diff --git a/modules/Bio/EnsEMBL/Utils/ConversionSupport.pm b/modules/Bio/EnsEMBL/Utils/ConversionSupport.pm
index c9f7b228ddd92930566044f15bee7481c4e3d75f..8a95b3536107be510bfda55bf285aadebcb1a304 100644
--- a/modules/Bio/EnsEMBL/Utils/ConversionSupport.pm
+++ b/modules/Bio/EnsEMBL/Utils/ConversionSupport.pm
@@ -78,15 +78,15 @@ use Data::Dumper;
=cut
sub new {
- my $class = shift;
- (my $serverroot = shift) or throw("You must supply a serverroot.");
- my $self = {
- '_serverroot' => $serverroot,
- '_param' => { interactive => 1 },
- '_warnings' => 0,
- };
- bless ($self, $class);
- return $self;
+ my $class = shift;
+ (my $serverroot = shift) or throw("You must supply a serverroot.");
+ my $self = {
+ '_serverroot' => $serverroot,
+ '_param' => { interactive => 1 },
+ '_warnings' => 0,
+ };
+ bless ($self, $class);
+ return $self;
}
=head2 parse_common_options
@@ -105,61 +105,59 @@ sub new {
=cut
sub parse_common_options {
- my $self = shift;
-
- # read commandline options
- my %h;
- Getopt::Long::Configure("pass_through");
- &GetOptions( \%h,
- 'dbname|db_name=s',
- 'host|dbhost|db_host=s',
- 'port|dbport|db_port=n',
- 'user|dbuser|db_user=s',
- 'pass|dbpass|db_pass=s',
- 'conffile|conf=s',
- 'logfile|log=s',
- 'logpath=s',
- 'logappend|log_append=s',
- 'verbose|v=s',
- 'interactive|i=s',
- 'dry_run|dry|n=s',
- 'help|h|?',
- );
-
-
- # reads config file
- my $conffile = $h{'conffile'} || $self->serverroot . "/sanger-plugins/vega/conf/ini-files/Conversion.ini";
- $conffile = abs_path($conffile);
- if (-e $conffile) {
- open(CONF, $conffile) or throw(
- "Unable to open configuration file $conffile for reading: $!");
- my $serverroot = $self->serverroot;
- while (<CONF>) {
- chomp;
+ my $self = shift;
- # remove comments
- s/^[#;].*//;
- s/\s+[;].*$//;
-
- # read options into internal parameter datastructure, removing whitespace
- next unless (/(\w\S*)\s*=\s*(\S*)\s*/);
- my $name = $1;
- my $val = $2;
- if ($val =~ /\$SERVERROOT/) {
- $val =~ s/\$SERVERROOT/$serverroot/g;
- $val = abs_path($val);
- }
- $self->param($name, $val);
- }
- $self->param('conffile', $conffile);
- } elsif ($conffile) {
- warning("Unable to open configuration file $conffile for reading: $!");
+ # read commandline options
+ my %h;
+ Getopt::Long::Configure("pass_through");
+ &GetOptions( \%h,
+ 'dbname|db_name=s',
+ 'host|dbhost|db_host=s',
+ 'port|dbport|db_port=n',
+ 'user|dbuser|db_user=s',
+ 'pass|dbpass|db_pass=s',
+ 'conffile|conf=s',
+ 'logfile|log=s',
+ 'logpath=s',
+ 'logappend|log_append=s',
+ 'verbose|v=s',
+ 'interactive|i=s',
+ 'dry_run|dry|n=s',
+ 'help|h|?',
+ );
+
+ # reads config file
+ my $conffile = $h{'conffile'} || $self->serverroot . "/sanger-plugins/vega/conf/ini-files/Conversion.ini";
+ $conffile = abs_path($conffile);
+ if (-e $conffile) {
+ open(CONF, $conffile) or throw(
+ "Unable to open configuration file $conffile for reading: $!");
+ my $serverroot = $self->serverroot;
+ while (<CONF>) {
+ chomp;
+
+ # remove comments
+ s/^[#;].*//;
+ s/\s+[;].*$//;
+
+ # read options into internal parameter datastructure, removing whitespace
+ next unless (/(\w\S*)\s*=\s*(\S*)\s*/);
+ my $name = $1;
+ my $val = $2;
+ if ($val =~ /\$SERVERROOT/) {
+ $val =~ s/\$SERVERROOT/$serverroot/g;
+ $val = abs_path($val);
+ }
+ $self->param($name, $val);
}
+ $self->param('conffile', $conffile);
+ } elsif ($conffile) {
+ warning("Unable to open configuration file $conffile for reading: $!");
+ }
-
- # override configured parameter with commandline options
- map { $self->param($_, $h{$_}) } keys %h;
- return(1);
+ # override configured parameter with commandline options
+ map { $self->param($_, $h{$_}) } keys %h;
+ return(1);
}
=head2 parse_extra_options
@@ -175,15 +173,15 @@ sub parse_common_options {
=cut
sub parse_extra_options {
- my ($self, @params) = @_;
- Getopt::Long::Configure("no_pass_through");
- eval {
- # catch warnings to pass to $self->error
- local $SIG{__WARN__} = sub { die @_; };
- &GetOptions(\%{ $self->{'_param'} }, @params);
- };
- $self->error($@) if $@;
- return(1);
+ my ($self, @params) = @_;
+ Getopt::Long::Configure("no_pass_through");
+ eval {
+ # catch warnings to pass to $self->error
+ local $SIG{__WARN__} = sub { die @_; };
+ &GetOptions(\%{ $self->{'_param'} }, @params);
+ };
+ $self->error($@) if $@;
+ return(1);
}
=head2 allowed_params
@@ -201,19 +199,19 @@ sub parse_extra_options {
=cut
sub allowed_params {
- my $self = shift;
+ my $self = shift;
- # setter
- if (@_) {
- @{ $self->{'_allowed_params'} } = @_;
- }
+ # setter
+ if (@_) {
+ @{ $self->{'_allowed_params'} } = @_;
+ }
- # getter
- if (ref($self->{'_allowed_params'}) eq 'ARRAY') {
- return @{ $self->{'_allowed_params'} };
- } else {
- return ();
- }
+ # getter
+ if (ref($self->{'_allowed_params'}) eq 'ARRAY') {
+ return @{ $self->{'_allowed_params'} };
+ } else {
+ return ();
+ }
}
=head2 get_common_params
@@ -229,20 +227,20 @@ sub allowed_params {
=cut
sub get_common_params {
- return qw(
- conffile
- dbname
- host
- port
- user
- pass
- logpath
- logfile
- logappend
- verbose
- interactive
- dry_run
- );
+ return qw(
+ conffile
+ dbname
+ host
+ port
+ user
+ pass
+ logpath
+ logfile
+ logappend
+ verbose
+ interactive
+ dry_run
+ );
}
=head2 get_loutre_params
@@ -256,13 +254,13 @@ sub get_common_params {
=cut
sub get_loutre_params {
- return qw(
- loutrehost
- loutreport
- loutreuser
- loutrepass
- loutredbname
- );
+ return qw(
+ loutrehost
+ loutreport
+ loutreuser
+ loutrepass
+ loutredbname
+ );
}
=head2 remove_vega_params
@@ -277,10 +275,10 @@ sub get_loutre_params {
=cut
sub remove_vega_params {
- my $self = shift;
- foreach my $param (qw(dbname host port user pass)) {
- $self->{'_param'}{$param} = undef;
- }
+ my $self = shift;
+ foreach my $param (qw(dbname host port user pass)) {
+ $self->{'_param'}{$param} = undef;
+ }
}
=head2 confirm_params
@@ -296,21 +294,21 @@ sub remove_vega_params {
=cut
sub confirm_params {
- my $self = shift;
+ my $self = shift;
- # print parameter table
- print "Running script with these parameters:\n\n";
- print $self->list_all_params;
+ # print parameter table
+ print "Running script with these parameters:\n\n";
+ print $self->list_all_params;
- if ($self->param('host') eq 'web-4-11') {
- # ask user if he wants to proceed
- exit unless $self->user_proceed("**************\n\n You're working on web-4-11! Is that correct and you want to continue ?\n\n**************");
- }
- else {
- # ask user if he wants to proceed
- exit unless $self->user_proceed("Continue?");
- }
- return(1);
+ if ($self->param('host') eq 'web-4-11') {
+ # ask user if he wants to proceed
+ exit unless $self->user_proceed("**************\n\n You're working on web-4-11! Is that correct and you want to continue ?\n\n**************");
+ }
+ else {
+ # ask user if he wants to proceed
+ exit unless $self->user_proceed("Continue?");
+ }
+ return(1);
}
=head2 list_all_params
@@ -324,12 +322,12 @@ sub confirm_params {
=cut
sub list_all_params {
- my $self = shift;
- my $txt = sprintf " %-21s%-40s\n", qw(PARAMETER VALUE);
- $txt .= " " . "-"x71 . "\n";
- $Text::Wrap::colums = 72;
- my @params = $self->allowed_params;
- foreach my $key (@params) {
+ my $self = shift;
+ my $txt = sprintf " %-21s%-40s\n", qw(PARAMETER VALUE);
+ $txt .= " " . "-"x71 . "\n";
+ $Text::Wrap::colums = 72;
+ my @params = $self->allowed_params;
+ foreach my $key (@params) {
my @vals = $self->param($key);
if (@vals) {
$txt .= Text::Wrap::wrap( sprintf(' %-21s', $key),