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lib/Bio/Graphics/Browser2/UserTracks.pm  view on Meta::CPAN

    warn "remote_bigbed_conf";
    return <<END;
[$dbname:database]
db_adaptor = Bio::DB::BigBed
db_args    = -bigbed $url
search options = none

>>>>>>>>>>>>>> cut here <<<<<<<<<<<<
[$track_id]
database        = $dbname
feature  = region
glyph    = segments
label density = 50
feature_limit = 500
bump     = fast
stranded = 1
height   = 4
bgcolor  = $color
fgcolor  = $color
key      = $filename segments
description = 

[$track_id\_coverage]
database        = $dbname
feature  = summary
glyph    = wiggle_whiskers
fgcolor  = black
height   = 50
autoscale = chromosome
key      = $filename coverage
description = 

END
}

sub _print_url {
    my $self = shift;
    my ($agent, $url, $fh) = @_;
    $agent->get($url,':content_cb' => sub { print $fh shift; });
}

# Sharing Link (File ID) - Generates the sharing link for a specific file.
sub sharing_link {
    my $self = shift;
    my $file = shift or return;
    return CGI::url(-full => 1, -path_info => 1) . "?share_link=" . $file;
}

# These methods are replaced by methods in Filesystem.pm and Database.pm
# Many of these functions are called asynchronously, if you want to connect an AJAX call to one of these functions add a hook in Action.pm
sub get_file_id { warn "get_file_id() has been called, without properly inheriting subclass Database.pm"; }
sub filename { warn "filename() has been called, without properly inheriting a subclass (like Filesystem.pm or Database.pm)"; }
sub nowfun { warn "nowfun() has been called, without properly inheriting subclass Database.pm"; }
sub get_uploaded_files { warn "get_uploaded_files() has been called, without properly inheriting a subclass (like Filesystem.pm or Database.pm)"; }
sub get_public_files { warn "get_public_files() has been called, without properly inheriting subclass Database.pm"; }
sub get_imported_files { warn "get_imported_files() has been called, without properly inheriting a subclass (like Filesystem.pm or Database.pm)"; }
sub get_shared_files { warn "get_shared_files() has been called, without properly inheriting subclass Database.pm"; }
sub share { warn "share() has been called, without properly inheriting subclass Database.pm"; }
sub unshare { warn "unshare() has been called, without properly inheriting subclass Database.pm"; }
sub field { warn "field() has been called, without properly inheriting subclass Database.pm"; }
sub update_modified { warn "update_modified() has been called, without properly inheriting subclass Database.pm"; }
sub created { warn "created() has been called, without properly inheriting a subclass (like Filesystem.pm or Database.pm)"; }
sub modified { warn "modified() has been called, without properly inheriting a subclass (like Filesystem.pm or Database.pm)"; }
sub description { warn "description() has been called, without properly inheriting a subclass (like Filesystem.pm or Database.pm)"; }
sub add_file { warn "add_file() has been called, without properly inheriting a subclass (like Filesystem.pm or Database.pm)"; }
sub delete_file { warn "delete_file() has been called, without properly inheriting a subclass (like Filesystem.pm or Database.pm)"; }
sub is_imported { warn "is_imported() has been called, without properly inheriting a subclass (like Filesystem.pm or Database.pm)"; }
sub permissions { warn "permissions() has been called, without properly inheriting subclass Database.pm"; }
sub is_mine { warn "is_mine() has been called, without properly inheriting a subclass (like Filesystem.pm or Database.pm)"; }
sub owner { warn "owner() has been called, without properly inheriting a subclass (like Filesystem.pm or Database.pm)"; }
sub is_shared_with_me { warn "is_shared_with_me() has been called, without properly inheriting subclass Database.pm"; }
sub file_type { warn "file_type() has been called, without properly inheriting a subclass (like Filesystem.pm or Database.pm)"; }
sub shared_with { warn "shared_with() has been called, without properly inheriting subclass Database.pm"; }
sub file_exists { warn "file_exists() has been called, without properly inheriting subclass Filesystem.pm"; }
sub change_userid { warn "change_userid() has been called, without properly inheriting a subclass (like Filesystem.pm or Database.pm)"; }
sub change_uploadsid { warn "change_uploadsid() has been called, without properly inheriting a subclass (like Filesystem.pm or Database.pm)"; }
sub close_database { }  # do nothing

package Bio::Graphics::Browser2::UserConf;

use base 'Tie::Handle';
use Symbol;

sub fh {
    my $class = shift;
    my $path  = shift;
    my $g = gensym;
    tie(*$g,$class,$path);
    return $g;
}

sub TIEHANDLE {
    my $class = shift;
    my $path  = shift;
    open my $f,$path or die "$path:$!";
    return bless {
	fh       => $f,
	seen_cut => 0,
	_db      => {},  # remember db names
	-didx    => 0,   # db indexes
    },$class;
}

sub READLINE {
    my $self = shift;
    my $fh   = $self->{fh};

    while (my $line = <$fh>) {
	$self->{_db}{$1} = $self->{_didx}++ if $line =~ /^\[(.+):database/;
	if ($line =~ /cut here/i) {
	    $self->{seen_cut}++;
	    next;
	}
	next unless $self->{seen_cut};
	$line =~ s/database\s*=\s*(.+)/database = database_$self->{_db}{$1} # do not change this!/;
	$line =~ s/\[(\w+?)_.+_(\d+)(:\d+)?\]/[$1_$2$3]/;
	return $line;
    }
    return;
}