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# Line 1  Line 1 
1    #
2    # Copyright (c) 2003-2006 University of Chicago and Fellowship
3    # for Interpretations of Genomes. All Rights Reserved.
4    #
5    # This file is part of the SEED Toolkit.
6    #
7    # The SEED Toolkit is free software. You can redistribute
8    # it and/or modify it under the terms of the SEED Toolkit
9    # Public License.
10    #
11    # You should have received a copy of the SEED Toolkit Public License
12    # along with this program; if not write to the University of Chicago
13    # at info@ci.uchicago.edu or the Fellowship for Interpretation of
14    # Genomes at veronika@thefig.info or download a copy from
15    # http://www.theseed.org/LICENSE.TXT.
16    #
17    
18  package Tracer;  package Tracer;
19    
20          require Exporter;          require Exporter;
21          @ISA = ('Exporter');          @ISA = ('Exporter');
22          @EXPORT = qw(Trace T TSetup QTrace Confess Cluck Min Max Assert);      @EXPORT = qw(Trace T TSetup QTrace Confess Cluck Min Max Assert Open OpenDir TICK StandardSetup EmergencyKey ETracing ScriptSetup ScriptFinish Insure ChDir Emergency);
23          @EXPORT_OK = qw(GetFile GetOptions Merge MergeOptions ParseCommand ParseRecord UnEscape);      @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;
29        use PageBuilder;
30        use Digest::MD5;
31        use File::Basename;
32        use File::Path;
33        use File::stat;
34        use LWP::UserAgent;
35        use Time::HiRes 'gettimeofday';
36        use URI::Escape;
37        use Time::Local;
38    
39  =head1 Tracing and Debugging Helpers  =head1 Tracing and Debugging Helpers
40    
41  =head2 Introduction  =head2 Tracing
42    
43  This package provides simple tracing for debugging and reporting purposes. To use it simply call the  This package provides simple tracing for debugging and reporting purposes. To use it simply call the
44  L</TSetup> method to set the options and call L</Trace> to write out trace messages. Each trace  L</TSetup> or L</ETracing> method to set the options and call L</Trace> to write out trace messages.
45  message has a I<trace level> and I<category> associated with it. In addition, the tracing package itself  L</TSetup> and L</ETracing> both establish a I<trace level> and a list of I<categories>. Similarly,
46  has a list of categories and a single trace level set by the B<TSetup> method. Only messages whose trace  each trace message has a I<trace level> and I<category> associated with it. Only messages whose trace
47  level is less than or equal to this package's trace level and whose category is activated will  level is less than or equal to the setup trace level and whose category is activated will
48  be written. Thus, a higher trace level on a message indicates that the message  be written. Thus, a higher trace level on a message indicates that the message
49  is less likely to be seen. A higher trace level passed to B<Setup> means more trace messages will  is less likely to be seen, while a higher trace level passed to B<TSetup> means more trace messages will
50  appear. To generate a trace message, use the following syntax.  appear.
51    
52    =head3 Putting Trace Messages in Your Code
53    
54  C<< Trace($message) if T(errors => 4); >>  To generate a trace message, use the following syntax.
55    
56        Trace($message) if T(errors => 4);
57    
58  This statement will produce a trace message if the trace level is 4 or more and the C<errors>  This statement will produce a trace message if the trace level is 4 or more and the C<errors>
59  category is active. Note that the special category C<main> is always active, so  category is active. There is a special category C<main> that is always active, so
60    
61  C<< Trace($message) if T(main => 4); >>      Trace($message) if T(main => 4);
62    
63  will trace if the trace level is 4 or more.  will trace if the trace level is 4 or more.
64    
# Line 34  Line 66 
66  following call is made in the B<Sprout> package, it will appear if the C<Sprout> category is  following call is made in the B<Sprout> package, it will appear if the C<Sprout> category is
67  active and the trace level is 2 or more.  active and the trace level is 2 or more.
68    
69  C<< Trace($message) if T(2); >>      Trace($message) if T(2);
70    
71    In scripts, where no package name is available, the category defaults to C<main>.
72    
73  To set up tracing, you call the C</Setup> method. The method takes as input a trace level, a list  =head3 Custom Tracing
74  of category names, and a set of options. The trace level and list of category names are  
75    Many programs have customized tracing configured using the L</TSetup> method. This is no longer
76    the preferred method, but a knowledge of how custom tracing works can make the more modern
77    L</Emergency Tracing> easier to understand.
78    
79    To set up custom tracing, you call the L</TSetup> method. The method takes as input a trace level,
80    a list of category names, and a destination. The trace level and list of category names are
81  specified as a space-delimited string. Thus  specified as a space-delimited string. Thus
82    
83  C<< TSetup('3 errors Sprout ERDB', 'HTML'); >>      TSetup('3 errors Sprout ERDB', 'TEXT');
84    
85    sets the trace level to 3, activates the C<errors>, C<Sprout>, and C<ERDB> categories, and
86    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
89    level 3 and writes the output to the standard error output. This sort of thing might be
90    useful in a CGI environment.
91    
92  sets the trace level to 3, activated the C<errors>, C<Sprout>, and C<ERDB> categories, and      TSetup('3 *', 'WARN');
 specifies that messages should be output as HTML paragraphs. The idea is to make it easier to  
 input tracing configuration on a web form.  
93    
94  In addition to HTML and file output for trace messages, you can specify that the trace messages  In addition standard error and file output for trace messages, you can specify that the trace messages
95  be queued. The messages can then be retrieved by calling the L</QTrace> method. This approach  be queued. The messages can then be retrieved by calling the L</QTrace> method. This approach
96  is useful if you are building a web page. Instead of having the trace messages interspersed with  is useful if you are building a web page. Instead of having the trace messages interspersed with
97  the page output, they can be gathered together and displayed at the end of the page. This makes  the page output, they can be gathered together and displayed at the end of the page. This makes
98  it easier to debug page formatting problems.  it easier to debug page formatting problems.
99    
100  Finally, you can specify that all trace messages be emitted as warnings.  Finally, you can specify that all trace messages be emitted to a file, or the standard output and
101    a file at the same time. To trace to a file, specify the filename with an output character in front
102    of it.
103    
104        TSetup('4 SQL', ">$fileName");
105    
106    To trace to the standard output and a file at the same time, put a C<+> in front of the angle
107    bracket.
108    
109        TSetup('3 *', "+>$fileName");
110    
111  The flexibility of tracing makes it superior to simple use of directives like C<die> and C<warn>.  The flexibility of tracing makes it superior to simple use of directives like C<die> and C<warn>.
112  Tracer calls can be left in the code with minimal overhead and then turned on only when needed.  Tracer calls can be left in the code with minimal overhead and then turned on only when needed.
113  Thus, debugging information is available and easily retrieved even when the application is  Thus, debugging information is available and easily retrieved even when the application is
114  being used out in the field.  being used out in the field.
115    
116    =head3 Trace Levels
117    
118    There is no hard and fast rule on how to use trace levels. The following is therefore only
119    a suggestion.
120    
121    =over 4
122    
123    =item Error 0
124    
125    Message indicates an error that may lead to incorrect results or that has stopped the
126    application entirely.
127    
128    =item Warning 1
129    
130    Message indicates something that is unexpected but that probably did not interfere
131    with program execution.
132    
133    =item Notice 2
134    
135    Message indicates the beginning or end of a major task.
136    
137    =item Information 3
138    
139    Message indicates a subtask. In the FIG system, a subtask generally relates to a single
140    genome. This would be a big loop that is not expected to execute more than 500 times or so.
141    
142    =item Detail 4
143    
144    Message indicates a low-level loop iteration.
145    
146    =back
147    
148    The format of trace messages is important because some utilities analyze trace files.
149    There are three fields-- the time stamp, the category name, and the text.
150    The time stamp is between square brackets and the category name between angle brackets.
151    After the category name there is a colon (C<:>) followed by the message text.
152    If the square brackets or angle brackets are missing, then the trace management
153    utilities assume that they are encountering a set of pre-formatted lines.
154    
155    Note, however, that this formatting is done automatically by the tracing functions. You
156    only need to know about it if you want to parse a trace file.
157    
158    =head3 Emergency Tracing
159    
160    Sometimes, you need a way for tracing to happen automatically without putting parameters
161    in a form or on the command line. Emergency tracing does this. You invoke emergency tracing
162    from the debug form, which is accessed from I<MySeedInstance>C</FIG/Html/SetPassword.html>.
163    Emergency tracing requires you specify a tracing key. For command-line tools, the key is
164    taken from the C<TRACING> environment variable. For web services, the key is taken from
165    a cookie. Either way, the key tells the tracing facility who you are, so that you control
166    the tracing in your environment without stepping on other users.
167    
168    The key can be anything you want. If you don't have a key, the C<SetPassword> page will
169    generate one for you.
170    
171    You can activate and de-activate emergency tracing from the debugging control panel, as
172    well as display the trace file itself.
173    
174    To enable emergency tracing in your code, call
175    
176        ETracing($cgi)
177    
178    from a web script and
179    
180        ETracing()
181    
182    from a command-line script.
183    
184    The web script will look for the tracing key in the cookies, and the command-line
185    script will look for it in the C<TRACING> environment variable. If you are
186    using the L</StandardScript> or L</StandardSetup> methods, emergency tracing
187    will be configured automatically.
188    
189    =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.
283    
284  my $Destination = "NONE";       # Description of where to send the trace output.  my $Destination = "NONE";       # Description of where to send the trace output.
285    my $TeeFlag = 0;            # TRUE if output is going to a file and to the
286                                # standard output
287  my %Categories = ( main => 1 );  my %Categories = ( main => 1 );
288                                                          # hash of active category names                                                          # hash of active category names
289  my $TraceLevel = 0;                     # trace level; a higher trace level produces more  my $TraceLevel = 0;                     # trace level; a higher trace level produces more
290                                                          # messages                                                          # messages
291  my @Queue = ();                         # queued list of trace messages.  my @Queue = ();                         # queued list of trace messages.
292    my $LastCategory = "main";  # name of the last category interrogated
293    my $SetupCount = 0;         # number of times TSetup called
294    my $AllTrace = 0;           # TRUE if we are tracing all categories.
295    
296  =head2 Public Methods  =head2 Public Methods
297    
# Line 90  Line 313 
313    
314  The destination for the trace output. To send the trace output to a file, specify the file  The destination for the trace output. To send the trace output to a file, specify the file
315  name preceded by a ">" symbol. If a double symbol is used (">>"), then the data is appended  name preceded by a ">" symbol. If a double symbol is used (">>"), then the data is appended
316  to the file. Otherwise the file is cleared before tracing begins. In addition to sending  to the file. Otherwise the file is cleared before tracing begins. Precede the first ">"
317  the trace messages to a file, you can specify a special destination. C<HTML> will cause  symbol with a C<+> to echo output to a file AND to the standard output. In addition to
318  tracing to the standard output with each line formatted as an HTML paragraph. C<TEXT>  sending the trace messages to a file, you can specify a special destination. C<HTML> will
319    cause tracing to the standard output with each line formatted as an HTML paragraph. C<TEXT>
320  will cause tracing to the standard output as ordinary text. C<ERROR> will cause trace  will cause tracing to the standard output as ordinary text. C<ERROR> will cause trace
321  messages to be sent to the standard error output as ordinary text. C<QUEUE> will cause trace  messages to be sent to the standard error output as ordinary text. C<QUEUE> will cause trace
322  messages to be stored in a queue for later retrieval by the L</QTrace> method. C<WARN> will  messages to be stored in a queue for later retrieval by the L</QTrace> method. C<WARN> will
# Line 110  Line 334 
334          my @categoryData = split /\s+/, $categoryList;          my @categoryData = split /\s+/, $categoryList;
335          # Extract the trace level.          # Extract the trace level.
336          $TraceLevel = shift @categoryData;          $TraceLevel = shift @categoryData;
337          # Build the category hash.      # Presume category-based tracing until we learn otherwise.
338        $AllTrace = 0;
339        # Build the category hash. Note that if we find a "*", we turn on non-category
340        # tracing. We must also clear away any pre-existing data.
341        %Categories = ( main => 1 );
342          for my $category (@categoryData) {          for my $category (@categoryData) {
343                  $Categories{$category} = 1;          if ($category eq '*') {
344                $AllTrace = 1;
345            } else {
346                $Categories{lc $category} = 1;
347            }
348          }          }
349          # Now we need to process the destination information. The most important special          # Now we need to process the destination information. The most important special
350          # case is the single ">", which requires we clear the file first. After doing      # cases are the single ">", which requires we clear the file first, and the
351          # so, we tack on another ">" sign so that future trace messages are appended.      # "+" prefix which indicates a double echo.
352        if ($target =~ m/^\+?>>?/) {
353            if ($target =~ m/^\+/) {
354                $TeeFlag = 1;
355                $target = substr($target, 1);
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 {
363                $Destination = $target;
364            }
365        } else {
366                  $Destination = uc($target);                  $Destination = uc($target);
367          }          }
368        # Increment the setup counter.
369        $SetupCount++;
370    }
371    
372    =head3 StandardSetup
373    
374    C<< my ($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
670    
671    C<< my $count = Tracer::Setups(); >>
672    
673    Return the number of times L</TSetup> has been called.
674    
675    This method allows for the creation of conditional tracing setups where, for example, we
676    may want to set up tracing if nobody else has done it before us.
677    
678    =cut
679    
680    sub Setups {
681        return $SetupCount;
682    }
683    
684    =head3 Open
685    
686    C<< my $handle = Open($fileHandle, $fileSpec, $message); >>
687    
688    Open a file.
689    
690    The I<$fileSpec> is essentially the second argument of the PERL C<open>
691    function. The mode is specified using Unix-like shell information. So, for
692    example,
693    
694        Open(\*LOGFILE, '>>/usr/spool/news/twitlog', "Could not open twit log.");
695    
696    would open for output appended to the specified file, and
697    
698        Open(\*DATASTREAM, "| sort -u >$outputFile", "Could not open $outputFile.");
699    
700    would open a pipe that sorts the records written and removes duplicates. Note
701    the use of file handle syntax in the Open call. To use anonymous file handles,
702    code as follows.
703    
704        my $logFile = Open(undef, '>>/usr/spool/news/twitlog', "Could not open twit log.");
705    
706    The I<$message> parameter is used if the open fails. If it is set to C<0>, then
707    the open returns TRUE if successful and FALSE if an error occurred. Otherwise, a
708    failed open will throw an exception and the third parameter will be used to construct
709    an error message. If the parameter is omitted, a standard message is constructed
710    using the file spec.
711    
712        Could not open "/usr/spool/news/twitlog"
713    
714    Note that the mode characters are automatically cleaned from the file name.
715    The actual error message from the file system will be captured and appended to the
716    message in any case.
717    
718        Could not open "/usr/spool/news/twitlog": file not found.
719    
720    In some versions of PERL the only error message we get is a number, which
721    corresponds to the C++ C<errno> value.
722    
723        Could not open "/usr/spool/news/twitlog": 6.
724    
725    =over 4
726    
727    =item fileHandle
728    
729    File handle. If this parameter is C<undef>, a file handle will be generated
730    and returned as the value of this method.
731    
732    =item fileSpec
733    
734    File name and mode, as per the PERL C<open> function.
735    
736    =item message (optional)
737    
738    Error message to use if the open fails. If omitted, a standard error message
739    will be generated. In either case, the error information from the file system
740    is appended to the message. To specify a conditional open that does not throw
741    an error if it fails, use C<0>.
742    
743    =item RETURN
744    
745    Returns the name of the file handle assigned to the file, or C<undef> if the
746    open failed.
747    
748    =back
749    
750    =cut
751    
752    sub Open {
753        # Get the parameters.
754        my ($fileHandle, $fileSpec, $message) = @_;
755        # Attempt to open the file.
756        my $rv = open $fileHandle, $fileSpec;
757        # If the open failed, generate an error message.
758        if (! $rv) {
759            # Save the system error message.
760            my $sysMessage = $!;
761            # See if we need a default message.
762            if (!$message) {
763                # Clean any obvious mode characters and leading spaces from the
764                # filename.
765                my ($fileName) = FindNamePart($fileSpec);
766                $message = "Could not open \"$fileName\"";
767            }
768            # Terminate with an error using the supplied message and the
769            # error message from the file system.
770            Confess("$message: $!");
771        }
772        # Return the file handle.
773        return $fileHandle;
774    }
775    
776    =head3 FindNamePart
777    
778    C<< my ($fileName, $start, $len) = Tracer::FindNamePart($fileSpec); >>
779    
780    Extract the portion of a file specification that contains the file name.
781    
782    A file specification is the string passed to an C<open> call. It specifies the file
783    mode and name. In a truly complex situation, it can specify a pipe sequence. This
784    method assumes that the file name is whatever follows the first angle bracket
785    sequence.  So, for example, in the following strings the file name is
786    C</usr/fig/myfile.txt>.
787    
788        >>/usr/fig/myfile.txt
789        </usr/fig/myfile.txt
790        | sort -u > /usr/fig/myfile.txt
791    
792    If the method cannot find a file name using its normal methods, it will return the
793    whole incoming string.
794    
795    =over 4
796    
797    =item fileSpec
798    
799    File specification string from which the file name is to be extracted.
800    
801    =item RETURN
802    
803    Returns a three-element list. The first element contains the file name portion of
804    the specified string, or the whole string if a file name cannot be found via normal
805    methods. The second element contains the start position of the file name portion and
806    the third element contains the length.
807    
808    =back
809    
810    =cut
811    #: Return Type $;
812    sub FindNamePart {
813        # Get the parameters.
814        my ($fileSpec) = @_;
815        # Default to the whole input string.
816        my ($retVal, $pos, $len) = ($fileSpec, 0, length $fileSpec);
817        # Parse out the file name if we can.
818        if ($fileSpec =~ m/(<|>>?)(.+?)(\s*)$/) {
819            $retVal = $2;
820            $len = length $retVal;
821            $pos = (length $fileSpec) - (length $3) - $len;
822        }
823        # Return the result.
824        return ($retVal, $pos, $len);
825    }
826    
827    =head3 OpenDir
828    
829    C<< my @files = OpenDir($dirName, $filtered, $flag); >>
830    
831    Open a directory and return all the file names. This function essentially performs
832    the functions of an C<opendir> and C<readdir>. If the I<$filtered> parameter is
833    set to TRUE, all filenames beginning with a period (C<.>), dollar sign (C<$>),
834    or pound sign (C<#>) and all filenames ending with a tilde C<~>) will be
835    filtered out of the return list. If the directory does not open and I<$flag> is not
836    set, an exception is thrown. So, for example,
837    
838        my @files = OpenDir("/Volumes/fig/contigs", 1);
839    
840    is effectively the same as
841    
842        opendir(TMP, "/Volumes/fig/contigs") || Confess("Could not open /Volumes/fig/contigs.");
843        my @files = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir(TMP);
844    
845    Similarly, the following code
846    
847        my @files = grep { $_ =~ /^\d/ } OpenDir("/Volumes/fig/orgs", 0, 1);
848    
849    Returns the names of all files in C</Volumes/fig/orgs> that begin with digits and
850    automatically returns an empty list if the directory fails to open.
851    
852    =over 4
853    
854    =item dirName
855    
856    Name of the directory to open.
857    
858    =item filtered
859    
860    TRUE if files whose names begin with a period (C<.>) should be automatically removed
861    from the list, else FALSE.
862    
863    =item flag
864    
865    TRUE if a failure to open is okay, else FALSE
866    
867    =back
868    
869    =cut
870    #: Return Type @;
871    sub OpenDir {
872        # Get the parameters.
873        my ($dirName, $filtered, $flag) = @_;
874        # Declare the return variable.
875        my @retVal = ();
876        # Open the directory.
877        if (opendir(my $dirHandle, $dirName)) {
878            # The directory opened successfully. Get the appropriate list according to the
879            # strictures of the filter parameter.
880            if ($filtered) {
881                @retVal = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir $dirHandle;
882            } else {
883                @retVal = readdir $dirHandle;
884            }
885        } elsif (! $flag) {
886            # Here the directory would not open and it's considered an error.
887            Confess("Could not open directory $dirName.");
888        }
889        # Return the result.
890        return @retVal;
891  }  }
892    
893  =head3 SetLevel  =head3 SetLevel
# Line 169  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($fileName); >>
# Line 370  Line 1169 
1169          my ($message) = @_;          my ($message) = @_;
1170          # Get the timestamp.          # Get the timestamp.
1171          my $timeStamp = Now();          my $timeStamp = Now();
1172          # Format the message.      # Format the message. Note we strip off any line terminators at the end.
1173          my $formatted = "$timeStamp $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 391  Line 1190 
1190         warn $message;         warn $message;
1191          } elsif ($Destination =~ m/^>>/) {          } elsif ($Destination =~ m/^>>/) {
1192                  # Write the trace message to an output file.                  # Write the trace message to an output file.
1193                  open TRACING, $Destination;          (open TRACING, $Destination) || die "Tracing open for \"$Destination\" failed: $!";
1194                  print TRACING "$formatted\n";                  print TRACING "$formatted\n";
1195                  close TRACING;                  close TRACING;
1196            # If the Tee flag is on, echo it to the standard output.
1197            if ($TeeFlag) {
1198                print "$formatted\n";
1199            }
1200          }          }
1201  }  }
1202    
# Line 436  Line 1239 
1239                  my ($category, $traceLevel) = @_;                  my ($category, $traceLevel) = @_;
1240                  if (!defined $traceLevel) {                  if (!defined $traceLevel) {
1241                          # Here we have no category, so we need to get the calling package.                          # Here we have no category, so we need to get the calling package.
1242                # The calling package is normally the first parameter. If it is
1243                # omitted, the first parameter will be the tracelevel. So, the
1244                # first thing we do is shift the so-called category into the
1245                # $traceLevel variable where it belongs.
1246                          $traceLevel = $category;                          $traceLevel = $category;
1247                          my ($package, $fileName, $line) = caller;                          my ($package, $fileName, $line) = caller;
1248              # If there is no calling package, we default to "main".              # If there is no calling package, we default to "main".
# Line 445  Line 1252 
1252                                  $category = $package;                                  $category = $package;
1253                          }                          }
1254                  }                  }
1255                  # Use the package and tracelevel to compute the result.          # Save the category name.
1256                  $retVal = ($traceLevel <= $TraceLevel && exists $Categories{$category});          $LastCategory = $category;
1257            # Convert it to lower case before we hash it.
1258            $category = lc $category;
1259            # 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}));
1266      }      }
1267          # Return the computed result.          # Return the computed result.
1268      return $retVal;      return $retVal;
# Line 528  Line 1344 
1344          return ($optionTable, @retVal);          return ($optionTable, @retVal);
1345  }  }
1346    
1347    =head3 Escape
1348    
1349    C<< my $codedString = Tracer::Escape($realString); >>
1350    
1351    Escape a string for use in a command length. Tabs will be replaced by C<\t>, new-lines
1352    replaced by C<\n>, carriage returns will be deleted, and backslashes will be doubled. The
1353    result is to reverse the effect of L</UnEscape>.
1354    
1355    =over 4
1356    
1357    =item realString
1358    
1359    String to escape.
1360    
1361    =item RETURN
1362    
1363    Escaped equivalent of the real string.
1364    
1365    =back
1366    
1367    =cut
1368    
1369    sub Escape {
1370        # Get the parameter.
1371        my ($realString) = @_;
1372        # Initialize the return variable.
1373        my $retVal = "";
1374        # Loop through the parameter string, looking for sequences to escape.
1375        while (length $realString > 0) {
1376            # Look for the first sequence to escape.
1377            if ($realString =~ /^(.*?)([\n\t\r\\])/) {
1378                # 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.
1380                $retVal .= $1;
1381                # Strip the processed section off the real string.
1382                $realString = substr $realString, (length $2) + (length $1);
1383                # Get the matched character.
1384                my $char = $2;
1385                # If we have a CR, we are done.
1386                if ($char ne "\r") {
1387                    # It's not a CR, so encode the escape sequence.
1388                    $char =~ tr/\t\n/tn/;
1389                    $retVal .= "\\" . $char;
1390                }
1391            } else {
1392                # Here there are no more escape sequences. The rest of the string is
1393                # transferred unmodified.
1394                $retVal .= $realString;
1395                $realString = "";
1396            }
1397        }
1398        # Return the result.
1399        return $retVal;
1400    }
1401    
1402  =head3 UnEscape  =head3 UnEscape
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 555  Line 1427 
1427          my ($codedString) = @_;          my ($codedString) = @_;
1428          # Initialize the return variable.          # Initialize the return variable.
1429          my $retVal = "";          my $retVal = "";
1430        # Only proceed if the incoming string is nonempty.
1431        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 576  Line 1454 
1454                          $codedString = "";                          $codedString = "";
1455                  }                  }
1456          }          }
1457        }
1458          # Return the result.          # Return the result.
1459          return $retVal;          return $retVal;
1460  }  }
# Line 673  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 688  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 700  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");
1627          if (!$ok) {      # Read the whole file into the return variable, stripping off any terminator
                 # If we had an error, trace it. We will automatically return a null value.  
                 Trace("Could not open \"$fileName\" for input.") if T(0);  
         } else {  
                 # Read the whole file into the return variable, stripping off an terminator  
1628          # characters.          # characters.
1629          my $lineCount = 0;          my $lineCount = 0;
1630                  while (my $line = <INPUTFILE>) {      while (my $line = <$handle>) {
1631              $lineCount++;              $lineCount++;
1632              $line =~ s/(\r|\n)+$//g;          $line = Strip($line);
1633                          push @retVal, $line;                          push @retVal, $line;
1634                  }                  }
1635                  # Close it.                  # Close it.
1636                  close INPUTFILE;      close $handle;
1637          my $actualLines = @retVal;          my $actualLines = @retVal;
         Trace("$lineCount lines read from $fileName. $actualLines processed.") if T(0);  
         }  
1638          # Return the file's contents in the desired format.          # Return the file's contents in the desired format.
1639      if (wantarray) {      if (wantarray) {
1640              return @retVal;              return @retVal;
# Line 726  Line 1643 
1643      }      }
1644  }  }
1645    
1646    =head3 PutFile
1647    
1648    C<< Tracer::PutFile($fileName, \@lines); >>
1649    
1650    Write out a file from a list of lines of text.
1651    
1652    =over 4
1653    
1654    =item fileName
1655    
1656    Name of the output file.
1657    
1658    =item lines
1659    
1660    Reference to a list of text lines. The lines will be written to the file in order, with trailing
1661    new-line characters. Alternatively, may be a string, in which case the string will be written without
1662    modification.
1663    
1664    =back
1665    
1666    =cut
1667    
1668    sub PutFile {
1669        # Get the parameters.
1670        my ($fileName, $lines) = @_;
1671        # Open the output file.
1672        my $handle = Open(undef, ">$fileName");
1673        if (ref $lines ne 'ARRAY') {
1674            # Here we have a scalar, so we write it raw.
1675            print $handle $lines;
1676        } else {
1677            # Write the lines one at a time.
1678            for my $line (@{$lines}) {
1679                print $handle "$line\n";
1680            }
1681        }
1682        # Close the output file.
1683        close $handle;
1684    }
1685    
1686  =head3 QTrace  =head3 QTrace
1687    
1688  C<< my $data = QTrace($format); >>  C<< my $data = QTrace($format); >>
# Line 747  Line 1704 
1704          my ($format) = @_;          my ($format) = @_;
1705          # Create the return variable.          # Create the return variable.
1706          my $retVal = "";          my $retVal = "";
1707        # Only proceed if there is an actual queue.
1708        if (@Queue) {
1709          # Process according to the format.          # Process according to the format.
1710          if ($format =~ m/^HTML$/i) {          if ($format =~ m/^HTML$/i) {
1711                  # Convert the queue into an HTML list.                  # Convert the queue into an HTML list.
# Line 762  Line 1721 
1721          }          }
1722          # Clear the queue.          # Clear the queue.
1723          @Queue = ();          @Queue = ();
1724        }
1725          # Return the formatted list.          # Return the formatted list.
1726          return $retVal;          return $retVal;
1727  }  }
# Line 770  Line 1730 
1730    
1731  C<< Confess($message); >>  C<< Confess($message); >>
1732    
1733  Trace the call stack and abort the program with the specified message. The stack  Trace the call stack and abort the program with the specified message. When used with
 trace will only appear if the trace level for this package is 1 or more. When used with  
1734  the OR operator and the L</Assert> method, B<Confess> can function as a debugging assert.  the OR operator and the L</Assert> method, B<Confess> can function as a debugging assert.
1735  So, for example  So, for example
1736    
# Line 793  Line 1752 
1752          # Get the parameters.          # Get the parameters.
1753          my ($message) = @_;          my ($message) = @_;
1754          # Trace the call stack.          # Trace the call stack.
1755          Cluck($message) if T(1);      Cluck($message);
1756          # Abort the program.          # Abort the program.
1757          croak(">>> $message");          croak(">>> $message");
1758  }  }
# Line 803  Line 1762 
1762  C<< Assert($condition1, $condition2, ... $conditionN); >>  C<< Assert($condition1, $condition2, ... $conditionN); >>
1763    
1764  Return TRUE if all the conditions are true. This method can be used in conjunction with  Return TRUE if all the conditions are true. This method can be used in conjunction with
1765  the OR operator and the L</Confess> method, B<Assert> can function as a debugging assert.  the OR operator and the L</Confess> method as a debugging assert.
1766  So, for example  So, for example
1767    
1768  C<< Assert($recNum >= 0) || Confess("Invalid record number $recNum."); >>  C<< Assert($recNum >= 0) || Confess("Invalid record number $recNum."); >>
# Line 924  Line 1883 
1883    
1884  =head3 AddToListMap  =head3 AddToListMap
1885    
1886  C<< Tracer::AddToListMap(\%hash, $key, $value); >>  C<< Tracer::AddToListMap(\%hash, $key, $value1, $value2, ... valueN); >>
1887    
1888  Add a key-value pair to a hash of lists. If no value exists for the key, a singleton list  Add a key-value pair to a hash of lists. If no value exists for the key, a singleton list
1889  is created for the key. Otherwise, the new value is pushed onto the list.  is created for the key. Otherwise, the new value is pushed onto the list.
# Line 939  Line 1898 
1898    
1899  Key for which the value is to be added.  Key for which the value is to be added.
1900    
1901  =item value  =item value1, value2, ... valueN
1902    
1903  Value to add to the key's value list.  List of values to add to the key's value list.
1904    
1905  =back  =back
1906    
# Line 949  Line 1908 
1908    
1909  sub AddToListMap {  sub AddToListMap {
1910      # Get the parameters.      # Get the parameters.
1911      my ($hash, $key, $value) = @_;      my ($hash, $key, @values) = @_;
1912      # Process according to whether or not the key already has a value.      # Process according to whether or not the key already has a value.
1913      if (! exists $hash->{$key}) {      if (! exists $hash->{$key}) {
1914          $hash->{$key} = [$value];          $hash->{$key} = [@values];
1915        } else {
1916            push @{$hash->{$key}}, @values;
1917        }
1918    }
1919    
1920    =head3 DebugMode
1921    
1922    C<< if (Tracer::DebugMode) { ...code... } >>
1923    
1924    Return TRUE if debug mode has been turned on, else abort.
1925    
1926    Certain CGI scripts are too dangerous to exist in the production
1927    environment. This method provides a simple way to prevent them
1928    from working unless they are explicitly turned on by creating a password
1929    cookie via the B<SetPassword> script.  If debugging mode
1930    is not turned on, an error will occur.
1931    
1932    =cut
1933    
1934    sub DebugMode {
1935        # Declare the return variable.
1936        my $retVal = 0;
1937        # Check the debug configuration.
1938        my $password = CGI::cookie("DebugMode");
1939        my $encrypted = Digest::MD5::md5_hex($password);
1940        if ($encrypted eq "252dec43280e0c0d6a75ffcec486e61d") {
1941            $retVal = 1;
1942        } else {
1943            # Here debug mode is off, so we generate an error.
1944            Confess("Cannot use this facility without logging in.");
1945        }
1946        # Return the determination indicator.
1947        return $retVal;
1948    }
1949    
1950    =head3 Strip
1951    
1952    C<< my $string = Tracer::Strip($line); >>
1953    
1954    Strip all line terminators off a string. This is necessary when dealing with files
1955    that may have been transferred back and forth several times among different
1956    operating environments.
1957    
1958    =over 4
1959    
1960    =item line
1961    
1962    Line of text to be stripped.
1963    
1964    =item RETURN
1965    
1966    The same line of text with all the line-ending characters chopped from the end.
1967    
1968    =back
1969    
1970    =cut
1971    
1972    sub Strip {
1973        # Get a copy of the parameter string.
1974        my ($string) = @_;
1975        my $retVal = (defined $string ? $string : "");
1976        # Strip the line terminator characters.
1977        $retVal =~ s/(\r|\n)+$//g;
1978        # Return the result.
1979        return $retVal;
1980    }
1981    
1982    =head3 Pad
1983    
1984    C<< my $paddedString = Tracer::Pad($string, $len, $left, $padChar); >>
1985    
1986    Pad a string to a specified length. The pad character will be a
1987    space, and the padding will be on the right side unless specified
1988    in the third parameter.
1989    
1990    =over 4
1991    
1992    =item string
1993    
1994    String to be padded.
1995    
1996    =item len
1997    
1998    Desired length of the padded string.
1999    
2000    =item left (optional)
2001    
2002    TRUE if the string is to be left-padded; otherwise it will be padded on the right.
2003    
2004    =item padChar (optional)
2005    
2006    Character to use for padding. The default is a space.
2007    
2008    =item RETURN
2009    
2010    Returns a copy of the original string with the pad character added to the
2011    specified end so that it achieves the desired length.
2012    
2013    =back
2014    
2015    =cut
2016    
2017    sub Pad {
2018        # Get the parameters.
2019        my ($string, $len, $left, $padChar) = @_;
2020        # Compute the padding character.
2021        if (! defined $padChar) {
2022            $padChar = " ";
2023        }
2024        # Compute the number of spaces needed.
2025        my $needed = $len - length $string;
2026        # Copy the string into the return variable.
2027        my $retVal = $string;
2028        # Only proceed if padding is needed.
2029        if ($needed > 0) {
2030            # Create the pad string.
2031            my $pad = $padChar x $needed;
2032            # Affix it to the return value.
2033            if ($left) {
2034                $retVal = $pad . $retVal;
2035            } else {
2036                $retVal .= $pad;
2037            }
2038        }
2039        # Return the result.
2040        return $retVal;
2041    }
2042    
2043    =head3 EOF
2044    
2045    This is a constant that is lexically greater than any useful string.
2046    
2047    =cut
2048    
2049    sub EOF {
2050        return "\xFF\xFF\xFF\xFF\xFF";
2051    }
2052    
2053    =head3 TICK
2054    
2055    C<< my @results = TICK($commandString); >>
2056    
2057    Perform a back-tick operation on a command. If this is a Windows environment, any leading
2058    dot-slash (C<./> will be removed. So, for example, if you were doing
2059    
2060        `./protein.cgi`
2061    
2062    from inside a CGI script, it would work fine in Unix, but would issue an error message
2063    in Windows complaining that C<'.'> is not a valid command. If instead you code
2064    
2065        TICK("./protein.cgi")
2066    
2067    it will work correctly in both environments.
2068    
2069    =over 4
2070    
2071    =item commandString
2072    
2073    The command string to pass to the system.
2074    
2075    =item RETURN
2076    
2077    Returns the standard output from the specified command, as a list.
2078    
2079    =back
2080    
2081    =cut
2082    #: Return Type @;
2083    sub TICK {
2084        # Get the parameters.
2085        my ($commandString) = @_;
2086        # Chop off the dot-slash if this is Windows.
2087        if ($FIG_Config::win_mode) {
2088            $commandString =~ s!^\./!!;
2089        }
2090        # Activate the command and return the result.
2091        return `$commandString`;
2092    }
2093    
2094    =head3 ScriptSetup
2095    
2096    C<< my ($cgi, $varHash) = ScriptSetup($noTrace); >>
2097    
2098    Perform standard tracing and debugging setup for scripts. The value returned is
2099    the CGI object followed by a pre-built variable hash.
2100    
2101    The C<Trace> form parameter is used to determine whether or not tracing is active and
2102    which trace modules (other than C<Tracer> itself) should be turned on. Specifying
2103    the C<CGI> trace module will trace parameter and environment information. Parameters are
2104    traced at level 3 and environment variables at level 4. To trace to a file instead of to
2105    the web page, set C<TF> to 1. At the end of the script, the client should call
2106    L</ScriptFinish> to output the web page.
2107    
2108    In some situations, it is not practical to invoke tracing via form parameters. For this
2109    situation, you can turn on emergency tracing from the debugging control panel.
2110    Tracing will then be turned on automatically for all programs that use the L</ETracing>
2111    method, which includes every program that uses this method or L</StandardSetup>.
2112    
2113    =over 4
2114    
2115    =item noTrace (optional)
2116    
2117    If specified, tracing will be suppressed. This is useful if the script wants to set up
2118    tracing manually.
2119    
2120    =item RETURN
2121    
2122    Returns a two-element list consisting of a CGI query object and a variable hash for
2123    the output page.
2124    
2125    =back
2126    
2127    =cut
2128    
2129    sub ScriptSetup {
2130        # Get the parameters.
2131        my ($noTrace) = @_;
2132        # Get the CGI query object.
2133        my $cgi = CGI->new();
2134        # Set up tracing if it's not suppressed.
2135        ETracing($cgi) unless $noTrace;
2136        # Create the variable hash.
2137        my $varHash = { results => '' };
2138        # Return the query object and variable hash.
2139        return ($cgi, $varHash);
2140    }
2141    
2142    =head3 ETracing
2143    
2144    C<< ETracing($parameter); >>
2145    
2146    Set up emergency tracing. Emergency tracing is tracing that is turned
2147    on automatically for any program that calls this method. The emergency
2148    tracing parameters are stored in a a file identified by a tracing key.
2149    If this method is called with a CGI object, then the tracing key is
2150    taken from a cookie. If it is called with no parameters, then the tracing
2151    key is taken from an environment variable. If it is called with a string,
2152    the tracing key is that string.
2153    
2154    =over 4
2155    
2156    =item parameter
2157    
2158    A parameter from which the tracing key is computed. If it is a scalar,
2159    that scalar is used as the tracing key. If it is a CGI object, the
2160    tracing key is taken from the C<IP> cookie. If it is omitted, the
2161    tracing key is taken from the C<TRACING> environment variable. If it
2162    is a CGI object and emergency tracing is not on, the C<Trace> and
2163    C<TF> parameters will be used to determine the type of tracing.
2164    
2165    =back
2166    
2167    =cut
2168    
2169    sub ETracing {
2170        # Get the parameter.
2171        my ($parameter) = @_;
2172        # Check for CGI mode.
2173        my $cgi = (ref $parameter eq 'CGI' ? $parameter : undef);
2174        # Default to no tracing except errors.
2175        my ($tracing, $dest) = ("0", "WARN");
2176        # Check for emergency tracing.
2177        my $tkey = EmergencyKey($parameter);
2178        my $emergencyFile = EmergencyFileName($tkey);
2179        if (-e $emergencyFile) {
2180            # We have the file. Read in the data.
2181            my @tracing = GetFile($emergencyFile);
2182            # Pull off the time limit.
2183            my $expire = shift @tracing;
2184            # Convert it to seconds.
2185            $expire *= 3600;
2186            # Check the file data.
2187            my $stat = stat($emergencyFile);
2188            my ($now) = gettimeofday;
2189            if ($now - $stat->mtime > $expire) {
2190                # Delete the expired file.
2191                unlink $emergencyFile;
2192      } else {      } else {
2193          push @{$hash->{$key}}, $value;              # Emergency tracing is on. Pull off the destination and
2194                # the trace level;
2195                $dest = shift @tracing;
2196                my $level = shift @tracing;
2197                # Convert the destination to a real tracing destination.
2198                # temp directory.
2199                $dest = EmergencyTracingDest($tkey, $dest);
2200                # Insure Tracer is specified.
2201                my %moduleHash = map { $_ => 1 } @tracing;
2202                $moduleHash{Tracer} = 1;
2203                # Set the trace parameter.
2204                $tracing = join(" ", $level, sort keys %moduleHash);
2205            }
2206        } elsif (defined $cgi) {
2207            # There's no emergency tracing, but we have a CGI object, so check
2208            # for tracing from the form parameters.
2209            if ($cgi->param('Trace')) {
2210                # Here the user has requested tracing via a form.
2211                $dest = ($cgi->param('TF') ? ">$FIG_Config::temp/Trace$$.log" : "QUEUE");
2212                $tracing = $cgi->param('Trace') . " Tracer";
2213            }
2214        }
2215        # Setup the tracing we've determined from all the stuff above.
2216        TSetup($tracing, $dest);
2217        # If we're a web script, trace the parameter and environment data.
2218        if (defined $cgi) {
2219            TraceParms($cgi);
2220        }
2221    }
2222    
2223    =head3 EmergencyFileName
2224    
2225    C<< my $fileName = Tracer::EmergencyFileName($tkey); >>
2226    
2227    Return the emergency tracing file name. This is the file that specifies
2228    the tracing information.
2229    
2230    =over 4
2231    
2232    =item tkey
2233    
2234    Tracing key for the current program.
2235    
2236    =item RETURN
2237    
2238    Returns the name of the file to contain the emergency tracing information.
2239    
2240    =back
2241    
2242    =cut
2243    
2244    sub EmergencyFileName {
2245        # Get the parameters.
2246        my ($tkey) = @_;
2247        # Compute the emergency tracing file name.
2248        return "$FIG_Config::temp/Emergency$tkey.txt";
2249    }
2250    
2251    =head3 EmergencyFileTarget
2252    
2253    C<< my $fileName = Tracer::EmergencyFileTarget($tkey); >>
2254    
2255    Return the emergency tracing target file name. This is the file that receives
2256    the tracing output for file-based tracing.
2257    
2258    =over 4
2259    
2260    =item tkey
2261    
2262    Tracing key for the current program.
2263    
2264    =item RETURN
2265    
2266    Returns the name of the file to contain the trace output.
2267    
2268    =back
2269    
2270    =cut
2271    
2272    sub EmergencyFileTarget {
2273        # Get the parameters.
2274        my ($tkey) = @_;
2275        # Compute the emergency tracing file name.
2276        return "$FIG_Config::temp/trace$tkey.log";
2277      }      }
2278    
2279    =head3 EmergencyTracingDest
2280    
2281    C<< my $dest = Tracer::EmergencyTracingDest($tkey, $myDest); >>
2282    
2283    This method converts an emergency tracing destination to a real
2284    tracing destination. The main difference is that if the
2285    destination is C<FILE> or C<APPEND>, we convert it to file
2286    output.
2287    
2288    =over 4
2289    
2290    =item tkey
2291    
2292    Tracing key for this environment.
2293    
2294    =item myDest
2295    
2296    Destination from the emergency tracing file.
2297    
2298    =item RETURN
2299    
2300    Returns a destination that can be passed into L</TSetup>.
2301    
2302    =back
2303    
2304    =cut
2305    
2306    sub EmergencyTracingDest {
2307        # Get the parameters.
2308        my ($tkey, $myDest) = @_;
2309        # Declare the return variable.
2310        my $retVal;
2311        # Process according to the destination value.
2312        if ($myDest eq 'FILE') {
2313            $retVal = ">" . EmergencyFileTarget($tkey);
2314        } elsif ($myDest eq 'APPEND') {
2315            $retVal = ">>" . EmergencyFileTarget($tkey);
2316        } else {
2317            $retVal = $myDest;
2318        }
2319        # Return the result.
2320        return $retVal;
2321    }
2322    
2323    =head3 Emergency
2324    
2325    C<< Emergency($key, $hours, $dest, $level, @modules); >>
2326    
2327    Turn on emergency tracing. This method can only be invoked over the web and is
2328    should not be called if debug mode is off. The caller specifies the duration of the
2329    emergency in hours, the desired tracing destination, the trace level,
2330    and a list of the trace modules to activate. For the length of the duration, when a
2331    program in an environment with the specified tracing key active invokes a Sprout
2332    CGI script, tracing will be turned on automatically. See L</TSetup> for more
2333    about tracing setup and L</ETracing> for more about emergency tracing.
2334    
2335    =over 4
2336    
2337    =item tkey
2338    
2339    The tracing key. This is used to identify the control file and the trace file.
2340    
2341    =item hours
2342    
2343    Number of hours to keep emergency tracing alive.
2344    
2345    =item dest
2346    
2347    Tracing destination. If no path information is specified for a file
2348    destination, it is put in the FIG temporary directory.
2349    
2350    =item level
2351    
2352    Tracing level. A higher level means more trace messages.
2353    
2354    =item modules
2355    
2356    A list of the tracing modules to activate.
2357    
2358    =back
2359    
2360    =cut
2361    
2362    sub Emergency {
2363        # Get the parameters.
2364        my ($tkey, $hours, $dest, $level, @modules) = @_;
2365        # Create the emergency file.
2366        my $specFile = EmergencyFileName($tkey);
2367        my $outHandle = Open(undef, ">$specFile");
2368        print $outHandle join("\n", $hours, $dest, $level, @modules, "");
2369    }
2370    
2371    =head3 EmergencyKey
2372    
2373    C<< my $tkey = EmergencyKey($parameter); >>
2374    
2375    Return the Key to be used for emergency tracing. This could be an IP address,
2376     a session ID, or a user name, depending on the environment.
2377    
2378    =over 4
2379    
2380    =item parameter
2381    
2382    Parameter defining the method for finding the tracing key. If it is a scalar,
2383    then it is presumed to be the tracing key itself. If it is a CGI object, then
2384    the tracing key is taken from the C<IP> cookie. Otherwise, the tracing key is
2385    taken from the C<TRACING> environment variable.
2386    
2387    =item RETURN
2388    
2389    Returns the key to be used for labels in emergency tracing.
2390    
2391    =back
2392    
2393    =cut
2394    
2395    sub EmergencyKey {
2396        # Get the parameters.
2397        my ($parameter) = @_;
2398        # Declare the return variable.
2399        my $retVal;
2400        # Determine the parameter type.
2401        if (! defined $parameter) {
2402            # Here we're supposed to check the environment.
2403            $retVal = $ENV{TRACING};
2404        } else {
2405            my $ptype = ref $parameter;
2406            if ($ptype eq 'CGI') {
2407                # Here we were invoked from a web page. Look for a cookie.
2408                $retVal = $parameter->cookie('IP');
2409            } elsif (! $ptype) {
2410                # Here the key was passed in.
2411                $retVal = $parameter;
2412            }
2413        }
2414        # If no luck finding a key, use the PID.
2415        if (! defined $retVal) {
2416            $retVal = $$;
2417        }
2418        # Return the result.
2419        return $retVal;
2420    }
2421    
2422    
2423    =head3 TraceParms
2424    
2425    C<< Tracer::TraceParms($cgi); >>
2426    
2427    Trace the CGI parameters at trace level CGI => 3 and the environment variables
2428    at level CGI => 4.
2429    
2430    =over 4
2431    
2432    =item cgi
2433    
2434    CGI query object containing the parameters to trace.
2435    
2436    =back
2437    
2438    =cut
2439    
2440    sub TraceParms {
2441        # Get the parameters.
2442        my ($cgi) = @_;
2443        if (T(CGI => 3)) {
2444            # Here we want to trace the parameter data.
2445            my @names = $cgi->param;
2446            for my $parmName (sort @names) {
2447                # Note we skip the Trace parameters, which are for our use only.
2448                if ($parmName ne 'Trace' && $parmName ne 'TF') {
2449                    my @values = $cgi->param($parmName);
2450                    Trace("CGI: $parmName = " . join(", ", @values));
2451                }
2452            }
2453            # Display the request method.
2454            my $method = $cgi->request_method();
2455            Trace("Method: $method");
2456        }
2457        if (T(CGI => 4)) {
2458            # Here we want the environment data too.
2459            for my $envName (sort keys %ENV) {
2460                Trace("ENV: $envName = $ENV{$envName}");
2461            }
2462        }
2463    }
2464    
2465    =head3 ScriptFinish
2466    
2467    C<< ScriptFinish($webData, $varHash); >>
2468    
2469    Output a web page at the end of a script. Either the string to be output or the
2470    name of a template file can be specified. If the second parameter is omitted,
2471    it is assumed we have a string to be output; otherwise, it is assumed we have the
2472    name of a template file. The template should have the variable C<DebugData>
2473    specified in any form that invokes a standard script. If debugging mode is turned
2474    on, a form field will be put in that allows the user to enter tracing data.
2475    Trace messages will be placed immediately before the terminal C<BODY> tag in
2476    the output, formatted as a list.
2477    
2478    A typical standard script would loook like the following.
2479    
2480        BEGIN {
2481            # Print the HTML header.
2482            print "CONTENT-TYPE: text/html\n\n";
2483        }
2484        use Tracer;
2485        use CGI;
2486        use FIG;
2487        # ... more uses ...
2488    
2489        my ($cgi, $varHash) = ScriptSetup();
2490        eval {
2491            # ... get data from $cgi, put it in $varHash ...
2492        };
2493        if ($@) {
2494            Trace("Script Error: $@") if T(0);
2495        }
2496        ScriptFinish("Html/MyTemplate.html", $varHash);
2497    
2498    The idea here is that even if the script fails, you'll see trace messages and
2499    useful output.
2500    
2501    =over 4
2502    
2503    =item webData
2504    
2505    A string containing either the full web page to be written to the output or the
2506    name of a template file from which the page is to be constructed. If the name
2507    of a template file is specified, then the second parameter must be present;
2508    otherwise, it must be absent.
2509    
2510    =item varHash (optional)
2511    
2512    If specified, then a reference to a hash mapping variable names for a template
2513    to their values. The template file will be read into memory, and variable markers
2514    will be replaced by data in this hash reference.
2515    
2516    =back
2517    
2518    =cut
2519    
2520    sub ScriptFinish {
2521        # Get the parameters.
2522        my ($webData, $varHash) = @_;
2523        # Check for a template file situation.
2524        my $outputString;
2525        if (defined $varHash) {
2526            # Here we have a template file. We need to determine the template type.
2527            my $template;
2528            if ($FIG_Config::template_url && $webData =~ /\.php$/) {
2529                $template = "$FIG_Config::template_url/$webData";
2530            } else {
2531                $template = "<<$webData";
2532            }
2533            $outputString = PageBuilder::Build($template, $varHash, "Html");
2534        } else {
2535            # Here the user gave us a raw string.
2536            $outputString = $webData;
2537        }
2538        # Check for trace messages.
2539        if ($Destination ne "NONE" && $TraceLevel > 0) {
2540            # We have trace messages, so we want to put them at the end of the body. This
2541            # is either at the end of the whole string or at the beginning of the BODY
2542            # end-tag.
2543            my $pos = length $outputString;
2544            if ($outputString =~ m#</body>#gi) {
2545                $pos = (pos $outputString) - 7;
2546            }
2547            # If the trace messages were queued, we unroll them. Otherwise, we display the
2548            # destination.
2549            my $traceHtml;
2550            if ($Destination eq "QUEUE") {
2551                $traceHtml = QTrace('Html');
2552            } elsif ($Destination =~ /^>>(.+)$/) {
2553                # Here the tracing output it to a file. We code it as a hyperlink so the user
2554                # can copy the file name into the clipboard easily.
2555                my $actualDest = $1;
2556                $traceHtml = "<p>Tracing output to $actualDest.</p>\n";
2557            } else {
2558                # Here we have one of the special destinations.
2559                $traceHtml = "<P>Tracing output type is $Destination.</p>\n";
2560            }
2561            substr $outputString, $pos, 0, $traceHtml;
2562        }
2563        # Write the output string.
2564        print $outputString;
2565    }
2566    
2567    =head3 Insure
2568    
2569    C<< Insure($dirName); >>
2570    
2571    Insure a directory is present.
2572    
2573    =over 4
2574    
2575    =item dirName
2576    
2577    Name of the directory to check. If it does not exist, it will be created.
2578    
2579    =back
2580    
2581    =cut
2582    
2583    sub Insure {
2584        my ($dirName) = @_;
2585        if (! -d $dirName) {
2586            Trace("Creating $dirName directory.") if T(2);
2587            eval { mkpath $dirName; };
2588            if ($@) {
2589                Confess("Error creating $dirName: $@");
2590            }
2591        }
2592    }
2593    
2594    =head3 ChDir
2595    
2596    C<< ChDir($dirName); >>
2597    
2598    Change to the specified directory.
2599    
2600    =over 4
2601    
2602    =item dirName
2603    
2604    Name of the directory to which we want to change.
2605    
2606    =back
2607    
2608    =cut
2609    
2610    sub ChDir {
2611        my ($dirName) = @_;
2612        if (! -d $dirName) {
2613            Confess("Cannot change to directory $dirName: no such directory.");
2614        } else {
2615            Trace("Changing to directory $dirName.") if T(4);
2616            my $okFlag = chdir $dirName;
2617            if (! $okFlag) {
2618                Confess("Error switching to directory $dirName.");
2619            }
2620        }
2621    }
2622    
2623    =head3 SendSMS
2624    
2625    C<< my $msgID = Tracer::SendSMS($phoneNumber, $msg); >>
2626    
2627    Send a text message to a phone number using Clickatell. The FIG_Config file must contain the
2628    user name, password, and API ID for the relevant account in the hash reference variable
2629    I<$FIG_Config::phone>, using the keys C<user>, C<password>, and C<api_id>. For
2630    example, if the user name is C<BruceTheHumanPet>, the password is C<silly>, and the API ID
2631    is C<2561022>, then the FIG_Config file must contain
2632    
2633        $phone =  { user => 'BruceTheHumanPet',
2634                    password => 'silly',
2635                    api_id => '2561022' };
2636    
2637    The original purpose of this method was to insure Bruce would be notified immediately when the
2638    Sprout Load terminates. Care should be taken if you do not wish Bruce to be notified immediately
2639    when you call this method.
2640    
2641    The message ID will be returned if successful, and C<undef> if an error occurs.
2642    
2643    =over 4
2644    
2645    =item phoneNumber
2646    
2647    Phone number to receive the message, in international format. A United States phone number
2648    would be prefixed by "1". A British phone number would be prefixed by "44".
2649    
2650    =item msg
2651    
2652    Message to send to the specified phone.
2653    
2654    =item RETURN
2655    
2656    Returns the message ID if successful, and C<undef> if the message could not be sent.
2657    
2658    =back
2659    
2660    =cut
2661    
2662    sub SendSMS {
2663        # Get the parameters.
2664        my ($phoneNumber, $msg) = @_;
2665        # Declare the return variable. If we do not change it, C<undef> will be returned.
2666        my $retVal;
2667        # Only proceed if we have phone support.
2668        if (! defined $FIG_Config::phone) {
2669            Trace("Phone support not present in FIG_Config.") if T(1);
2670        } else {
2671            # Get the phone data.
2672            my $parms = $FIG_Config::phone;
2673            # Get the Clickatell URL.
2674            my $url = "http://api.clickatell.com/http/";
2675            # Create the user agent.
2676            my $ua = LWP::UserAgent->new;
2677            # Request a Clickatell session.
2678            my $resp = $ua->post("$url/sendmsg", { user => $parms->{user},
2679                                         password => $parms->{password},
2680                                         api_id => $parms->{api_id},
2681                                         to => $phoneNumber,
2682                                         text => $msg});
2683            # Check for an error.
2684            if (! $resp->is_success) {
2685                Trace("Alert failed.") if T(1);
2686            } else {
2687                # Get the message ID.
2688                my $rstring = $resp->content;
2689                if ($rstring =~ /^ID:\s+(.*)$/) {
2690                    $retVal = $1;
2691                } else {
2692                    Trace("Phone attempt failed with $rstring") if T(1);
2693                }
2694            }
2695        }
2696        # Return the result.
2697        return $retVal;
2698    }
2699    
2700    =head3 CommaFormat
2701    
2702    C<< my $formatted = Tracer::CommaFormat($number); >>
2703    
2704    Insert commas into a number.
2705    
2706    =over 4
2707    
2708    =item number
2709    
2710    A sequence of digits.
2711    
2712    =item RETURN
2713    
2714    Returns the same digits with commas strategically inserted.
2715    
2716    =back
2717    
2718    =cut
2719    
2720    sub CommaFormat {
2721        # Get the parameters.
2722        my ($number) = @_;
2723        # Pad the length up to a multiple of three.
2724        my $padded = "$number";
2725        $padded = " " . $padded while length($padded) % 3 != 0;
2726        # This is a fancy PERL trick. The parentheses in the SPLIT pattern
2727        # cause the delimiters to be included in the output stream. The
2728        # GREP removes the empty strings in between the delimiters.
2729        my $retVal = join(",", grep { $_ ne '' } split(/(...)/, $padded));
2730        # Clean out the spaces.
2731        $retVal =~ s/ //g;
2732        # Return the result.
2733        return $retVal;
2734    }
2735    =head3 SetPermissions
2736    
2737    C<< Tracer::SetPermissions($dirName, $group, $mask, %otherMasks); >>
2738    
2739    Set the permissions for a directory and all the files and folders inside it.
2740    In addition, the group ownership will be changed to the specified value.
2741    
2742    This method is more vulnerable than most to permission and compatability
2743    problems, so it does internal error recovery.
2744    
2745    =over 4
2746    
2747    =item dirName
2748    
2749    Name of the directory to process.
2750    
2751    =item group
2752    
2753    Name of the group to be assigned.
2754    
2755    =item mask
2756    
2757    Permission mask. Bits that are C<1> in this mask will be ORed into the
2758    permission bits of any file or directory that does not already have them
2759    set to 1.
2760    
2761    =item otherMasks
2762    
2763    Map of search patterns to permission masks. If a directory name matches
2764    one of the patterns, that directory and all its members and subdirectories
2765    will be assigned the new pattern. For example, the following would
2766    assign 01664 to most files, but would use 01777 for directories named C<tmp>.
2767    
2768        Tracer::SetPermissions($dirName, 'fig', 01664, '^tmp$' => 01777);
2769    
2770    The list is ordered, so the following would use 0777 for C<tmp1> and
2771    0666 for C<tmp>, C<tmp2>, or C<tmp3>.
2772    
2773        Tracer::SetPermissions($dirName, 'fig', 01664, '^tmp1' => 0777,
2774                                                       '^tmp' => 0666);
2775    
2776    Note that the pattern matches are all case-insensitive, and only directory
2777    names are matched, not file names.
2778    
2779    =back
2780    
2781    =cut
2782    
2783    sub SetPermissions {
2784        # Get the parameters.
2785        my ($dirName, $group, $mask, @otherMasks) = @_;
2786        # Set up for error recovery.
2787        eval {
2788            # Switch to the specified directory.
2789            ChDir($dirName);
2790            # Get the group ID.
2791            my $gid = getgrnam($group);
2792            # Get the mask for tracing.
2793            my $traceMask = sprintf("%04o", $mask) . "($mask)";
2794            Trace("Fixing permissions for directory $dirName using group $group($gid) and mask $traceMask.") if T(2);
2795            my $fixCount = 0;
2796            my $lookCount = 0;
2797            # @dirs will be a stack of directories to be processed.
2798            my @dirs = (getcwd());
2799            while (scalar(@dirs) > 0) {
2800                # Get the current directory.
2801                my $dir = pop @dirs;
2802                # Check for a match to one of the specified directory names. To do
2803                # that, we need to pull the individual part of the name off of the
2804                # whole path.
2805                my $simpleName = $dir;
2806                if ($dir =~ m!/([^/]+)$!) {
2807                    $simpleName = $1;
2808                }
2809                Trace("Simple directory name for $dir is $simpleName.") if T(4);
2810                # Search for a match.
2811                my $match = 0;
2812                my $i;
2813                for ($i = 0; $i < $#otherMasks && ! $match; $i += 2) {
2814                    my $pattern = $otherMasks[$i];
2815                    if ($simpleName =~ /$pattern/i) {
2816                        $match = 1;
2817                    }
2818                }
2819                # Check for a match. Note we use $i-1 because the loop added 2
2820                # before terminating due to the match.
2821                if ($match && $otherMasks[$i-1] != $mask) {
2822                    # This directory matches one of the incoming patterns, and it's
2823                    # a different mask, so we process it recursively with that mask.
2824                    SetPermissions($dir, $group, $otherMasks[$i-1], @otherMasks);
2825                } else {
2826                    # Here we can process normally. Get all of the non-hidden members.
2827                    my @submems = OpenDir($dir, 1);
2828                    for my $submem (@submems) {
2829                        # Get the full name.
2830                        my $thisMem = "$dir/$submem";
2831                        Trace("Checking member $thisMem.") if T(4);
2832                        $lookCount++;
2833                        if ($lookCount % 1000 == 0) {
2834                            Trace("$lookCount members examined. Current is $thisMem. Mask is $traceMask") if T(3);
2835                        }
2836                        # Fix the group.
2837                        chown -1, $gid, $thisMem;
2838                        # Insure this member is not a symlink.
2839                        if (! -l $thisMem) {
2840                            # Get its info.
2841                            my $fileInfo = stat $thisMem;
2842                            # Only proceed if we got the info. Otherwise, it's a hard link
2843                            # and we want to skip it anyway.
2844                            if ($fileInfo) {
2845                                my $fileMode = $fileInfo->mode;
2846                                if (($fileMode & $mask) != $mask) {
2847                                    # Fix this member.
2848                                    $fileMode |= $mask;
2849                                    chmod $fileMode, $thisMem;
2850                                    $fixCount++;
2851                                }
2852                                # If it's a subdirectory, stack it.
2853                                if (-d $thisMem) {
2854                                    push @dirs, $thisMem;
2855                                }
2856                            }
2857                        }
2858                    }
2859                }
2860            }
2861            Trace("$lookCount files and directories processed, $fixCount fixed.") if T(2);
2862        };
2863        # Check for an error.
2864        if ($@) {
2865            Confess("SetPermissions error: $@");
2866        }
2867    }
2868    
2869    =head3 CompareLists
2870    
2871    C<< my ($inserted, $deleted) = Tracer::CompareLists(\@newList, \@oldList, $keyIndex); >>
2872    
2873    Compare two lists of tuples, and return a hash analyzing the differences. The lists
2874    are presumed to be sorted alphabetically by the value in the $keyIndex column.
2875    The return value contains a list of items that are only in the new list
2876    (inserted) and only in the old list (deleted).
2877    
2878    =over 4
2879    
2880    =item newList
2881    
2882    Reference to a list of new tuples.
2883    
2884    =item oldList
2885    
2886    Reference to a list of old tuples.
2887    
2888    =item keyIndex (optional)
2889    
2890    Index into each tuple of its key field. The default is 0.
2891    
2892    =item RETURN
2893    
2894    Returns a 2-tuple consisting of a reference to the list of items that are only in the new
2895    list (inserted) followed by a reference to the list of items that are only in the old
2896    list (deleted).
2897    
2898    =back
2899    
2900    =cut
2901    
2902    sub CompareLists {
2903        # Get the parameters.
2904        my ($newList, $oldList, $keyIndex) = @_;
2905        if (! defined $keyIndex) {
2906            $keyIndex = 0;
2907        }
2908        # Declare the return variables.
2909        my ($inserted, $deleted) = ([], []);
2910        # Loop through the two lists simultaneously.
2911        my ($newI, $oldI) = (0, 0);
2912        my ($newN, $oldN) = (scalar @{$newList}, scalar @{$oldList});
2913        while ($newI < $newN || $oldI < $oldN) {
2914            # Get the current object in each list. Note that if one
2915            # of the lists is past the end, we'll get undef.
2916            my $newItem = $newList->[$newI];
2917            my $oldItem = $oldList->[$oldI];
2918            if (! defined($newItem) || defined($oldItem) && $newItem->[$keyIndex] gt $oldItem->[$keyIndex]) {
2919                # The old item is not in the new list, so mark it deleted.
2920                push @{$deleted}, $oldItem;
2921                $oldI++;
2922            } elsif (! defined($oldItem) || $oldItem->[$keyIndex] gt $newItem->[$keyIndex]) {
2923                # The new item is not in the old list, so mark it inserted.
2924                push @{$inserted}, $newItem;
2925                $newI++;
2926            } else {
2927                # The item is in both lists, so push forward.
2928                $oldI++;
2929                $newI++;
2930            }
2931        }
2932        # Return the result.
2933        return ($inserted, $deleted);
2934    }
2935    
2936    =head3 GetLine
2937    
2938    C<< my @data = Tracer::GetLine($handle); >>
2939    
2940    Read a line of data from a tab-delimited file.
2941    
2942    =over 4
2943    
2944    =item handle
2945    
2946    Open file handle from which to read.
2947    
2948    =item RETURN
2949    
2950    Returns a list of the fields in the record read. The fields are presumed to be
2951    tab-delimited. If we are at the end of the file, then an empty list will be
2952    returned. If an empty line is read, a single list item consisting of a null
2953    string will be returned.
2954    
2955    =back
2956    
2957    =cut
2958    
2959    sub GetLine {
2960        # Get the parameters.
2961        my ($handle) = @_;
2962        # Declare the return variable.
2963        my @retVal = ();
2964        # Read from the file.
2965        my $line = <$handle>;
2966        # Only proceed if we found something.
2967        if (defined $line) {
2968            # Remove the new-line.
2969            chomp $line;
2970            # If the line is empty, return a single empty string; otherwise, parse
2971            # it into fields.
2972            if ($line eq "") {
2973                push @retVal, "";
2974            } else {
2975                push @retVal, split /\t/,$line;
2976            }
2977        }
2978        # Return the result.
2979        return @retVal;
2980    }
2981    
2982    =head3 PutLine
2983    
2984    C<< Tracer::PutLine($handle, \@fields); >>
2985    
2986    Write a line of data to a tab-delimited file. The specified field values will be
2987    output in tab-separated form, with a trailing new-line.
2988    
2989    =over 4
2990    
2991    =item handle
2992    
2993    Output file handle.
2994    
2995    =item fields
2996    
2997    List of field values.
2998    
2999    =back
3000    
3001    =cut
3002    
3003    sub PutLine {
3004        # Get the parameters.
3005        my ($handle, $fields) = @_;
3006        # Write the data.
3007        print $handle join("\t", @{$fields}) . "\n";
3008    }
3009    
3010    =head3 GenerateURL
3011    
3012    C<< my $queryUrl = Tracer::GenerateURL($page, %parameters); >>
3013    
3014    Generate a GET-style URL for the specified page with the specified parameter
3015    names and values. The values will be URL-escaped automatically. So, for
3016    example
3017    
3018        Tracer::GenerateURL("form.cgi", type => 1, string => "\"high pass\" or highway")
3019    
3020    would return
3021    
3022        form.cgi?type=1&string=%22high%20pass%22%20or%20highway
3023    
3024    =over 4
3025    
3026    =item page
3027    
3028    Page URL.
3029    
3030    =item parameters
3031    
3032    Hash mapping parameter names to parameter values.
3033    
3034    =item RETURN
3035    
3036    Returns a GET-style URL that goes to the specified page and passes in the
3037    specified parameters and values.
3038    
3039    =back
3040    
3041    =cut
3042    
3043    sub GenerateURL {
3044        # Get the parameters.
3045        my ($page, %parameters) = @_;
3046        # Prime the return variable with the page URL.
3047        my $retVal = $page;
3048        # Loop through the parameters, creating parameter elements in a list.
3049        my @parmList = map { "$_=" . uri_escape($parameters{$_}) } keys %parameters;
3050        # If the list is nonempty, tack it on.
3051        if (@parmList) {
3052            $retVal .= "?" . join("&", @parmList);
3053        }
3054        # Return the result.
3055        return $retVal;
3056  }  }
3057    
3058  1;  1;

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