Add SampleSheet code

use warnings;

use Cwd;

use File::Copy;

use FindBin qw($RealBin $RealScript);

use IPC::Open3;

use Symbol qw(gensym);

# $DRIVECOMMAND is the path to the drive command

my $DRIVECOMMAND = '/home/bufferbox/gopath/bin/drive';

# $DRIVEPATH is the path to the drive folder containing samplesheets

my $DRIVEPATH = '/home/bufferbox/gdrive/NS Samplesheets';

# Next, let's make a big list of global variables.  These all initially start

# out as undefined, and are filled in as we go along.

		dolog(<<"EOF");

We were unable to find a LibraryID inside RunParameters.xml.

EOF

		log_failure("Could not find a LibraryID",

			    'run', $RUNFOLDER, "$RealBin/email-recipients.txt",

			    $LOGPATH, $LOG);

		email_failure("Could not find a LibraryID",

			      'run', $RUNFOLDER,

			      "$RealBin/email-recipients.txt", $LOGPATH, \$LOG,

		              $RealBin, $RealScript);

		return;

	}

	# Go into the drive folder

	dolog("Checking gdrive folder\n");

	chdir($DRIVEPATH) or do {

		dolog(<<"EOF");

Unable to access the Google Drive folder containing the samplesheets.

The folder we are trying to access is: $DRIVEPATH

EOF

		email_failure("Could not access gdrive folder", 'run',		                              $RUNFOLDER, "$RealBin/email-recipients.txt",

			      $LOGPATH, \$LOG, $RealBin, $RealScript);

		return;

	};

	# Run our first drive pull

	my $drive_exit_code;

	dolog("Running drive pull\n");

	$drive_exit_code = drive_run($DRIVECOMMAND, 'pull', '-no-prompt',

		                     '-verbose', '.');

	return unless defined($drive_exit_code);

	# If we got return code 13, then we need to fix clashes and re-pull

	while ($drive_exit_code == 13) {

		$drive_exit_code = drive_run($DRIVECOMMAND, 'pull',

			                     '-no-prompt', '-verbose',

					     '-fix-clashes');

		return unless defined($drive_exit_code);

		$drive_exit_code = drive_run($DRIVECOMMAND, 'pull',

			                     '-no-prompt', '-verbose', '.');

		return unless defined($drive_exit_code);

	}

	# Find our samplesheet

	dolog("Drive running complete!  Checking for samplesheet.\n");

	my @samplesheets = glob "$DRIVEPATH/$LIBRARYID SampleSheet*.csv";

	dolog('Found ' . scalar(@samplesheets) . " candidate(s).\n");

	# Pick exactly which samplesheet to use

	my $samplesheet_path;

	if (scalar(@samplesheets) == 0) {

		dolog("No samplesheets found!\n");

		email_failure("No samplesheets found for $LIBRARYID", 'run',

			      $RUNFOLDER, "$RealBin/email-recipients.txt",

			      $LOGPATH, \$LOG, $RealBin, $RealScript);

		return;

	} elsif (scalar(@samplesheets) == 1) {

		$samplesheet_path = $samplesheets[0];

	} else {

		# Get the last-modified time for each samplesheet

		my %samplesheet_dates;

		foreach my $samplesheet (@samplesheets) {

			my $mtime = (stat($samplesheet))[9];

			dolog("Samplesheet $samplesheet last modified $mtime\n.");

			$samplesheet_dates{$samplesheet} = $mtime;

		}

		# Sort the samplesheets, and get the newest

		my @sorted_samplesheets = sort {

			$samplesheet_dates{$a} <=> $samplesheet_dates{$b};

		} keys(%samplesheet_dates);

		$samplesheet_path = pop @sorted_samplesheets;

	}

	dolog("Using samplesheet at path $samplesheet_path\n");

	# Copy the SampleSheet into place

	if (-r "$RUNFOLDER/SampleSheet.csv") {

		dolog(<<"EOF");

We found an existing SampleSheet.csv.

We are renaming this to SampleSheet.csv.old.

(If that file exists, we'll add another ".old" to that one, and so on, and ....)

EOF

		directory_rename("$RUNFOLDER/SampleSheet.csv");

	}

	File::Copy::copy($samplesheet_path, "$RUNFOLDER/SampleSheet.csv") or do {

		dolog(<<"EOF");

We were unable to copy the SampleSheet, because of an error.

The file we tried to copy is: $samplesheet_path

The destination was: $RUNFOLDER/SampleSheet.csv

The error is: $!

EOF

		email_failure('Unable to copy SampleSheet.csv into place', 'run',

			      $RUNFOLDER, "$RealBin/email-recipients.txt",

			      $LOGPATH, \$LOG, $RealBin, $RealScript);

	};

	dolog("Samplesheet copied\n");

	# Check to see if we have any Project directories

	my $basecalls_path = "$RUNFOLDER/Data/Intensities/BaseCalls";

	my $basecalls_handle;

	my ($msg) = @_;

	return log_msg($LOGHANDLE, \$LOG, $msg);

}

# drive_run: Run the drive command, and return.

# Returns the exit code, or undef on failure.

sub drive_run {

	my @drive_options = @_;

	# Output some header stuff

	dolog('Drive command: ' . join(' ', @drive_options) . "\n");

	dolog("Drive command output:\n");

	dolog("==========================================================\n");

	# Actually spawn the command

	my $input_handle;

	my $output_handle = gensym();

	my $drive_buffer = '';

	my $drive_pid;

	eval {

		$drive_pid = open3($input_handle, $output_handle, 0,

			           @drive_options);

	};

	if ($@) {

		dolog(<<"EOF");

There was a problem running the drive command.

The error we got was: $@

EOF

		email_failure('Problem runnig the drive command', 'run',

			      $RUNFOLDER, "$RealBin/email-recipients.txt",

			      $LOGPATH, \$LOG, $RealBin, $RealScript);

		return undef;

	}

	close($input_handle);

	# Send any output to the log, and then clean up

	while (read($output_handle, $drive_buffer, 10)) {

		dolog($drive_buffer);

		$drive_buffer = '';

	}

	waitpid($drive_pid, 0);

	close($output_handle);

	# Get and return the exit code

	my $drive_exit_code = $? >> 8;

	dolog("==========================================================\n");

	dolog("The drive program returned exit code $drive_exit_code\n");

	return $drive_exit_code;

}