ /^(.*?)\\(\\|n|t|r)/) {
1438                  # 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
1439                  # 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.
1440                  $retVal .= $1;                  $retVal .= $1;
1441                  $codedString = substr $codedString, (2 + length $1);                  $codedString = substr $codedString, (2 + length $1);
1442                  # Decode the escape sequence.                  # Get the escape value.
1443                  my $char = $2;                  my $char = $2;
1444                  $char =~ tr/\\btn/\\ \t\n/;                  # If we have a "\r", we are done.
1445                    if ($char ne 'r') {
1446                        # Here it's not an 'r', so we convert it.
1447                        $char =~ tr/\\tn/\\\t\n/;
1448                  $retVal .= $char;                  $retVal .= $char;
1449                    }
1450              } else {              } else {
1451                  # 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
1452                  # transferred unmodified.                  # transferred unmodified.
# Line 1020  Line 1552 
1552      return @inputList;      return @inputList;
1553  }  }
1554    
1555    =head3 Percent
1556    
1557    C<< my $percent = Tracer::Percent($number, $base); >>
1558    
1559    Returns the percent of the base represented by the given number. If the base
1560    is zero, returns zero.
1561    
1562    =over 4
1563    
1564    =item number
1565    
1566    Percent numerator.
1567    
1568    =item base
1569    
1570    Percent base.
1571    
1572    =item RETURN
1573    
1574    Returns the percentage of the base represented by the numerator.
1575    
1576    =back
1577    
1578    =cut
1579    
1580    sub Percent {
1581        # Get the parameters.
1582        my ($number, $base) = @_;
1583        # Declare the return variable.
1584        my $retVal = 0;
1585        # Compute the percent.
1586        if ($base != 0) {
1587            $retVal = $number * 100 / $base;
1588        }
1589        # Return the result.
1590        return $retVal;
1591    }
1592    
1593  =head3 GetFile  =head3 GetFile
1594    
1595  C<< my @fileContents = Tracer::GetFile($fileName); >>  C<< my @fileContents = Tracer::GetFile($fileName); >>
1596    
1597  Return the entire contents of a file.      or
1598    
1599    C<< my $fileContents = Tracer::GetFile($fileName); >>
1600    
1601    Return the entire contents of a file. In list context, line-ends are removed and
1602    each line is a list element. In scalar context, line-ends are replaced by C<\n>.
1603    
1604  =over 4  =over 4
1605    
# Line 1035  Line 1610 
1610  =item RETURN  =item RETURN
1611    
1612  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.
1613  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
1614    the file, an empty list will be returned.
1615    
1616  =back  =back
1617    
# Line 1047  Line 1623 
1623      # Declare the return variable.      # Declare the return variable.
1624      my @retVal = ();      my @retVal = ();
1625      # Open the file for input.      # Open the file for input.
1626      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 {  
1627          # Read the whole file into the return variable, stripping off any terminator          # Read the whole file into the return variable, stripping off any terminator
1628          # characters.          # characters.
1629          my $lineCount = 0;          my $lineCount = 0;
1630          while (my $line = <INPUTFILE>) {      while (my $line = <$handle>) {
1631              $lineCount++;              $lineCount++;
1632              $line = Strip($line);              $line = Strip($line);
1633              push @retVal, $line;              push @retVal, $line;
1634          }          }
1635          # Close it.          # Close it.
1636          close INPUTFILE;      close $handle;
1637          my $actualLines = @retVal;          my $actualLines = @retVal;
1638      }      Trace("$actualLines lines read from file $fileName.") if T(File => 2);
1639      # Return the file's contents in the desired format.      # Return the file's contents in the desired format.
1640      if (wantarray) {      if (wantarray) {
1641          return @retVal;          return @retVal;
# Line 1072  Line 1644 
1644      }      }
1645  }  }
1646    
1647    =head3 PutFile
1648    
1649    C<< Tracer::PutFile($fileName, \@lines); >>
1650    
1651    Write out a file from a list of lines of text.
1652    
1653    =over 4
1654    
1655    =item fileName
1656    
1657    Name of the output file.
1658    
1659    =item lines
1660    
1661    Reference to a list of text lines. The lines will be written to the file in order, with trailing
1662    new-line characters. Alternatively, may be a string, in which case the string will be written without
1663    modification.
1664    
1665    =back
1666    
1667    =cut
1668    
1669    sub PutFile {
1670        # Get the parameters.
1671        my ($fileName, $lines) = @_;
1672        # Open the output file.
1673        my $handle = Open(undef, ">$fileName");
1674        # Count the lines written.
1675        if (ref $lines ne 'ARRAY') {
1676            # Here we have a scalar, so we write it raw.
1677            print $handle $lines;
1678            Trace("Scalar put to file $fileName.") if T(File => 3);
1679        } else {
1680            # Write the lines one at a time.
1681            my $count = 0;
1682            for my $line (@{$lines}) {
1683                print $handle "$line\n";
1684                $count++;
1685            }
1686            Trace("$count lines put to file $fileName.") if T(File => 3);
1687        }
1688        # Close the output file.
1689        close $handle;
1690    }
1691    
1692  =head3 QTrace  =head3 QTrace
1693    
1694  C<< my $data = QTrace($format); >>  C<< my $data = QTrace($format); >>
# Line 1151  Line 1768 
1768  C<< Assert($condition1, $condition2, ... $conditionN); >>  C<< Assert($condition1, $condition2, ... $conditionN); >>
1769    
1770  Return TRUE if all the conditions are true. This method can be used in conjunction with  Return TRUE if all the conditions are true. This method can be used in conjunction with
1771  the OR operator and the L</Confess> method, B<Assert> can function as a debugging assert.  the OR operator and the L</Confess> method as a debugging assert.
1772  So, for example  So, for example
1773    
1774  C<< Assert($recNum >= 0) || Confess("Invalid record number $recNum."); >>  C<< Assert($recNum >= 0) || Confess("Invalid record number $recNum."); >>
# Line 1272  Line 1889 
1889    
1890  =head3 AddToListMap  =head3 AddToListMap
1891    
1892  C<< Tracer::AddToListMap(\%hash, $key, $value); >>  C<< Tracer::AddToListMap(\%hash, $key, $value1, $value2, ... valueN); >>
1893    
1894  Add a key-value pair to a hash of lists. If no value exists for the key, a singleton list  Add a key-value pair to a hash of lists. If no value exists for the key, a singleton list
1895  is created for the key. Otherwise, the new value is pushed onto the list.  is created for the key. Otherwise, the new value is pushed onto the list.
# Line 1287  Line 1904 
1904    
1905  Key for which the value is to be added.  Key for which the value is to be added.
1906    
1907  =item value  =item value1, value2, ... valueN
1908    
1909  Value to add to the key's value list.  List of values to add to the key's value list.
1910    
1911  =back  =back
1912    
# Line 1297  Line 1914 
1914    
1915  sub AddToListMap {  sub AddToListMap {
1916      # Get the parameters.      # Get the parameters.
1917      my ($hash, $key, $value) = @_;      my ($hash, $key, @values) = @_;
1918      # Process according to whether or not the key already has a value.      # Process according to whether or not the key already has a value.
1919      if (! exists $hash->{$key}) {      if (! exists $hash->{$key}) {
1920          $hash->{$key} = [$value];          $hash->{$key} = [@values];
1921      } else {      } else {
1922          push @{$hash->{$key}}, $value;          push @{$hash->{$key}}, @values;
1923      }      }
1924  }  }
1925    
# Line 1310  Line 1927 
1927    
1928  C<< if (Tracer::DebugMode) { ...code... } >>  C<< if (Tracer::DebugMode) { ...code... } >>
1929    
1930  Return TRUE if debug mode has been turned on, else output an error  Return TRUE if debug mode has been turned on, else abort.
 page and return FALSE.  
1931    
1932  Certain CGI scripts are too dangerous to exist in the production  Certain CGI scripts are too dangerous to exist in the production
1933  environment. This method provides a simple way to prevent them  environment. This method provides a simple way to prevent them
1934  from working unless they are explicitly turned on by creating a password  from working unless they are explicitly turned on by creating a password
1935  cookie via the B<SetPassword> script.  If debugging mode  cookie via the B<SetPassword> script.  If debugging mode
1936  is not turned on, an error web page will be output directing the  is not turned on, an error will occur.
 user to enter in the correct password.  
1937    
1938  =cut  =cut
1939    
# Line 1331  Line 1946 
1946      if ($encrypted eq "252dec43280e0c0d6a75ffcec486e61d") {      if ($encrypted eq "252dec43280e0c0d6a75ffcec486e61d") {
1947          $retVal = 1;          $retVal = 1;
1948      } else {      } else {
1949          # Here debug mode is off, so we generate an error page.          # Here debug mode is off, so we generate an error.
1950          my $pageString = PageBuilder::Build("<Html/ErrorPage.html", {}, "Html");          Confess("Cannot use this facility without logging in.");
         print $pageString;  
1951      }      }
1952      # Return the determination indicator.      # Return the determination indicator.
1953      return $retVal;      return $retVal;
# Line 1364  Line 1978 
1978  sub Strip {  sub Strip {
1979      # Get a copy of the parameter string.      # Get a copy of the parameter string.
1980      my ($string) = @_;      my ($string) = @_;
1981      my $retVal = $string;      my $retVal = (defined $string ? $string : "");
1982      # Strip the line terminator characters.      # Strip the line terminator characters.
1983      $retVal =~ s/(\r|\n)+$//g;      $retVal =~ s/(\r|\n)+$//g;
1984      # Return the result.      # Return the result.
# Line 1432  Line 2046 
2046      return $retVal;      return $retVal;
2047  }  }
2048    
2049    =head3 EOF
2050    
2051    This is a constant that is lexically greater than any useful string.
2052    
2053    =cut
2054    
2055    sub EOF {
2056        return "\xFF\xFF\xFF\xFF\xFF";
2057    }
2058    
2059  =head3 TICK  =head3 TICK
2060    
2061  C<< my @results = TICK($commandString); >>  C<< my @results = TICK($commandString); >>
# Line 1473  Line 2097 
2097      return `$commandString`;      return `$commandString`;
2098  }  }
2099    
2100    =head3 ScriptSetup
2101    
2102    C<< my ($cgi, $varHash) = ScriptSetup($noTrace); >>
2103    
2104    Perform standard tracing and debugging setup for scripts. The value returned is
2105    the CGI object followed by a pre-built variable hash.
2106    
2107    The C<Trace> form parameter is used to determine whether or not tracing is active and
2108    which trace modules (other than C<Tracer> itself) should be turned on. Specifying
2109    the C<CGI> trace module will trace parameter and environment information. Parameters are
2110    traced at level 3 and environment variables at level 4. To trace to a file instead of to
2111    the web page, set C<TF> to 1. At the end of the script, the client should call
2112    L</ScriptFinish> to output the web page.
2113    
2114    In some situations, it is not practical to invoke tracing via form parameters. For this
2115    situation, you can turn on emergency tracing from the debugging control panel.
2116    Tracing will then be turned on automatically for all programs that use the L</ETracing>
2117    method, which includes every program that uses this method or L</StandardSetup>.
2118    
2119    =over 4
2120    
2121    =item noTrace (optional)
2122    
2123    If specified, tracing will be suppressed. This is useful if the script wants to set up
2124    tracing manually.
2125    
2126    =item RETURN
2127    
2128    Returns a two-element list consisting of a CGI query object and a variable hash for
2129    the output page.
2130    
2131    =back
2132    
2133    =cut
2134    
2135    sub ScriptSetup {
2136        # Get the parameters.
2137        my ($noTrace) = @_;
2138        # Get the CGI query object.
2139        my $cgi = CGI->new();
2140        # Set up tracing if it's not suppressed.
2141        ETracing($cgi) unless $noTrace;
2142        # Create the variable hash.
2143        my $varHash = { results => '' };
2144        # Return the query object and variable hash.
2145        return ($cgi, $varHash);
2146    }
2147    
2148    =head3 ETracing
2149    
2150    C<< ETracing($parameter); >>
2151    
2152    Set up emergency tracing. Emergency tracing is tracing that is turned
2153    on automatically for any program that calls this method. The emergency
2154    tracing parameters are stored in a a file identified by a tracing key.
2155    If this method is called with a CGI object, then the tracing key is
2156    taken from a cookie. If it is called with no parameters, then the tracing
2157    key is taken from an environment variable. If it is called with a string,
2158    the tracing key is that string.
2159    
2160    =over 4
2161    
2162    =item parameter
2163    
2164    A parameter from which the tracing key is computed. If it is a scalar,
2165    that scalar is used as the tracing key. If it is a CGI object, the
2166    tracing key is taken from the C<IP> cookie. If it is omitted, the
2167    tracing key is taken from the C<TRACING> environment variable. If it
2168    is a CGI object and emergency tracing is not on, the C<Trace> and
2169    C<TF> parameters will be used to determine the type of tracing.
2170    
2171    =back
2172    
2173    =cut
2174    
2175    sub ETracing {
2176        # Get the parameter.
2177        my ($parameter) = @_;
2178        # Check for CGI mode.
2179        my $cgi = (ref $parameter eq 'CGI' ? $parameter : undef);
2180        # Default to no tracing except errors.
2181        my ($tracing, $dest) = ("0", "WARN");
2182        # Check for emergency tracing.
2183        my $tkey = EmergencyKey($parameter);
2184        my $emergencyFile = EmergencyFileName($tkey);
2185        if (-e $emergencyFile) {
2186            # We have the file. Read in the data.
2187            my @tracing = GetFile($emergencyFile);
2188            # Pull off the time limit.
2189            my $expire = shift @tracing;
2190            # Convert it to seconds.
2191            $expire *= 3600;
2192            # Check the file data.
2193            my $stat = stat($emergencyFile);
2194            my ($now) = gettimeofday;
2195            if ($now - $stat->mtime > $expire) {
2196                # Delete the expired file.
2197                unlink $emergencyFile;
2198            } else {
2199                # Emergency tracing is on. Pull off the destination and
2200                # the trace level;
2201                $dest = shift @tracing;
2202                my $level = shift @tracing;
2203                # Convert the destination to a real tracing destination.
2204                # temp directory.
2205                $dest = EmergencyTracingDest($tkey, $dest);
2206                # Insure Tracer is specified.
2207                my %moduleHash = map { $_ => 1 } @tracing;
2208                $moduleHash{Tracer} = 1;
2209                # Set the trace parameter.
2210                $tracing = join(" ", $level, sort keys %moduleHash);
2211            }
2212        } elsif (defined $cgi) {
2213            # There's no emergency tracing, but we have a CGI object, so check
2214            # for tracing from the form parameters.
2215            if ($cgi->param('Trace')) {
2216                # Here the user has requested tracing via a form.
2217                $dest = ($cgi->param('TF') ? ">$FIG_Config::temp/Trace$$.log" : "QUEUE");
2218                $tracing = $cgi->param('Trace') . " Tracer";
2219            }
2220        }
2221        # Setup the tracing we've determined from all the stuff above.
2222        TSetup($tracing, $dest);
2223        # If we're a web script, trace the parameter and environment data.
2224        if (defined $cgi) {
2225            TraceParms($cgi);
2226        }
2227    }
2228    
2229    =head3 EmergencyFileName
2230    
2231    C<< my $fileName = Tracer::EmergencyFileName($tkey); >>
2232    
2233    Return the emergency tracing file name. This is the file that specifies
2234    the tracing information.
2235    
2236    =over 4
2237    
2238    =item tkey
2239    
2240    Tracing key for the current program.
2241    
2242    =item RETURN
2243    
2244    Returns the name of the file to contain the emergency tracing information.
2245    
2246    =back
2247    
2248    =cut
2249    
2250    sub EmergencyFileName {
2251        # Get the parameters.
2252        my ($tkey) = @_;
2253        # Compute the emergency tracing file name.
2254        return "$FIG_Config::temp/Emergency$tkey.txt";
2255    }
2256    
2257    =head3 EmergencyFileTarget
2258    
2259    C<< my $fileName = Tracer::EmergencyFileTarget($tkey); >>
2260    
2261    Return the emergency tracing target file name. This is the file that receives
2262    the tracing output for file-based tracing.
2263    
2264    =over 4
2265    
2266    =item tkey
2267    
2268    Tracing key for the current program.
2269    
2270    =item RETURN
2271    
2272    Returns the name of the file to contain the trace output.
2273    
2274    =back
2275    
2276    =cut
2277    
2278    sub EmergencyFileTarget {
2279        # Get the parameters.
2280        my ($tkey) = @_;
2281        # Compute the emergency tracing file name.
2282        return "$FIG_Config::temp/trace$tkey.log";
2283    }
2284    
2285    =head3 EmergencyTracingDest
2286    
2287    C<< my $dest = Tracer::EmergencyTracingDest($tkey, $myDest); >>
2288    
2289    This method converts an emergency tracing destination to a real
2290    tracing destination. The main difference is that if the
2291    destination is C<FILE> or C<APPEND>, we convert it to file
2292    output.
2293    
2294    =over 4
2295    
2296    =item tkey
2297    
2298    Tracing key for this environment.
2299    
2300    =item myDest
2301    
2302    Destination from the emergency tracing file.
2303    
2304    =item RETURN
2305    
2306    Returns a destination that can be passed into L</TSetup>.
2307    
2308    =back
2309    
2310    =cut
2311    
2312    sub EmergencyTracingDest {
2313        # Get the parameters.
2314        my ($tkey, $myDest) = @_;
2315        # Declare the return variable.
2316        my $retVal;
2317        # Process according to the destination value.
2318        if ($myDest eq 'FILE') {
2319            $retVal = ">" . EmergencyFileTarget($tkey);
2320        } elsif ($myDest eq 'APPEND') {
2321            $retVal = ">>" . EmergencyFileTarget($tkey);
2322        } else {
2323            $retVal = $myDest;
2324        }
2325        # Return the result.
2326        return $retVal;
2327    }
2328    
2329    =head3 Emergency
2330    
2331    C<< Emergency($key, $hours, $dest, $level, @modules); >>
2332    
2333    Turn on emergency tracing. This method can only be invoked over the web and is
2334    should not be called if debug mode is off. The caller specifies the duration of the
2335    emergency in hours, the desired tracing destination, the trace level,
2336    and a list of the trace modules to activate. For the length of the duration, when a
2337    program in an environment with the specified tracing key active invokes a Sprout
2338    CGI script, tracing will be turned on automatically. See L</TSetup> for more
2339    about tracing setup and L</ETracing> for more about emergency tracing.
2340    
2341    =over 4
2342    
2343    =item tkey
2344    
2345    The tracing key. This is used to identify the control file and the trace file.
2346    
2347    =item hours
2348    
2349    Number of hours to keep emergency tracing alive.
2350    
2351    =item dest
2352    
2353    Tracing destination. If no path information is specified for a file
2354    destination, it is put in the FIG temporary directory.
2355    
2356    =item level
2357    
2358    Tracing level. A higher level means more trace messages.
2359    
2360    =item modules
2361    
2362    A list of the tracing modules to activate.
2363    
2364    =back
2365    
2366    =cut
2367    
2368    sub Emergency {
2369        # Get the parameters.
2370        my ($tkey, $hours, $dest, $level, @modules) = @_;
2371        # Create the emergency file.
2372        my $specFile = EmergencyFileName($tkey);
2373        my $outHandle = Open(undef, ">$specFile");
2374        print $outHandle join("\n", $hours, $dest, $level, @modules, "");
2375    }
2376    
2377    =head3 EmergencyKey
2378    
2379    C<< my $tkey = EmergencyKey($parameter); >>
2380    
2381    Return the Key to be used for emergency tracing. This could be an IP address,
2382     a session ID, or a user name, depending on the environment.
2383    
2384    =over 4
2385    
2386    =item parameter
2387    
2388    Parameter defining the method for finding the tracing key. If it is a scalar,
2389    then it is presumed to be the tracing key itself. If it is a CGI object, then
2390    the tracing key is taken from the C<IP> cookie. Otherwise, the tracing key is
2391    taken from the C<TRACING> environment variable.
2392    
2393    =item RETURN
2394    
2395    Returns the key to be used for labels in emergency tracing.
2396    
2397    =back
2398    
2399    =cut
2400    
2401    sub EmergencyKey {
2402        # Get the parameters.
2403        my ($parameter) = @_;
2404        # Declare the return variable.
2405        my $retVal;
2406        # Determine the parameter type.
2407        if (! defined $parameter) {
2408            # Here we're supposed to check the environment.
2409            $retVal = $ENV{TRACING};
2410        } else {
2411            my $ptype = ref $parameter;
2412            if ($ptype eq 'CGI') {
2413                # Here we were invoked from a web page. Look for a cookie.
2414                $retVal = $parameter->cookie('IP');
2415            } elsif (! $ptype) {
2416                # Here the key was passed in.
2417                $retVal = $parameter;
2418            }
2419        }
2420        # If no luck finding a key, use the PID.
2421        if (! defined $retVal) {
2422            $retVal = $$;
2423        }
2424        # Return the result.
2425        return $retVal;
2426    }
2427    
2428    
2429    =head3 TraceParms
2430    
2431    C<< Tracer::TraceParms($cgi); >>
2432    
2433    Trace the CGI parameters at trace level CGI => 3 and the environment variables
2434    at level CGI => 4.
2435    
2436    =over 4
2437    
2438    =item cgi
2439    
2440    CGI query object containing the parameters to trace.
2441    
2442    =back
2443    
2444    =cut
2445    
2446    sub TraceParms {
2447        # Get the parameters.
2448        my ($cgi) = @_;
2449        if (T(CGI => 3)) {
2450            # Here we want to trace the parameter data.
2451            my @names = $cgi->param;
2452            for my $parmName (sort @names) {
2453                # Note we skip the Trace parameters, which are for our use only.
2454                if ($parmName ne 'Trace' && $parmName ne 'TF') {
2455                    my @values = $cgi->param($parmName);
2456                    Trace("CGI: $parmName = " . join(", ", @values));
2457                }
2458            }
2459            # Display the request method.
2460            my $method = $cgi->request_method();
2461            Trace("Method: $method");
2462        }
2463        if (T(CGI => 4)) {
2464            # Here we want the environment data too.
2465            for my $envName (sort keys %ENV) {
2466                Trace("ENV: $envName = $ENV{$envName}");
2467            }
2468        }
2469    }
2470    
2471    =head3 ScriptFinish
2472    
2473    C<< ScriptFinish($webData, $varHash); >>
2474    
2475    Output a web page at the end of a script. Either the string to be output or the
2476    name of a template file can be specified. If the second parameter is omitted,
2477    it is assumed we have a string to be output; otherwise, it is assumed we have the
2478    name of a template file. The template should have the variable C<DebugData>
2479    specified in any form that invokes a standard script. If debugging mode is turned
2480    on, a form field will be put in that allows the user to enter tracing data.
2481    Trace messages will be placed immediately before the terminal C<BODY> tag in
2482    the output, formatted as a list.
2483    
2484    A typical standard script would loook like the following.
2485    
2486        BEGIN {
2487            # Print the HTML header.
2488            print "CONTENT-TYPE: text/html\n\n";
2489        }
2490        use Tracer;
2491        use CGI;
2492        use FIG;
2493        # ... more uses ...
2494    
2495        my ($cgi, $varHash) = ScriptSetup();
2496        eval {
2497            # ... get data from $cgi, put it in $varHash ...
2498        };
2499        if ($@) {
2500            Trace("Script Error: $@") if T(0);
2501        }
2502        ScriptFinish("Html/MyTemplate.html", $varHash);
2503    
2504    The idea here is that even if the script fails, you'll see trace messages and
2505    useful output.
2506    
2507    =over 4
2508    
2509    =item webData
2510    
2511    A string containing either the full web page to be written to the output or the
2512    name of a template file from which the page is to be constructed. If the name
2513    of a template file is specified, then the second parameter must be present;
2514    otherwise, it must be absent.
2515    
2516    =item varHash (optional)
2517    
2518    If specified, then a reference to a hash mapping variable names for a template
2519    to their values. The template file will be read into memory, and variable markers
2520    will be replaced by data in this hash reference.
2521    
2522    =back
2523    
2524    =cut
2525    
2526    sub ScriptFinish {
2527        # Get the parameters.
2528        my ($webData, $varHash) = @_;
2529        # Check for a template file situation.
2530        my $outputString;
2531        if (defined $varHash) {
2532            # Here we have a template file. We need to determine the template type.
2533            my $template;
2534            if ($FIG_Config::template_url && $webData =~ /\.php$/) {
2535                $template = "$FIG_Config::template_url/$webData";
2536            } else {
2537                $template = "<<$webData";
2538            }
2539            $outputString = PageBuilder::Build($template, $varHash, "Html");
2540        } else {
2541            # Here the user gave us a raw string.
2542            $outputString = $webData;
2543        }
2544        # Check for trace messages.
2545        if ($Destination ne "NONE" && $TraceLevel > 0) {
2546            # We have trace messages, so we want to put them at the end of the body. This
2547            # is either at the end of the whole string or at the beginning of the BODY
2548            # end-tag.
2549            my $pos = length $outputString;
2550            if ($outputString =~ m#</body>#gi) {
2551                $pos = (pos $outputString) - 7;
2552            }
2553            # If the trace messages were queued, we unroll them. Otherwise, we display the
2554            # destination.
2555            my $traceHtml;
2556            if ($Destination eq "QUEUE") {
2557                $traceHtml = QTrace('Html');
2558            } elsif ($Destination =~ /^>>(.+)$/) {
2559                # Here the tracing output it to a file. We code it as a hyperlink so the user
2560                # can copy the file name into the clipboard easily.
2561                my $actualDest = $1;
2562                $traceHtml = "<p>Tracing output to $actualDest.</p>\n";
2563            } else {
2564                # Here we have one of the special destinations.
2565                $traceHtml = "<P>Tracing output type is $Destination.</p>\n";
2566            }
2567            substr $outputString, $pos, 0, $traceHtml;
2568        }
2569        # Write the output string.
2570        print $outputString;
2571    }
2572    
2573    =head3 Insure
2574    
2575    C<< Insure($dirName); >>
2576    
2577    Insure a directory is present.
2578    
2579    =over 4
2580    
2581    =item dirName
2582    
2583    Name of the directory to check. If it does not exist, it will be created.
2584    
2585    =back
2586    
2587    =cut
2588    
2589    sub Insure {
2590        my ($dirName) = @_;
2591        if (! -d $dirName) {
2592            Trace("Creating $dirName directory.") if T(File => 2);
2593            eval { mkpath $dirName; };
2594            if ($@) {
2595                Confess("Error creating $dirName: $@");
2596            }
2597        }
2598    }
2599    
2600    =head3 ChDir
2601    
2602    C<< ChDir($dirName); >>
2603    
2604    Change to the specified directory.
2605    
2606    =over 4
2607    
2608    =item dirName
2609    
2610    Name of the directory to which we want to change.
2611    
2612    =back
2613    
2614    =cut
2615    
2616    sub ChDir {
2617        my ($dirName) = @_;
2618        if (! -d $dirName) {
2619            Confess("Cannot change to directory $dirName: no such directory.");
2620        } else {
2621            Trace("Changing to directory $dirName.") if T(File => 4);
2622            my $okFlag = chdir $dirName;
2623            if (! $okFlag) {
2624                Confess("Error switching to directory $dirName.");
2625            }
2626        }
2627    }
2628    
2629    =head3 SendSMS
2630    
2631    C<< my $msgID = Tracer::SendSMS($phoneNumber, $msg); >>
2632    
2633    Send a text message to a phone number using Clickatell. The FIG_Config file must contain the
2634    user name, password, and API ID for the relevant account in the hash reference variable
2635    I<$FIG_Config::phone>, using the keys C<user>, C<password>, and C<api_id>. For
2636    example, if the user name is C<BruceTheHumanPet>, the password is C<silly>, and the API ID
2637    is C<2561022>, then the FIG_Config file must contain
2638    
2639        $phone =  { user => 'BruceTheHumanPet',
2640                    password => 'silly',
2641                    api_id => '2561022' };
2642    
2643    The original purpose of this method was to insure Bruce would be notified immediately when the
2644    Sprout Load terminates. Care should be taken if you do not wish Bruce to be notified immediately
2645    when you call this method.
2646    
2647    The message ID will be returned if successful, and C<undef> if an error occurs.
2648    
2649    =over 4
2650    
2651    =item phoneNumber
2652    
2653    Phone number to receive the message, in international format. A United States phone number
2654    would be prefixed by "1". A British phone number would be prefixed by "44".
2655    
2656    =item msg
2657    
2658    Message to send to the specified phone.
2659    
2660    =item RETURN
2661    
2662    Returns the message ID if successful, and C<undef> if the message could not be sent.
2663    
2664    =back
2665    
2666    =cut
2667    
2668    sub SendSMS {
2669        # Get the parameters.
2670        my ($phoneNumber, $msg) = @_;
2671        # Declare the return variable. If we do not change it, C<undef> will be returned.
2672        my $retVal;
2673        # Only proceed if we have phone support.
2674        if (! defined $FIG_Config::phone) {
2675            Trace("Phone support not present in FIG_Config.") if T(1);
2676        } else {
2677            # Get the phone data.
2678            my $parms = $FIG_Config::phone;
2679            # Get the Clickatell URL.
2680            my $url = "http://api.clickatell.com/http/";
2681            # Create the user agent.
2682            my $ua = LWP::UserAgent->new;
2683            # Request a Clickatell session.
2684            my $resp = $ua->post("$url/sendmsg", { user => $parms->{user},
2685                                         password => $parms->{password},
2686                                         api_id => $parms->{api_id},
2687                                         to => $phoneNumber,
2688                                         text => $msg});
2689            # Check for an error.
2690            if (! $resp->is_success) {
2691                Trace("Alert failed.") if T(1);
2692            } else {
2693                # Get the message ID.
2694                my $rstring = $resp->content;
2695                if ($rstring =~ /^ID:\s+(.*)$/) {
2696                    $retVal = $1;
2697                } else {
2698                    Trace("Phone attempt failed with $rstring") if T(1);
2699                }
2700            }
2701        }
2702        # Return the result.
2703        return $retVal;
2704    }
2705    
2706    =head3 CommaFormat
2707    
2708    C<< my $formatted = Tracer::CommaFormat($number); >>
2709    
2710    Insert commas into a number.
2711    
2712    =over 4
2713    
2714    =item number
2715    
2716    A sequence of digits.
2717    
2718    =item RETURN
2719    
2720    Returns the same digits with commas strategically inserted.
2721    
2722    =back
2723    
2724    =cut
2725    
2726    sub CommaFormat {
2727        # Get the parameters.
2728        my ($number) = @_;
2729        # Pad the length up to a multiple of three.
2730        my $padded = "$number";
2731        $padded = " " . $padded while length($padded) % 3 != 0;
2732        # This is a fancy PERL trick. The parentheses in the SPLIT pattern
2733        # cause the delimiters to be included in the output stream. The
2734        # GREP removes the empty strings in between the delimiters.
2735        my $retVal = join(",", grep { $_ ne '' } split(/(...)/, $padded));
2736        # Clean out the spaces.
2737        $retVal =~ s/ //g;
2738        # Return the result.
2739        return $retVal;
2740    }
2741    =head3 SetPermissions
2742    
2743    C<< Tracer::SetPermissions($dirName, $group, $mask, %otherMasks); >>
2744    
2745    Set the permissions for a directory and all the files and folders inside it.
2746    In addition, the group ownership will be changed to the specified value.
2747    
2748    This method is more vulnerable than most to permission and compatability
2749    problems, so it does internal error recovery.
2750    
2751    =over 4
2752    
2753    =item dirName
2754    
2755    Name of the directory to process.
2756    
2757    =item group
2758    
2759    Name of the group to be assigned.
2760    
2761    =item mask
2762    
2763    Permission mask. Bits that are C<1> in this mask will be ORed into the
2764    permission bits of any file or directory that does not already have them
2765    set to 1.
2766    
2767    =item otherMasks
2768    
2769    Map of search patterns to permission masks. If a directory name matches
2770    one of the patterns, that directory and all its members and subdirectories
2771    will be assigned the new pattern. For example, the following would
2772    assign 01664 to most files, but would use 01777 for directories named C<tmp>.
2773    
2774        Tracer::SetPermissions($dirName, 'fig', 01664, '^tmp$' => 01777);
2775    
2776    The list is ordered, so the following would use 0777 for C<tmp1> and
2777    0666 for C<tmp>, C<tmp2>, or C<tmp3>.
2778    
2779        Tracer::SetPermissions($dirName, 'fig', 01664, '^tmp1' => 0777,
2780                                                       '^tmp' => 0666);
2781    
2782    Note that the pattern matches are all case-insensitive, and only directory
2783    names are matched, not file names.
2784    
2785    =back
2786    
2787    =cut
2788    
2789    sub SetPermissions {
2790        # Get the parameters.
2791        my ($dirName, $group, $mask, @otherMasks) = @_;
2792        # Set up for error recovery.
2793        eval {
2794            # Switch to the specified directory.
2795            ChDir($dirName);
2796            # Get the group ID.
2797            my $gid = getgrnam($group);
2798            # Get the mask for tracing.
2799            my $traceMask = sprintf("%04o", $mask) . "($mask)";
2800            Trace("Fixing permissions for directory $dirName using group $group($gid) and mask $traceMask.") if T(File => 2);
2801            my $fixCount = 0;
2802            my $lookCount = 0;
2803            # @dirs will be a stack of directories to be processed.
2804            my @dirs = (getcwd());
2805            while (scalar(@dirs) > 0) {
2806                # Get the current directory.
2807                my $dir = pop @dirs;
2808                # Check for a match to one of the specified directory names. To do
2809                # that, we need to pull the individual part of the name off of the
2810                # whole path.
2811                my $simpleName = $dir;
2812                if ($dir =~ m!/([^/]+)$!) {
2813                    $simpleName = $1;
2814                }
2815                Trace("Simple directory name for $dir is $simpleName.") if T(File => 4);
2816                # Search for a match.
2817                my $match = 0;
2818                my $i;
2819                for ($i = 0; $i < $#otherMasks && ! $match; $i += 2) {
2820                    my $pattern = $otherMasks[$i];
2821                    if ($simpleName =~ /$pattern/i) {
2822                        $match = 1;
2823                    }
2824                }
2825                # Check for a match. Note we use $i-1 because the loop added 2
2826                # before terminating due to the match.
2827                if ($match && $otherMasks[$i-1] != $mask) {
2828                    # This directory matches one of the incoming patterns, and it's
2829                    # a different mask, so we process it recursively with that mask.
2830                    SetPermissions($dir, $group, $otherMasks[$i-1], @otherMasks);
2831                } else {
2832                    # Here we can process normally. Get all of the non-hidden members.
2833                    my @submems = OpenDir($dir, 1);
2834                    for my $submem (@submems) {
2835                        # Get the full name.
2836                        my $thisMem = "$dir/$submem";
2837                        Trace("Checking member $thisMem.") if T(4);
2838                        $lookCount++;
2839                        if ($lookCount % 1000 == 0) {
2840                            Trace("$lookCount members examined. Current is $thisMem. Mask is $traceMask") if T(File => 3);
2841                        }
2842                        # Fix the group.
2843                        chown -1, $gid, $thisMem;
2844                        # Insure this member is not a symlink.
2845                        if (! -l $thisMem) {
2846                            # Get its info.
2847                            my $fileInfo = stat $thisMem;
2848                            # Only proceed if we got the info. Otherwise, it's a hard link
2849                            # and we want to skip it anyway.
2850                            if ($fileInfo) {
2851                                my $fileMode = $fileInfo->mode;
2852                                if (($fileMode & $mask) != $mask) {
2853                                    # Fix this member.
2854                                    $fileMode |= $mask;
2855                                    chmod $fileMode, $thisMem;
2856                                    $fixCount++;
2857                                }
2858                                # If it's a subdirectory, stack it.
2859                                if (-d $thisMem) {
2860                                    push @dirs, $thisMem;
2861                                }
2862                            }
2863                        }
2864                    }
2865                }
2866            }
2867            Trace("$lookCount files and directories processed, $fixCount fixed.") if T(File => 2);
2868        };
2869        # Check for an error.
2870        if ($@) {
2871            Confess("SetPermissions error: $@");
2872        }
2873    }
2874    
2875    =head3 CompareLists
2876    
2877    C<< my ($inserted, $deleted) = Tracer::CompareLists(\@newList, \@oldList, $keyIndex); >>
2878    
2879    Compare two lists of tuples, and return a hash analyzing the differences. The lists
2880    are presumed to be sorted alphabetically by the value in the $keyIndex column.
2881    The return value contains a list of items that are only in the new list
2882    (inserted) and only in the old list (deleted).
2883    
2884    =over 4
2885    
2886    =item newList
2887    
2888    Reference to a list of new tuples.
2889    
2890    =item oldList
2891    
2892    Reference to a list of old tuples.
2893    
2894    =item keyIndex (optional)
2895    
2896    Index into each tuple of its key field. The default is 0.
2897    
2898    =item RETURN
2899    
2900    Returns a 2-tuple consisting of a reference to the list of items that are only in the new
2901    list (inserted) followed by a reference to the list of items that are only in the old
2902    list (deleted).
2903    
2904    =back
2905    
2906    =cut
2907    
2908    sub CompareLists {
2909        # Get the parameters.
2910        my ($newList, $oldList, $keyIndex) = @_;
2911        if (! defined $keyIndex) {
2912            $keyIndex = 0;
2913        }
2914        # Declare the return variables.
2915        my ($inserted, $deleted) = ([], []);
2916        # Loop through the two lists simultaneously.
2917        my ($newI, $oldI) = (0, 0);
2918        my ($newN, $oldN) = (scalar @{$newList}, scalar @{$oldList});
2919        while ($newI < $newN || $oldI < $oldN) {
2920            # Get the current object in each list. Note that if one
2921            # of the lists is past the end, we'll get undef.
2922            my $newItem = $newList->[$newI];
2923            my $oldItem = $oldList->[$oldI];
2924            if (! defined($newItem) || defined($oldItem) && $newItem->[$keyIndex] gt $oldItem->[$keyIndex]) {
2925                # The old item is not in the new list, so mark it deleted.
2926                push @{$deleted}, $oldItem;
2927                $oldI++;
2928            } elsif (! defined($oldItem) || $oldItem->[$keyIndex] gt $newItem->[$keyIndex]) {
2929                # The new item is not in the old list, so mark it inserted.
2930                push @{$inserted}, $newItem;
2931                $newI++;
2932            } else {
2933                # The item is in both lists, so push forward.
2934                $oldI++;
2935                $newI++;
2936            }
2937        }
2938        # Return the result.
2939        return ($inserted, $deleted);
2940    }
2941    
2942    =head3 GetLine
2943    
2944    C<< my @data = Tracer::GetLine($handle); >>
2945    
2946    Read a line of data from a tab-delimited file.
2947    
2948    =over 4
2949    
2950    =item handle
2951    
2952    Open file handle from which to read.
2953    
2954    =item RETURN
2955    
2956    Returns a list of the fields in the record read. The fields are presumed to be
2957    tab-delimited. If we are at the end of the file, then an empty list will be
2958    returned. If an empty line is read, a single list item consisting of a null
2959    string will be returned.
2960    
2961    =back
2962    
2963    =cut
2964    
2965    sub GetLine {
2966        # Get the parameters.
2967        my ($handle) = @_;
2968        # Declare the return variable.
2969        my @retVal = ();
2970        Trace("File position is " . tell($handle) . ". EOF flag is " . eof($handle) . ".") if T(File => 4);
2971        # Read from the file.
2972        my $line = <$handle>;
2973        # Only proceed if we found something.
2974        if (defined $line) {
2975            # Remove the new-line.
2976            chomp $line;
2977            Trace("Line read: $line") if T(File => 4);
2978            # If the line is empty, return a single empty string; otherwise, parse
2979            # it into fields.
2980            if ($line eq "") {
2981                push @retVal, "";
2982            } else {
2983                push @retVal, split /\t/,$line;
2984            }
2985        } else {
2986            # Trace the reason the read failed.
2987            Trace("End of file: $!") if T(File => 3);
2988        }
2989        # Return the result.
2990        return @retVal;
2991    }
2992    
2993    =head3 PutLine
2994    
2995    C<< Tracer::PutLine($handle, \@fields); >>
2996    
2997    Write a line of data to a tab-delimited file. The specified field values will be
2998    output in tab-separated form, with a trailing new-line.
2999    
3000    =over 4
3001    
3002    =item handle
3003    
3004    Output file handle.
3005    
3006    =item fields
3007    
3008    List of field values.
3009    
3010    =back
3011    
3012    =cut
3013    
3014    sub PutLine {
3015        # Get the parameters.
3016        my ($handle, $fields) = @_;
3017        # Write the data.
3018        print $handle join("\t", @{$fields}) . "\n";
3019    }
3020    
3021    =head3 GenerateURL
3022    
3023    C<< my $queryUrl = Tracer::GenerateURL($page, %parameters); >>
3024    
3025    Generate a GET-style URL for the specified page with the specified parameter
3026    names and values. The values will be URL-escaped automatically. So, for
3027    example
3028    
3029        Tracer::GenerateURL("form.cgi", type => 1, string => "\"high pass\" or highway")
3030    
3031    would return
3032    
3033        form.cgi?type=1&string=%22high%20pass%22%20or%20highway
3034    
3035    =over 4
3036    
3037    =item page
3038    
3039    Page URL.
3040    
3041    =item parameters
3042    
3043    Hash mapping parameter names to parameter values.
3044    
3045    =item RETURN
3046    
3047    Returns a GET-style URL that goes to the specified page and passes in the
3048    specified parameters and values.
3049    
3050    =back
3051    
3052    =cut
3053    
3054    sub GenerateURL {
3055        # Get the parameters.
3056        my ($page, %parameters) = @_;
3057        # Prime the return variable with the page URL.
3058        my $retVal = $page;
3059        # Loop through the parameters, creating parameter elements in a list.
3060        my @parmList = map { "$_=" . uri_escape($parameters{$_}) } keys %parameters;
3061        # If the list is nonempty, tack it on.
3062        if (@parmList) {
3063            $retVal .= "?" . join("&", @parmList);
3064        }
3065        # Return the result.
3066        return $retVal;
3067    }
3068    
3069  1;  1;

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