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Commit f09df535 authored by Steve Trevanion's avatar Steve Trevanion
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whitespace

parent 50959091
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Showing with 123 additions and 125 deletions
modules/Bio/EnsEMBL/Utils/ConversionSupport.pm
View file @ f09df535
......@@ -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),
......
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