https://github.com/galaxyproject/galaxy
Tip revision: 2faef5510fc86c2454ed72d65c70302b5bd050a0 authored by mvdbeek on 27 February 2020, 18:42:00 UTC
Update version to 20.01
Update version to 20.01
Tip revision: 2faef55
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;
}