Rendering (#443)

* display from where is comming the config by default * re-activate progress bar and display AGAT HEADER even for sq script. Display by default origin of the config file
NBISweden · Mar 20, 2024 · 6bff76e · 6bff76e
1 parent 39e841d
commit 6bff76e
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Showing 3 changed files with 12 additions and 7 deletions.
diff --git a/lib/AGAT/AGAT.pm b/lib/AGAT/AGAT.pm
@@ -140,10 +140,15 @@ MESSAGE
 sub get_agat_config{
 	my ($args)=@_;
 
+	# Print the header. Put here because get_agat_config it the first function call for _sp_ and _sq_ screen
+	print AGAT::AGAT::get_agat_header();
+
 	my ($config_file_provided);
 	if( defined($args->{config_file_in}) ) { $config_file_provided = $args->{config_file_in};}
 
+	# Get the config file
 	my $config_file_checked = get_config({type => "local", config_file_in => $config_file_provided}); #try local first, if none will take the original
+	# Load the config
 	my $config = load_config({ config_file => $config_file_checked});
 	check_config({ config => $config});
 	return $config;

diff --git a/lib/AGAT/Config.pm b/lib/AGAT/Config.pm
@@ -84,7 +84,7 @@ sub get_config{
 	# -------------- INPUT --------------
 	# -- Declare all variables and fill them --
 	my ( $verbose, $log, $debug, $type, $config_file_in ) ;
-	if( ! defined($args->{verbose}) ) { $verbose = undef;} else{ $verbose = $args->{verbose}; }
+	if( ! defined($args->{verbose}) ) { $verbose = 1;} else{ $verbose = $args->{verbose}; }
 	if( ! defined($args->{log}) ) { $log = undef;} else{ $log = $args->{log}; }
 	if( ! defined($args->{debug}) ) { $debug = undef;} else{ $debug = $args->{debug}; }
 	if( ! defined($args->{type}) ) { $type = "local";} else{ $type = $args->{type};}
@@ -104,24 +104,24 @@ sub get_config{
 		if ($type eq "local") {
 			$path = $run_dir."/".$config_file;
 			if (-e $path){
-				dual_print($log, "Using $config_file file found in your working directory.\n", $verbose );
+				dual_print($log, "=> Using $config_file config file found in your working directory.\n", $verbose );
 			} else {
 				$path = undef;
 			}
 		}
 		#otherwise use the standard location ones
 		if (! $path) { 
 			$path = dist_file('AGAT', $config_file);
-			dual_print($log, "Using standard $path file\n", $verbose );
+			dual_print($log, "=> Using standard $path config file\n", $verbose );
 		}
 	}
 	# Config file provided we must load this one !
 	else{
 		if (-e $config_file_in){
 			$path = $config_file_in;
-			dual_print($log, "Using provided config file $path.\n", $verbose );
+			dual_print($log, "=> Using provided config file $path.\n", $verbose );
 		} else{
-			warn "Config file $config_file_in does not exist! Please check the path!"; exit;
+			warn "=> Config file $config_file_in does not exist! Please check the path!"; exit;
 		}
 	}
 	return $path;

diff --git a/lib/AGAT/OmniscientI.pm b/lib/AGAT/OmniscientI.pm
@@ -156,7 +156,8 @@ sub slurp_gff3_file_JD {
 	}
 
 	# +----------------- Print header ------------------+
-	dual_print ($log, AGAT::AGAT::get_agat_header(), $verbose);
+	# Printed to screen by get_agat_config at the very beginning so here we just to want to report the header in the log
+	dual_print ($log, AGAT::AGAT::get_agat_header(), 0);
 
 	# +----------------- debug param  ------------------+
 	$debug = $config->{debug};
@@ -370,7 +371,6 @@ sub slurp_gff3_file_JD {
 
 		# -------------- Set progress bar ---------------------
 		my $nb_line_read=0;
-		my $progress_bar=undef;
  		if  ( $progress_bar and $nb_line_feature ){
 			$progress_bar = Term::ProgressBar->new({
 					name  => 'Parsing',