galaxy/contrib/gls.pl

#/!/usr/bin/env perl -w

=head1 NAME

 gls

=head1 DESCRIPTION

 Display the files generated by the current user within the local instance of Galaxy.
 Information is grouped by user's Galaxy histories and ordered by date/time
 
=head1 OPTIONS

	- i|info        = show more info about file [default = no]
	- e|error       = show error files [default = no]
	- d|dirname     = show files from this dirname (ie, history name) only (NOTE. if history name contains spaces, it should be quoted)
	- n|nocontent   = show empty files [default = no]
	- a|altuser     = supply an alternative username (nb, admin only)
	- h|help        = help
	- m|man         = man

=head1 AUTHOR

 Simon McGowan, CBRG [Computational Biology Research Group, Oxford University, UK]

=head1 Update Record

 23/09/2010  001  S.McGowan  first written

=cut



use strict;
use Data::Dumper;
use DBI;
use Getopt::Long;
use Pod::Usage;

my $show_file_info = 0;
my $show_error_files = 0;
my $show_empty_files = 0;
my $help = 0;
my $man = 0;
my $alt_user;
my $selected_dir;

GetOptions(
	'h|help'=>\$help,
	'm|man'=>\$man,
	'i|info'=>\$show_file_info,
	'e|error'=>\$show_error_files,
	'a|altuser=s'=>\$alt_user,
	'n|nocontent'=>\$show_empty_files,
	'd|dirname=s'=>\$selected_dir
); 

pod2usage(1) if $help;
pod2usage(-verbose=>2) if $man;

my %history_data;
my %file_data;


############  CONFIG  ########################################
# list of admin usernames:
my %admin;
$admin{simonmcg} = '';
$admin{stevetay} = '';

# institute email domain
my $email_domain = '@molbiol.ox.ac.uk';

# mysql db
my $mysql_database = 'galaxy';
my $mysql_host = 'xxxxxxxx';
my $mysql_username = 'xxxxxxxx';
my $mysql_password = 'xxxxxxxx';

# file path
my $db_root_dir = '/wwwdata/galaxy-prod/database/files/';
##############################################################

#-----------------------------------------------------------------------------------

my $current_user = getlogin();  

# allow admin to list any user's galaxy files:
if (exists($admin{$current_user}))
{
	if ($alt_user)  {$current_user = $alt_user;}
} 

&get_data;

&print_galaxy_data;

exit();

#-----------------------------------------------------------------------------------

sub get_data
{
	my $dbh = DBI->connect("DBI:mysql:database=$mysql_database;host=" . $mysql_host, $mysql_username, $mysql_password, {'RaiseError' => 1});
	
	my $sql = "SELECT h.id, h.name, h.create_time, hda.dataset_id, hda.update_time, hda.name, hda.info, hda.blurb, hda.extension, d.file_size
	FROM history h, history_dataset_association hda, galaxy_user g, dataset d
	WHERE g.email = '$current_user$email_domain'
	AND g.id = h.user_id
	AND h.id = hda.history_id
	AND hda.dataset_id = d.id";	
	
	my $sth = $dbh->prepare($sql) or die("Failed to prepare statement $sql\n"); 
	$sth->execute() or die("Can't perform SQL $sql : $DBI::errstr\n");	
	while (my $ref = $sth->fetch)
	{
		my ($history_id, $history_name, $create_time, $dataset_id, $dataset_time, $dataset_name, $info, $blurb, $ext, $file_size) = @{$ref};
		
		#print "$history_id, $history_name, $create_time, $dataset_id, $dataset_time, $dataset_name, $info, $blurb, $ext, $file_size\n\n";
		
		$history_data{$history_id}{create_time} = $create_time;
		$history_data{$history_id}{history_name} = $history_name;
		
		$file_data{$history_id}{$dataset_id}{dataset_update_time} = $dataset_time;
		$file_data{$history_id}{$dataset_id}{dataset_name} = $dataset_name;
		$file_data{$history_id}{$dataset_id}{info} = $info;
		$file_data{$history_id}{$dataset_id}{blurb} = $blurb;		
		$file_data{$history_id}{$dataset_id}{file_size} = $file_size;		
		$file_data{$history_id}{$dataset_id}{ext} = $ext;
	}	
	$sth->finish;
}

sub print_galaxy_data
{
	foreach my $hist_id (sort numerically keys %history_data)
	{
		my $hist_name = $history_data{$hist_id}{history_name};
		if ($selected_dir)
		{
			# if the user has opted to see just one dir...
			unless($hist_name eq $selected_dir) {next;}
		}
		
		my $hist_date = $history_data{$hist_id}{create_time};
		
		print "\n";
		print "$hist_date - $hist_name\n";
		
		foreach my $dataset_id (sort numerically keys %{$file_data{$hist_id}})
		{
			my $dataset_time = $file_data{$hist_id}{$dataset_id}{dataset_update_time};
			my $dataset_name = $file_data{$hist_id}{$dataset_id}{dataset_name};
			my $info = $file_data{$hist_id}{$dataset_id}{info};
			my $blurb = $file_data{$hist_id}{$dataset_id}{blurb};
			my $file_size = $file_data{$hist_id}{$dataset_id}{file_size};
			my $ext = $file_data{$hist_id}{$dataset_id}{ext};
			my $file_path = &derive_file_path($dataset_id);
			
			if (($blurb) and ($blurb eq 'empty'))
			{
				unless ($show_empty_files) {next;}
			}
			if (($blurb) and ($blurb eq 'error'))
			{
				unless ($show_error_files) {next;}
			}
			
			print "\t$dataset_time - $dataset_name";
			print " $file_path";
			if ($show_file_info)
			{
				print " [size:$file_size; type:$ext;";
				if (($info) and ($blurb)) { print " $info; $blurb"; }
				elsif ($info) { print " $info"; }
				elsif ($blurb) { print " $blurb"; }
				print ']';
			}
			print "\n";
		}
	}
}

sub derive_file_path
{
	my ($dataset_id) = @_;
	my $dir = sprintf("%06d", $dataset_id);
	$dir =~ s/\d\d\d$//;
	my $full_path = $db_root_dir . $dir . '/dataset_' . $dataset_id . '.dat';
	return ($full_path);	
}

sub numerically
{
	$a <=> $b;
}