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bin/gbrowse_metadb_config.pl  view on Meta::CPAN

	return;
    }
    return $userid;
}

# Check Files (Uploads ID, Data Source) - Makes sure a user's files are in the database, add them if not.
sub check_files {
    my $userid      = shift or die "No user ID given, please check the gbrowse_metadb_config.pl script.\n";
    my $uploadsid   = shift or die "No uploads ID given, please check the gbrowse_metadb_config.pl script.\n";
    my $data_source = shift or die "No data source given, please check the gbrowse_metadb_config.pl script.\n";
    
    # Get the files from the database.
    my $files_in_db = $database->selectcol_arrayref("SELECT path FROM uploads WHERE userid=? AND data_source=?", 
						    undef, $userid, $data_source);
    my @files_in_db = @$files_in_db;
    
    # Get the files in the folder.
    my $path = $globals->user_dir($data_source, $uploadsid);
    my @files_in_folder;
    opendir D, $path;
    while (my $dir = readdir(D)) {
	next if $dir =~ /^\.+$/;
	push @files_in_folder, $dir;
    }
    closedir(D);
	
    my $all_ok = 1;
    foreach my $file (@files_in_folder) {
	my $found = grep(/$file/, @files_in_db);
	unless ($found) {
	    print STDERR "\n" unless $line_counter++;
	    add_file($file, $userid, $uploadsid, $data_source, $file) &&
		print STDERR "- File \"$file\" found in the \"$data_source/$uploadsid\" folder without metadata, added to database.\n";
	    $all_ok = 0;
	}
    }
    return $all_ok;
}

# Fix Permissions () - Grants the web user the required privileges on all databases.
sub fix_permissions {
    my (undef, $db_name) = $dsn =~ /.*:(database=)?([^;]+)/;
    $db_name ||= "gbrowse_login";
    ($type)    = $dsn =~ /^dbi:([^:]+)/i unless defined $type;

    if ($type =~ /mysql/i) {
	my ($db_user) = $dsn =~ /user=([^;]+)/i;
	my ($db_pass) = $dsn =~ /password=([^;]+)/i;
	$db_pass    ||= '';
	warn "GRANT ALL PRIVILEGES on $db_name.* TO '$db_user'\@'%' IDENTIFIED BY '$db_pass'";
	$database->do("GRANT ALL PRIVILEGES on $db_name.* TO '$db_user'\@'%' IDENTIFIED BY '$db_pass'")
	    or die DBI->errstr;
    }
}

sub fix_session_permissions {
    print STDERR "Fixing permissions in sessions directory\n";
    my $globals     = Bio::Graphics::Browser2->open_globals;
    my $session_dir = $globals->session_dir;
    my $webuser     = GBrowse::ConfigData->config('wwwuser');
    system "sudo chown -R $webuser $session_dir";
}

sub fix_sqlite_permissions {
    my (undef, $db_name) = $dsn =~ /.*:(database=)?([^;]+)/;
    $db_name ||= "gbrowse_login";

    my ($path) = $dsn =~ /dbname=([^;]+)/i;
    ($path) = $dsn =~ /DBI:SQLite:([^;]+)/i unless $path;
    die "Couldn't figure out location of database index from $dsn" unless $path;

    my $user    = GBrowse::ConfigData->config('wwwuser');
    my $group   = get_group_from_user($user);

    my $dir = dirname($path);
    unless (-e $dir) {
	my $parent = dirname($dir);
	if (-w $parent) {
	    mkdir $parent;
	} else {
	    print STDERR "Using sudo to create $parent directory. You may be prompted for your login password now.\n";
	    system "sudo mkdir $parent";
	}
    }
    my $file_owner = -e $path ? getpwuid((stat($path))[4]) : '';
    my $dir_owner  = -e $dir  ? getpwuid((stat($dir))[4])  : '';

    # Check if we need to, to avoid unnecessary printing/sudos.
    unless ($group) {
	print STDERR "Unable to look up group for $user. Will not change ownerships on $path.\n";
	print STDERR "You should do this manually to give the Apache web server read/write access to $path.\n";
	return;
    }

    if (-e $path && $user ne $file_owner) {
	print STDERR "Using sudo to set $path ownership to $user:$group. You may be prompted for your login password now.\n";
	system "sudo chown $user $path" ;
	system "sudo chgrp $group $path";
	system "sudo chmod 0644 $path";
    }
    if (-e $dir && $user ne $dir_owner) {
	print STDERR "Using sudo to set $dir ownership to $user:$group. You may be prompted for your login password now.\n";
	system "sudo chown $user $dir";
	system "sudo chgrp $group $dir";
	system "sudo chmod 0755 $dir";
    }
}

# Create Database() - Creates the database specified (or the default gbrowse_login database).
sub create_mysql_database {
    my (undef, $db_name) = $dsn =~ /.*:(database=)?([^;]+)/;
    $db_name ||= "gbrowse_login";
    unless (DBI->connect($dsn)) {
        if ($dsn =~ /mysql/i) {
            print STDERR "Could not log into $db_name database, creating and/or fixing login permissions...\n";
            
            my ($admin_user, $admin_pass);
            if ($admin) {
                ($admin_user) = $admin =~ /^(.*):/;
                ($admin_pass) = $admin =~ /:(.*)$/;
            }
            
            $admin_user ||= prompt("Please enter the MySQL administrator user", "root");
            $admin_pass ||= prompt("Please enter the MySQL administrator password", "",1);

	    my ($db_user) = $dsn =~ /user=([^;]+)/i;
	    my ($db_pass) = $dsn =~ /password=([^;]+)/i;
	    $db_pass    ||= '';

            my $test_dbi = DBI->connect("DBI:mysql:database=mysql;user=$admin_user;password=$admin_pass;");
            $test_dbi->do("CREATE DATABASE IF NOT EXISTS $db_name");
	    $test_dbi->do("GRANT ALL PRIVILEGES on $db_name.* TO '$db_user'\@'%' IDENTIFIED BY '$db_pass'");
	    print STDERR "Database created!\n" unless DBI->errstr;
        }
    }
    # SQLite will create the file/database upon first connection.
}

# Add File (Full Path, Owner's Uploads ID, Data Source) - Adds $file to the database under a specified owner.
# Database.pm's add_file() is dependant too many outside variables, not enough time to re-structure.
sub add_file {    
    my $filename    = shift;
    my $userid      = shift;
    my $uploadsid   = shift;
    my $data_source = shift;
    my $full_path   = shift;

    my $imported = ($filename =~ /^(ftp|http|das)_/)? 1 : 0;
    my $description = "";
    my $shared = "private";

    my $trackid = md5_hex($uploadsid.$filename.$data_source);
    my $now = nowfun();
    $database->do("INSERT INTO uploads (trackid, userid, path, description, imported, creation_date, modification_date, sharing_policy, data_source) VALUES (?, ?, ?, ?, ?, $now, $now, ?, ?)", undef, $trackid, $userid, $filename, $description, $import...
    return $trackid;
}

# Now Function - return the database-dependent function for determining current date & time
sub nowfun {
    return ($type =~ /sqlite/i)? "datetime('now','localtime')" : 'NOW()';
}

# Escape Enums (type string) - If the string contains an ENUM, returns a compatible data type that works with SQLite.