Move misc. code into a separate file

#!/usr/bin/perl -w

use strict;

use warnings;

use Cwd;

# This is a support script, which is loaded by the various "bbox-workflow"

# programs.  It is not meant to be executed directly.

#

# This support script has miscellaneous code.

# 

# NOTE: This code relies heavily on dolog, which must be loaded into the same

# scope as this code, or else things will fail.

# This file is Copyright (C) 2016 The Board of Trustees of the Leland Stanford

# Jr. University.  All rights reserved.

# barcode_path: Given a runfolder, return the path to the laneBarcode.html file.

# $runfolder: The path to the runfolder to search.

# Returns a path, or undef if the file wasn't found.

sub barcode_path {

	my ($runfolder) = @_;

	# Start by appeding what we know about the path

	my $html_path = "$runfolder/Data/Intensities/BaseCalls/Reports/html";

	# Look in our html_path for a directory

	my $html_handle;

	my $html_dir;

	opendir($html_handle, $html_path) or do {

		dolog(<<"EOF");

We have just run into problems trying to find the laneBarcode.html file

The directory we tried to access is: $html_path

The error we got is: $!

EOF

		return undef;

	};

	while (my $candidate = readdir($html_handle)) {

		next unless -d "$html_path/$candidate";

		$html_dir = "$html_path/$candidate";

	}

	closedir($html_handle);

	# If we found our directory, then return the full path

	if (defined($html_dir)) {

		return "$html_dir/all/all/all/laneBarcode.html";

	} else {

		return undef;

	}

}

# validate_path: Make sure a path (a directory) is readable, executable, and is

# a directory.

# $path: The path to validate.

# Returns the absolute path, or undef if there was a problem.

sub validate_path {

	my ($path) = @_;

	if (   (-r $path)

	    && (-x $path)

	    && (-d $path)

	) {

		$path = Cwd::abs_path($path);

		return $path;

	} else {

		return undef;

	}

}

# directory_rename: Append .old to a directory.

# $path: The path to the directory to rename.

sub directory_rename {

	my ($path) = @_;

	my $new_name = "$path.old";

	if (-r $new_name) {

		directory_rename($new_name);

	}

	rename($path, $new_name);

}

# End on a true value.

1;

require 'bbox-delivery-code.pl';

require 'bbox-email-code.pl';

require 'bbox-log-lock-code.pl';

require 'bbox-misc-code.pl';

# First, let's set our "constants".  These are settings that aren't likely to

	my ($msg) = @_;

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

}

# Given a runfolder, return the path to the laneBarcode.html file

sub barcode_path {

	my ($runfolder) = @_;

	# Start by appeding what we know about the path

	my $html_path = "$runfolder/Data/Intensities/BaseCalls/Reports/html";

	# Look in our html_path for a directory

	my $html_handle;

	my $html_dir;

	opendir($html_handle, $html_path) or do {

		dolog(<<"EOF");

We have just run into problems trying to find the laneBarcode.html file

The directory we tried to access is: $html_path

The error we got is: $!

EOF

		return undef;

	};

	while (my $candidate = readdir($html_handle)) {

		next unless -d "$html_path/$candidate";

		$html_dir = "$html_path/$candidate";

	}

	closedir($html_handle);

	# If we found our directory, then return the full path

	if (defined($html_dir)) {

		return "$html_dir/all/all/all/laneBarcode.html";

	} else {

		return undef;

	}

}

# Make sure a path is valid

sub validate_path {

	my ($path) = @_;

	if (   (-r $path)

	    && (-x $path)

	    && (-d $path)

	) {

		$path = Cwd::abs_path($path);

		return $path;

	} else {

		return undef;

	}

}

# Append .old to a directory

sub directory_rename {

	my ($path) = @_;

	my $new_name = "$path.old";

	if (-r $new_name) {

		directory_rename($new_name);

	}

	rename($path, $new_name);

}