From 7511fdd8589b5272bdbb79508f1a186def235faa Mon Sep 17 00:00:00 2001
From: Patrick Meidl <pm2@sanger.ac.uk>
Date: Fri, 29 Jun 2007 14:37:25 +0000
Subject: [PATCH] introduced loglevels
---
modules/Bio/EnsEMBL/Utils/Logger.pm | 192 +++++++++++++++-------------
1 file changed, 105 insertions(+), 87 deletions(-)
diff --git a/modules/Bio/EnsEMBL/Utils/Logger.pm b/modules/Bio/EnsEMBL/Utils/Logger.pm
index 490d0cddf7..70c0f73c74 100644
--- a/modules/Bio/EnsEMBL/Utils/Logger.pm
+++ b/modules/Bio/EnsEMBL/Utils/Logger.pm
@@ -49,8 +49,17 @@ no warnings 'uninitialized';
use FindBin qw($Bin $Script);
use POSIX qw(strftime);
use Bio::EnsEMBL::Utils::Argument qw(rearrange);
-use Bio::EnsEMBL::Utils::Exception qw(throw warning);
-
+use Bio::EnsEMBL::Utils::Exception qw(throw);
+use Bio::EnsEMBL::Utils::ScriptUtils qw(parse_bytes);
+
+my %level_defs = (
+ 'error' => 1,
+ 'warn' => 2,
+ 'warning' => 2,
+ 'info' => 3,
+ 'debug' => 4,
+ 'verbose' => 4,
+);
=head2 new
@@ -59,7 +68,7 @@ use Bio::EnsEMBL::Utils::Exception qw(throw warning);
'/path/to/ensembl');
Description : constructor
Return type : Bio::EnsEMBL::Utils::ConversionSupport object
- Exceptions : thrown if no serverroot is provided
+ Exceptions : thrown on invalid loglevel
Caller : general
=cut
@@ -68,8 +77,8 @@ sub new {
my $caller = shift;
my $class = ref($caller) || $caller;
- my ($logfile, $logpath, $logappend, $verbose, $is_component) = rearrange(
- ['LOGFILE', 'LOGPATH', 'LOGAPPEND', 'VERBOSE', 'IS_COMPONENT'], @_);
+ my ($logfile, $logpath, $logappend, $loglevel, $is_component) = rearrange(
+ ['LOGFILE', 'LOGPATH', 'LOGAPPEND', 'LOGLEVEL', 'IS_COMPONENT'], @_);
my $self = { '_warnings' => 0, };
bless ($self, $class);
@@ -78,14 +87,22 @@ sub new {
$self->logfile($logfile);
$self->logpath($logpath);
$self->logappend($logappend);
- $self->verbose($verbose);
$self->is_component($is_component);
+
+ $loglevel ||= 'info';
+ if ($loglevel =~ /^\d+$/ and $loglevel > 0 and $loglevel < 5) {
+ $self->{'loglevel'} = $loglevel;
+ } elsif ($level_defs{lc($loglevel)}) {
+ $self->{'loglevel'} = $level_defs{lc($loglevel)};
+ } else {
+ throw('Unknown loglevel: $loglevel.');
+ }
return $self;
}
-=head2 log
+=head2 log_generic
Arg[1] : String $txt - the text to log
Arg[2] : Int $indent - indentation level for log message
@@ -100,11 +117,17 @@ sub new {
=cut
-sub log {
- my ($self, $txt, $indent) = @_;
+sub log_generic {
+ my ($self, $txt, $indent, $stamped) = @_;
$indent ||= 0;
my $fh = $self->log_filehandle;
+
+ # append timestamp and memory usage to log text if requested
+ if ($stamped) {
+ $txt =~ s/(\n*)$//;
+ $txt .= " ".$self->date_and_mem.$1;
+ }
# strip off leading linebreaks so that indenting doesn't break
$txt =~ s/^(\n*)//;
@@ -118,32 +141,7 @@ sub log {
}
-=head2 log_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 $self->log and increases the warning counter.
- Return type : true on success
- Exceptions : none
- Caller : general
-
-=cut
-
-sub log_warning {
- my ($self, $txt, $indent) = @_;
-
- $txt = "WARNING: " . $txt;
- $self->log($txt, $indent);
-
- $self->{'_warnings'}++;
-
- return(1);
-}
-
-
-=head2 log_error
+=head2 error
Arg[1] : String $txt - the error text to log
Arg[2] : Int $indent - indentation level for log message
@@ -156,64 +154,77 @@ sub log_warning {
=cut
-sub log_error {
- my ($self, $txt, $indent) = @_;
+sub error {
+ my ($self, $txt, $indent, $stamped) = @_;
+
+ return(0) unless ($self->{'loglevel'} >= 1);
$txt = "ERROR: ".$txt;
- $self->log($txt, $indent);
+ $self->log_generic($txt, $indent, $stamped);
- $self->log("\nExiting prematurely.\n\n");
- $self->log("Runtime: ".$self->runtime." ".$self->date_and_mem."\n\n");
+ $self->log_generic("\nExiting prematurely.\n\n");
+ $self->log_generic("Runtime: ".$self->runtime." ".$self->date_and_mem."\n\n");
exit(1);
}
-=head2 log_verbose
+=head2 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_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
+ $support->log_warning('Log foo.\n', 1);
+ Description : Logs a message via $self->log and increases the warning counter.
+ Return type : true on success
Exceptions : none
Caller : general
=cut
-sub log_verbose {
- my ($self, $txt, $indent) = @_;
+sub warning {
+ my ($self, $txt, $indent, $stamped) = @_;
+
+ return(0) unless ($self->{'loglevel'} >= 2);
+
+ $txt = "WARNING: " . $txt;
+ $self->log_generic($txt, $indent, $stamped);
+
+ $self->{'_warnings'}++;
+
+ return(1);
+}
+
+
+sub info {
+ my ($self, $txt, $indent, $stamped) = @_;
- return(0) unless $self->verbose;
+ return(0) unless ($self->{'loglevel'} >= 3);
- $self->log($txt, $indent);
+ $self->log_generic($txt, $indent, $stamped);
return(1);
}
-=head2 log_stamped
+=head2 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_stamped('Log this stamped message.\n', 1);
- Description : Appends timestamp and memory usage to a message and logs it via
- $self->log
- Return type : TRUE on success
+ $support->log_verbose('Log this verbose message.\n', 1);
+ Description : Logs a message via $self->log if --verbose option was used
+ Return type : TRUE on success, FALSE if not verbose
Exceptions : none
Caller : general
=cut
-sub log_stamped {
- my ($self, $txt, $indent) = @_;
-
- # append timestamp and memory usage to log text
- $txt =~ s/(\n*)$//;
- $txt .= " ".$self->date_and_mem.$1;
-
- $self->log($txt, $indent);
+sub debug {
+ my ($self, $txt, $indent, $stamped) = @_;
+
+ return(0) unless ($self->{'loglevel'} >= 4);
+
+ $self->log_generic($txt, $indent, $stamped);
return(1);
}
@@ -235,7 +246,7 @@ sub log_progress {
my $log_str = "\r".(' 'x$indent)."$curr/$max (".int($curr/$max*100)."\%$mem)";
$log_str .= "\n" if ($curr == $max);
- $self->log($log_str);
+ $self->info($log_str);
}
}
@@ -259,7 +270,7 @@ sub log_progressbar {
my $log_str = "\r".(' 'x$indent)."[".('='x$index).(' 'x(20-$index))."] ${percent}\%";
$log_str .= "\n" if ($curr == $self->{'_progress'}->{$name}->{'max_val'});
- $self->log($log_str);
+ $self->info($log_str);
# increment counters
$self->{'_progress'}->{$name}->{'index'}++;
@@ -391,12 +402,12 @@ sub init_log {
my $script = "$hostname:$Bin/$Script";
my $user = `whoami`;
chomp $user;
- $self->log("Script: $script\nDate: ".$self->date."\nUser: $user\n");
+ $self->info("Script: $script\nDate: ".$self->date."\nUser: $user\n");
# print parameters the script is running with
if ($params) {
- $self->log("Parameters:\n\n");
- $self->log($params);
+ $self->info("Parameters:\n\n");
+ $self->info($params);
}
}
@@ -418,9 +429,9 @@ sub init_log {
sub finish_log {
my $self = shift;
- $self->log("\nAll done for $Script.\n");
- $self->log($self->warnings." warnings. ");
- $self->log("Runtime: ".$self->runtime." ".$self->date_and_mem."\n\n");
+ $self->info("\nAll done for $Script.\n");
+ $self->info($self->warning_count." warnings. ");
+ $self->info("Runtime: ".$self->runtime." ".$self->date_and_mem."\n\n");
return(1);
}
@@ -459,6 +470,7 @@ sub date_and_mem {
my $date = strftime "%Y-%m-%d %T", localtime;
my $mem = `ps -p $$ -o vsz |tail -1`;
chomp $mem;
+ $mem = parse_bytes($mem*1000);
return "[$date, mem $mem]";
}
@@ -496,7 +508,7 @@ sub mem {
}
-=head2 warnings
+=head2 warning_count
Example : print LOG "There were ".$support->warnings." warnings.\n";
Description : Returns the number of warnings encountered while running the
@@ -507,7 +519,7 @@ sub mem {
=cut
-sub warnings {
+sub warning_count {
my $self = shift;
return $self->{'_warnings'};
}
@@ -582,31 +594,37 @@ sub logappend {
=cut
-sub verbose {
+sub is_component {
my $self = shift;
- $self->{'_verbose'} = shift if (@_);
- return $self->{'_verbose'};
+ $self->{'_is_component'} = shift if (@_);
+ return $self->{'_is_component'};
}
-=head2
+#
+# deprecated methods (left here for backwards compatibility
+#
+sub log_error {
+ return $_[0]->error(@_);
+}
- Arg[1] :
- Example :
- Description :
- Return type :
- Exceptions :
- Caller :
- Status :
+sub log_warning {
+ return $_[0]->warning(@_);
+}
-=cut
+sub log {
+ return $_[0]->info(@_);
+}
-sub is_component {
- my $self = shift;
- $self->{'_is_component'} = shift if (@_);
- return $self->{'_is_component'};
+sub log_verbose {
+ return $_[0]->debug(@_);
}
+sub log_stamped {
+ return $_[0]->log(@_, 1);
+}
+
+
1;
--
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