Bio::EnsEMBL::Utils::Logger Class Reference

Public Member Functions
public Bio::EnsEMBL::Utils::ConversionSupport	new ()
public Boolean	log_generic ()
public void	error ()
public Boolean	warning ()
public	info ()
public Boolean	debug ()
public	log_progress ()
public	log_progressbar ()
public	init_progress ()
public Filehandle	log_filehandle ()
public	extract_log_identifier ()
public Filehandle	init_log ()
public Boolean	finish_log ()
public	runtime ()
public String	date_and_mem ()
public	time_and_mem ()
public String	date ()
public String	mem ()
public Int	warning_count ()
public	logfile ()
public	log_auto_id ()
public	logauto ()
public	create_auto_logfile ()
public	logpath ()
public	logappend ()
public	is_component ()
public	loglevel ()
public	log_error ()
public	log_warning ()
public	log ()
public	log_verbose ()
public	log_stamped ()

Detailed Description

Synopsis

my $serverroot = '/path/to/ensembl';
my $suport = new Bio::EnsEMBL::Utils::ConversionSupport($serverroot);
 
# parse common options
$support->parse_common_options;
 
# parse extra options for your script
$support->parse_extra_options( 'string_opt=s', 'numeric_opt=n' );
 
# ask user if he wants to run script with these parameters
$support->confirm_params;
 
# see individual method documentation for more stuff

Description

This module is a collection of common methods and provides helper
functions for the Vega release and schema conversion scripts. Amongst
others, it reads options from a config file, parses commandline options
and does logging.

Definition at line 36 of file Logger.pm.

Member Function Documentation

create_auto_logfile()

public Bio::EnsEMBL::Utils::Logger::create_auto_logfile

(

)

  Arg[1]      : 
  Example     :

  Description : 
  Return type : 
  Exceptions  : 
  Caller      : 
  Status      : At Risk
              : under development

Code:

date()

public String Bio::EnsEMBL::Utils::Logger::date

(

)

  Example     :

print "Date: " . $support->date . "\n";

  Description : Prints a nicely formatted timestamp (YYYY-DD-MM hh:mm:ss)
  Return type : String - the timestamp
  Exceptions  : none
  Caller      : general

Code:

date_and_mem()

public String Bio::EnsEMBL::Utils::Logger::date_and_mem

(

)

  Example     :

print LOG "Time, memory usage: ".$support->date_and_mem."\n";

  Description : Prints a timestamp and the memory usage of your script.
  Return type : String - timestamp and memory usage
  Exceptions  : none
  Caller      : general

Code:

debug()

public Boolean Bio::EnsEMBL::Utils::Logger::debug

(

)

  Arg[1]      : String $txt - the warning text to log
  Arg[2]      : Int $indent - indentation level for log message
  Example     :

my $log = $support->log_filehandle;
               $support->log_verbose('Log this verbose message.\n', 1);

  Description : Logs a message via $self->log if --verbose option was used
  Return type : TRUE on success, FALSE if not verbose
  Exceptions  : none
  Caller      : general

Code:

error()

public void Bio::EnsEMBL::Utils::Logger::error

(

)

  Arg[1]      : String $txt - the error text to log
  Arg[2]      : Int $indent - indentation level for log message
  Example     :

my $log = $support->log_filehandle;
               $support->log_error('Log foo.\n', 1);

  Description : Logs a message via $self->log and exits the script.
  Return type : none
  Exceptions  : none
  Caller      : general

Code:

extract_log_identifier()

public Bio::EnsEMBL::Utils::Logger::extract_log_identifier

(

)

  Arg[1]      : 
  Example     :

  Description : 
  Return type : 
  Exceptions  : 
  Caller      : 
  Status      :

Code:

finish_log()

public Boolean Bio::EnsEMBL::Utils::Logger::finish_log

(

)

  Example     :

$support->finish_log;

  Description : Writes footer information to a logfile. This includes the
                number of logged warnings, timestamp and memory footprint.
  Return type : TRUE on success
  Exceptions  : none
  Caller      : general

Code:

info()

public Bio::EnsEMBL::Utils::Logger::info

(

)

Undocumented method

Code:

init_log()

public Filehandle Bio::EnsEMBL::Utils::Logger::init_log

(

)

  Example     :

$support->init_log;

  Description : Opens a filehandle to the logfile and prints some header
                information to this file. This includes script name, date, user
                running the script and parameters the script will be running
                with.
  Return type : Filehandle - the log filehandle
  Exceptions  : none
  Caller      : general

Code:

init_progress()

public Bio::EnsEMBL::Utils::Logger::init_progress

(

)

Undocumented method

Code:

is_component()

public Bio::EnsEMBL::Utils::Logger::is_component

(

)

  Arg[1]      : 
  Example     :

  Description : 
  Return type : 
  Exceptions  : 
  Caller      : 
  Status      :

Code:

log()

public Bio::EnsEMBL::Utils::Logger::log

(

)

Undocumented method

Code:

log_auto_id()

public Bio::EnsEMBL::Utils::Logger::log_auto_id

(

)

  Arg[1]      : 
  Example     :

  Description : 
  Return type : 
  Exceptions  : 
  Caller      : 
  Status      :

Code:

log_error()

public Bio::EnsEMBL::Utils::Logger::log_error

(

)

Undocumented method

Code:

log_filehandle()

public Filehandle Bio::EnsEMBL::Utils::Logger::log_filehandle

(

)

  Arg[1]      : (optional) String $mode - file access mode
  Example     :

 my $log = $support->log_filehandle;
@section autotoc_md33 print to the filehandle
                print $log 'Lets start logging...\n';
@section autotoc_md34 log via the wrapper $self->log()
                $support->log('Another log message.\n');

  Description : Returns a filehandle for logging (STDERR by default, logfile if
                set from config or commandline). You can use the filehandle
                directly to print to, or use the smart wrapper $self->log().
                Logging mode (truncate or append) can be set by passing the
                mode as an argument to log_filehandle(), or with the
                --logappend commandline option (default: truncate)
  Return type : Filehandle - the filehandle to log to
  Exceptions  : thrown if logfile can't be opened
  Caller      : general

Code:

log_generic()

public Boolean Bio::EnsEMBL::Utils::Logger::log_generic

(

)

  Arg[1]      : String $txt - the text to log
  Arg[2]      : Int $indent - indentation level for log message
  Example     :

my $log = $support->log_filehandle;
               $support->log('Log foo.\n', 1);

  Description : Logs a message to the filehandle initialised by calling
                $self->log_filehandle(). You can supply an indentation level
                to get nice hierarchical log messages.
  Return type : true on success
  Exceptions  : thrown when no filehandle can be obtained
  Caller      : general

Code:

log_progress()

public Bio::EnsEMBL::Utils::Logger::log_progress

(

)

Undocumented method

Code:

log_progressbar()

public Bio::EnsEMBL::Utils::Logger::log_progressbar

(

)

Undocumented method

Code:

log_stamped()

public Bio::EnsEMBL::Utils::Logger::log_stamped

(

)

Undocumented method

Code:

log_verbose()

public Bio::EnsEMBL::Utils::Logger::log_verbose

(

)

Undocumented method

Code:

log_warning()

public Bio::EnsEMBL::Utils::Logger::log_warning

(

)

Undocumented method

Code:

logappend()

public Bio::EnsEMBL::Utils::Logger::logappend

(

)

  Arg[1]      : 
  Example     :

  Description : 
  Return type : 
  Exceptions  : 
  Caller      : 
  Status      :

Code:

logauto()

public Bio::EnsEMBL::Utils::Logger::logauto

(

)

Undocumented method

Code:

logfile()

public Bio::EnsEMBL::Utils::Logger::logfile

(

)

  Arg[1]      : 
  Example     :

  Description : Getter and setter for the logfile
  Return type :
  Exceptions  : 
  Caller      : 
  Status      :

Code:

loglevel()

public Bio::EnsEMBL::Utils::Logger::loglevel

(

)

Undocumented method

Code:

logpath()

public Bio::EnsEMBL::Utils::Logger::logpath

(

)

  Arg[1]      : 
  Example     :

  Description : 
  Return type : 
  Exceptions  : 
  Caller      : 
  Status      :

Code:

mem()

public String Bio::EnsEMBL::Utils::Logger::mem

(

)

  Example     :

print "Memory usage: " . $support->mem . "\n";

  Description : Prints the memory used by your script. Not sure about platform
                dependence of this call ...
  Return type : String - memory usage
  Exceptions  : none
  Caller      : general

Code:

new()

public Bio::EnsEMBL::Utils::ConversionSupport Bio::EnsEMBL::Utils::Logger::new

(

)

  Arg[1]      : String $serverroot - root directory of your ensembl sandbox
  Example     :

my $support = new Bio::EnsEMBL::Utils::ConversionSupport(
                                       '/path/to/ensembl');

  Description : constructor
  Return type : Bio::EnsEMBL::Utils::ConversionSupport object
  Exceptions  : thrown on invalid loglevel
  Caller      : general

Code:

runtime()

public Bio::EnsEMBL::Utils::Logger::runtime

(

)

Undocumented method

Code:

time_and_mem()

public Bio::EnsEMBL::Utils::Logger::time_and_mem

(

)

Undocumented method

Code:

warning()

public Boolean Bio::EnsEMBL::Utils::Logger::warning

(

)

  Arg[1]      : String $txt - the warning text to log
  Arg[2]      : Int $indent - indentation level for log message
  Example     :

my $log = $support->log_filehandle;
               $support->log_warning('Log foo.\n', 1);

  Description : Logs a message via $self->log and increases the warning counter.
  Return type : true on success
  Exceptions  : none
  Caller      : general

Code:

warning_count()

public Int Bio::EnsEMBL::Utils::Logger::warning_count

(

)

  Example     :

print LOG "There were ".$support->warnings." warnings.\n";

  Description : Returns the number of warnings encountered while running the
                script (the warning counter is increased by $self->log_warning).
  Return type : Int - number of warnings
  Exceptions  : none
  Caller      : general

Code:

---

The documentation for this class was generated from the following file:

• ensembl/modules/Bio/EnsEMBL/Utils/Logger.pm