Commit c430a853 authored by Karl Kornel's avatar Karl Kornel
Browse files

Move locking and logging code into a different file

parent 28e03ae7

bbox-delivery-code.pl

+11 −11
Original line number Diff line number Diff line
@@ -24,7 +24,7 @@ use File::Copy; 
# $script_name: The name of the script being run.

sub deliver {

	my ($runfolder, $project, $email, $log, $bin_path, $script_name) = @_;

	log_msg("Starting delivery for $project\n");

	dolog("Starting delivery for $project\n");



	# Extract the username

	$project =~ m{\AProject_(.+)\z}xims;
@@ -42,7 +42,7 @@ sub deliver { 


	# If we don't find anything, send an email and return

	if (!scalar(@homedirs)) {

		log_msg("No home directory found for $username!\n");

		dolog("No home directory found for $username!\n");

		email_delivery_manual("$project_path/$project", $email,

			              $script_name);

		return 1;
@@ -51,7 +51,7 @@ sub deliver { 


	# Now, let's get to work

	# Start by getting the user's UID and GID.

	log_msg("Will do delivery to user $username\n");

	dolog("Will do delivery to user $username\n");

	my @homedir_stat = stat($homedir);

	my $homedir_mode = $homedir_stat[2] & 07777;

	my $homedir_uid = $homedir_stat[4];
@@ -73,8 +73,8 @@ sub deliver { 
		}

	}

	my $destination = "$homedir/$runfolder_name$runfolder_suffix";

	log_msg("Will deliver files to $destination ");

	log_msg(sprintf("(mode %o)\n", $homedir_mode));

	dolog("Will deliver files to $destination ");

	dolog(sprintf("(mode %o)\n", $homedir_mode));



	# Create the directory to hold everything

	mkdir($destination, $homedir_mode);
@@ -110,7 +110,7 @@ sub deliver_directory { 
	# Start listing the source directory contents

	my $source_handle;

	opendir($source_handle, $source) or do {

		log_msg(<<"EOF");

		dolog(<<"EOF");

We were unable to read the source directory for our copy.

The directory we tried to read is: $source

The error we got is: $!
@@ -126,13 +126,13 @@ EOF 
		# Work out the file/directory target and mode

		my $target = "$destination/$item";

		my $mode = (stat("$source/$item"))[2] & 07777;

		log_msg("$source/$item -> $target, ");

		log_msg(sprintf("mode %o\n", $mode));

		dolog("$source/$item -> $target, ");

		dolog(sprintf("mode %o\n", $mode));



		# Files are easy enough to copy

		if (-f "$source/$item") {

			File::Copy::copy("$source/$item", $target) or do {

				log_msg(<<"EOF");

				dolog(<<"EOF");

We were unable to copy $item to its destination, because of an error.

The file we tried to copy is: $source/$item

The destination was: $target
@@ -155,8 +155,8 @@ EOF 


		# Skip other stuff

		else {

			log_msg("Skipping $source/$item, which is neither a ");

			log_msg("file nor a directory.\n");

			dolog("Skipping $source/$item, which is neither a ");

			dolog("file nor a directory.\n");

		}

	}

bbox-email-code.pl

+21 −21
Original line number Diff line number Diff line
@@ -24,10 +24,10 @@ sub check_email { 


	# Only create if the file doesn't exist

	if (! -r $path) {

		log_msg("Missing $path.  Creating now.\n");

		dolog("Missing $path.  Creating now.\n");

		my $email_handle;

		open($email_handle, '>', $path) or do {

			log_msg(<<"EOF");

			dolog(<<"EOF");

We are having problems creating one of our configuration files.

The file we are trying to create is: $path

The error we are getting is: $!
@@ -147,7 +147,7 @@ EOF 
	my $log_handle;

	my $log_body = '';

	open($log_handle, '<', $log_path) or do {

		log_msg(<<"EOF");

		dolog(<<"EOF");

We have just encounted a problem when trying to re-open our log file.

The file we were trying to read is: $log_path

The error we got is: $!
@@ -178,7 +178,7 @@ EOF 
	my $barcode_handle;

	my $barcode_body = '';

	open($barcode_handle, '<', $barcode_path) or do {

		log_msg(<<"EOF");

		dolog(<<"EOF");

We have just encountered a roblem when trying to open the landBarcode HTML file.

The file we were trying to read is: $barcode_path

The error we got is: $!
@@ -203,8 +203,8 @@ EOF 
		],

		parts      => [ $email_body, $email_log, $email_barcode ],

	);

	log_msg('Sending a ' . length($email->as_string) . '-byte email to ');

	log_msg(email_recipients($config) . "\n");

	dolog('Sending a ' . length($email->as_string) . '-byte email to ');

	dolog(email_recipients($config) . "\n");



	# Send the email

	my $email_sender = Email::Send->new({
@@ -215,7 +215,7 @@ EOF 
	});

	my $send_result = $email_sender->send($email->as_string);

	if (!$send_result) {

		log_msg("Error sending email: $send_result\n");

		dolog("Error sending email: $send_result\n");

		return 0;

	}
@@ -284,7 +284,7 @@ EOF 
		my $log_handle;

		my $log_body = '';

		open($log_handle, '<', $log_path) or do {

			log_msg(<<"EOF");

			dolog(<<"EOF");

We have just encounted a problem when trying to re-open our log file.

This happened while trying to report an error.

The file we were trying to read is: $log_path
@@ -312,8 +312,8 @@ EOF 
		],

		parts      => [ $email_body, $email_file ],

	);

	log_msg('Sending a ' . length($email->as_string) . '-byte email to ');

	log_msg(email_recipients($config) . "\n");

	dolog('Sending a ' . length($email->as_string) . '-byte email to ');

	dolog(email_recipients($config) . "\n");



	# Send the email

	my $email_sender = Email::Send->new({
@@ -324,7 +324,7 @@ EOF 
	});

	my $send_result = $email_sender->send($email->as_string);

	if (!$send_result) {

		log_msg("Error sending email: $send_result\n");

		dolog("Error sending email: $send_result\n");

		return 0;

	}
@@ -376,8 +376,8 @@ EOF 
		],

		parts      => [ $email_body ],

	);

	log_msg('Sending a ' . length($email->as_string) . '-byte email to ');

	log_msg(email_recipients($config) . "\n");

	dolog('Sending a ' . length($email->as_string) . '-byte email to ');

	dolog(email_recipients($config) . "\n");



	# Send the email

	my $email_sender = Email::Send->new({
@@ -388,7 +388,7 @@ EOF 
	});

	my $send_result = $email_sender->send($email->as_string);

	if (!$send_result) {

		log_msg("Error sending email: $send_result\n");

		dolog("Error sending email: $send_result\n");

		return 0;

	}
@@ -444,8 +444,8 @@ EOF 
		],

		parts      => [ $email_body ],

	);

	log_msg('Sending a ' . length($email->as_string) . '-byte email to ');

	log_msg(email_recipients($config) . "\n");

	dolog('Sending a ' . length($email->as_string) . '-byte email to ');

	dolog(email_recipients($config) . "\n");



	# Send the email

	my $email_sender = Email::Send->new({
@@ -456,7 +456,7 @@ EOF 
	});

	my $send_result = $email_sender->send($email->as_string);

	if (!$send_result) {

		log_msg("Error sending email: $send_result\n");

		dolog("Error sending email: $send_result\n");

		return 0;

	}
@@ -531,7 +531,7 @@ EOF 
		my $log_handle;

		my $log_body = '';

		open($log_handle, '<', $log_path) or do {

			log_msg(<<"EOF");

			dolog(<<"EOF");

We have just encounted a problem when trying to re-open our log file.

This happened while trying to report an error.

The file we were trying to read is: $log_path
@@ -556,8 +556,8 @@ EOF 
		],

		parts      => [ $email_body, $email_file ],

	);

	log_msg('Sending a ' . length($email->as_string) . '-byte email to ');

	log_msg(email_recipients($config) . "\n");

	dolog('Sending a ' . length($email->as_string) . '-byte email to ');

	dolog(email_recipients($config) . "\n");



	# Send the email

	my $email_sender = Email::Send->new({
@@ -568,7 +568,7 @@ EOF 
	});

	my $send_result = $email_sender->send($email->as_string);

	if (!$send_result) {

		log_msg("Error sending email: $send_result\n");

		dolog("Error sending email: $send_result\n");

		return 0;

	}

bbox-log-lock-code.pl

0 → 100644
+158 −0
Original line number Diff line number Diff line 
#!/usr/bin/perl -w



use strict;

use warnings;



use Fcntl qw(:flock);





# 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 all of the lockfile and logging code.





# log_open: Open our log file, naming any file in place.

# $log_path: The path to the log file, which might exist.

# $log_ref: A reference to a scalar, whose content is written to the log.

# Returns an open file handle, or false.

sub log_open {

	my ($log_path, $log_ref) = @_;

	my $log_handle;



	# If our log file exists, then rename it by appending ".old".

	if (-r $log_path) {

		log_rename($log_path);

	}



	# Try opening our log file, and set autoflush.

	# autoflush, in particular, is important: If we don't do that, and we

	# have to send the log file somewhere, it might not all be written to

	# disk.

	open($log_handle, '>', $log_path) or do {

		dolog(<<"EOL");

We are having trouble opening the log file.

The file we tried to create is: $log_path

The error we got is: $!

EOL

		return 0;

	};

	my $old_handle = select($log_handle);

	$| = 1;

	select($old_handle);



	# Put a header into the log file.

	# Also, if we have anything in our holding variable, output it.

	my $start_time = localtime(time());

	print $log_handle <<"EOL";

This is the log of the bbox-workflow program!

This log file was started on: $start_time

If you need help, please email research-computing-support\@stanford.edu

EOL

	if (defined($log_ref)) {

		print $log_handle ${$log_ref};

		${$log_ref} = '';

	}



	# The log is ready to go!

	return $log_handle;

}



# log_rename: Rename a log file, by appending .old

# We make this a separate subroutine because we might recurse.

# $file: The file to rename.

sub log_rename {

	my ($file) = @_;

	if (-r "$file.old") {

		log_rename("$file.old");

	}

	rename($file, "$file.old");

	return 1;

}



# log_close: Close the log.

# $log_handle: An open file handle.

sub log_close {

	my ($log_handle) = @_;

	return unless defined($log_handle);

	my $end_time = localtime(time());

	print $log_handle <<"EOL";

The time is now $end_time.

Logging complete!

EOL

	close($log_handle);

	return 1;

}

	

# log_msg: Log stuff.

# $log_handle: A file handle, or undef.

# $log_ref: A scalar reference, to write the log file if $log_handle is undef.

# $message: The message to log.

sub log_msg {

	my ($log_handle, $log_ref, $message) = @_;



	# First, print the log entry to standard output

	print $message;



	# Next, if the log file is open, output it there.

	# If the log file isn't open, then write to our holding variable.

	if (defined($log_handle)) {

		print $log_handle $message;

	} else {

		${$log_ref} .= $message;

	}

}



# lock_get: Create and lock our lock file.

# $lock_path: The path to the lock file.

# $log_path: The path to where the log should be.

# Returns a file handle, or false.

sub lock_get {

	my ($lock_path, $log_path) = @_;

	my $lock_handle;



	# First, open the lock file, in append mode.

	# We open in append mode because we don't want to change anything

	# immediately.  We'll wait for the lock first.

	open ($lock_handle, '>>', $lock_path) or do {

		dolog(<<"EOL");

We have just tried to create/open the following file:

$lock_path

However, we got this error: $!

This should not happen.  Please contact Support!

EOL

		return 0;

	};



	# Actually take the lock.  If already locked, fail immediately.

	flock($lock_handle, LOCK_EX | LOCK_NB) or do {

		dolog(<<"EOL");

It appears that the run folder you specified is already being actively worked

on by another instance of the workflow program.  You should wait for that other

instance to complete.  To see what it's doing, you can look at the log file,

which should be here: $log_path

EOL

		return 0;

	};



	# We are locked!  Turn on autoflush, write our process ID, and return.

	my $old_handle = select($lock_handle);

	$| = 1;

	select($old_handle);

	truncate($lock_handle, 0);

	print $lock_handle "$$\n";

	dolog("Lock file $lock_path locked.\n");

	return 1;

}



# lock_release: Release our lock.

# $lock_path: The path to the lock file.

# $lock_handle: A file handle, or undef.

sub lock_release {

	my ($lock_path, $lock_handle) = @_;

	return unless defined($lock_handle);

	unlink($lock_path);

	flock($lock_handle, LOCK_UN);

	close($lock_handle);

	return 1;

}

bbox-workflow-miseq

+59 −178
Original line number Diff line number Diff line
@@ -5,7 +5,6 @@ use warnings; 


use Cwd;

use FindBin qw($RealBin $RealScript);

use Fcntl qw(:flock);

use IPC::Open3;

use Symbol qw(gensym);
@@ -13,7 +12,7 @@ use Symbol qw(gensym); 
use lib qw($RealBin);

require 'bbox-delivery-code.pl';

require 'bbox-email-code.pl';



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





# First, let's set our "constants".  These are settings that aren't likely to
@@ -76,7 +75,7 @@ check_email("$RealBin/email-recipients.txt"); 


# We should have at least one argument from the command line

if (scalar(@ARGV) < 1) {

	log_msg(<<"EOL");

	dolog(<<"EOL");

Please specify an action to perform, like 'scan' or 'run'.

For example: $RealScript scan NextSeq

Or: $RealScript run NextSeq/160804-NS500126-123-BDGEJMGM
@@ -148,7 +147,7 @@ EOF 
$possible_actions{scan} = sub {

	# Get the search directory from the command line

	if (scalar(@ARGV) < 1) {

		log_msg(<<"EOL");

		dolog(<<"EOL");

When using the `scan` action, please provide the path to a directory to search.

For example: $RealScript scan MiSeq

EOL
@@ -159,19 +158,19 @@ EOL 
	# Make sure the search folder is valid, and also set $SEARCHFOLDER

	$SEARCHFOLDER = validate_path($candidate_searchfolder);

	if (!defined($SEARCHFOLDER)) {

		log_msg(<<"EOL");

		dolog(<<"EOL");

The search folder you provided does not exist, is not a directory, or cannot

be read.  Please re-run your command with a valid folder path.

The path your provided is: $candidate_searchfolder

EOL

		exit 1;

	}

	log_msg("Searching $SEARCHFOLDER for candidate runfolders...\n");

	dolog("Searching $SEARCHFOLDER for candidate runfolders...\n");



	# Open the search folder, and start looking at what's inside

	my $searchfolder_handle;

	opendir($searchfolder_handle, $SEARCHFOLDER) or do {

		log_msg(<<"EOL");

		dolog(<<"EOL");

We just got an error when trying to open a directory.

The directory we tried accessing is: $SEARCHFOLDER

The error message we received is: $!
@@ -179,34 +178,34 @@ EOL 
		exit 1;

	};

	while (my $candidate_runfolder = readdir($searchfolder_handle)) {

		log_msg("Found candidate $candidate_runfolder\n");

		dolog("Found candidate $candidate_runfolder\n");



		# Skip dot files

		if ($candidate_runfolder =~ m{\A[.]}xims) {

			log_msg("... Skipping dotfile.\n");

			dolog("... Skipping dotfile.\n");

			next;

		}



		# Skip non-directories

		if (! -d "$SEARCHFOLDER/$candidate_runfolder") {

			log_msg("... Skipping.  Not a directory.\n");

			dolog("... Skipping.  Not a directory.\n");

			next;

		}



		# Skip if we have a workflow-complete.txt file

		if (-r "$SEARCHFOLDER/$candidate_runfolder/workflow-complete.txt") {

			log_msg("... workflow-complete.txt found.  Skipping.\n");

			dolog("... workflow-complete.txt found.  Skipping.\n");

			next;

		}

		

		# Skip if we have a workflow-lock.txt file

		if (-r "$SEARCHFOLDER/$candidate_runfolder/workflow-lock.txt") {

			log_msg("... workflow-lock.txt found.  Skipping.\n");

			dolog("... workflow-lock.txt found.  Skipping.\n");

			next;

		}



		# We have a candidate!  Run against it, and exit

		log_msg("Time to run!\n");

		dolog("Time to run!\n");

		closedir($searchfolder_handle);

		unshift @ARGV, "$SEARCHFOLDER/$candidate_runfolder";

		&{$possible_actions{run}}();
@@ -214,7 +213,7 @@ EOL 
	}



	# If we hit this point, we didn't find anything, so exit

	log_msg("No viable candidates found.  Exiting.\n");

	dolog("No viable candidates found.  Exiting.\n");

	closedir($searchfolder_handle);

	return 1;

};
@@ -222,7 +221,7 @@ EOL 
$possible_actions{run} = sub {

	# Get the run folder from the command line

	if (scalar(@ARGV) < 1) {

		log_msg(<<"EOL");

		dolog(<<"EOL");

When using the `run` action, please provide the path to the run folder.

For example: $RealScript run 160804-NS500126-0555-ABCDEFG

EOL
@@ -233,7 +232,7 @@ EOL 
	# Make sure the run folder is valid, and also set $RUNFOLDER

	$RUNFOLDER = validate_path($candidate_runfolder);

	if (!defined($RUNFOLDER)) {

		log_msg(<<"EOL");

		dolog(<<"EOL");

The run folder you provided does not exist, is not a directory, or cannot be

read.  Please re-run your command with a valid folder path.

The path you provided is: $candidate_runfolder
@@ -247,17 +246,19 @@ EOL 
	$LOCKPATH = "$RUNFOLDER/workflow-lock.txt";



	# Get a lock on our run folder

	lock_get() or exit(1);

	$LOCKHANDLE = lock_get($LOCKPATH, $LOGPATH);

	exit(1) unless $LOCKHANDLE;



	# Start logging to file

	log_open() or exit(1);

	$LOGHANDLE = log_open($LOGPATH, \$LOG);

	exit(1) unless $LOGHANDLE;



	# Wait for RTAComplete.txt to appear

	log_msg("Waiting for $RUNFOLDER/RTAComplete.txt to appear...\n");

	dolog("Waiting for $RUNFOLDER/RTAComplete.txt to appear...\n");

	while ($TIMEOUT1 > 0) {

		# If the file exists, then stop the loop

		if (-r "$RUNFOLDER/RTAComplete.txt") {

			log_msg("File found!\n");

			dolog("File found!\n");

			last;

		}
@@ -267,7 +268,7 @@ EOL 
	}

	# If we timed out, then exit.

	if ($TIMEOUT1 == 0) {

		log_msg("Gave up waiting for $RUNFOLDER/RTAComplete.txt\n");

		dolog("Gave up waiting for $RUNFOLDER/RTAComplete.txt\n");

		log_failure("Gave up waiting for RTAComplete.txt to appear",

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

		            $LOGPATH, $LOG);
@@ -278,7 +279,7 @@ EOL 
	my $basecalls_path = "$RUNFOLDER/Data/Intensities/BaseCalls";

	my $basecalls_handle;

	opendir($basecalls_handle, $basecalls_path) or do {

		log_msg(<<"EOF");

		dolog(<<"EOF");

The BaseCalls directory does not exist, is not a directory, or cannot be read.

Please make sure you are running this command with a valid run folder!

The directory we are trying to open is: $basecalls_path
@@ -297,7 +298,7 @@ EOF 
		                   }xims;



		# Rename the directory (this might recurse)

		log_msg(<<"EOF");

		dolog(<<"EOF");

We found an existing Project directory: $1.

We are renaming this to $1.old.

(If that directory already exists, we'll add another ".old" to that one,
@@ -308,10 +309,10 @@ EOF 
	}



	# Get ready to run the analysis command

	log_msg("Running the analysis!\n");

	log_msg("Analysis command: " . join(' ', @RUNCOMMAND) . "\n");

	log_msg("Analysys command output:\n");

	log_msg("==========================================================\n");

	dolog("Running the analysis!\n");

	dolog("Analysis command: " . join(' ', @RUNCOMMAND) . "\n");

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

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



	# Actually run the analysis command.

	# We send all output to the log directly.  We also make a file handle
@@ -324,7 +325,7 @@ EOF 
	                         0, @RUNCOMMAND);

	close($input_handle);

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

		log_msg($analysis_buffer);

		dolog($analysis_buffer);

		$analysis_buffer = '';

	}

	waitpid($analysis_pid, 0);
@@ -332,12 +333,12 @@ EOF 


	# Clean up from the analysis command

	my $analysis_exit_code = $? >> 8;

	log_msg("==========================================================\n");

	log_msg("The analysis program returned exit code $analysis_exit_code\n");

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

	dolog("The analysis program returned exit code $analysis_exit_code\n");



	# Send an email regarding the analysis

	if ($analysis_exit_code == 0) {

		log_msg("That's good! 8-)\n");

		dolog("That's good! 8-)\n");

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

		               $LOGPATH, $RealBin, $RealScript) or do {

			email_failure('Problems sending the post-analysis mail',
@@ -346,18 +347,18 @@ EOF 
				      $LOG, $RealBin, $RealScript);

		};

	} else {

		log_msg("That's bad 8-(\n");

		dolog("That's bad 8-(\n");

		email_failure('The analysis program had an error',

		              'run', $RUNFOLDER,

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

		              $RealBin, $RealScript);

	}



	log_msg("Creating workflow-complete.txt marker file\n");

	dolog("Creating workflow-complete.txt marker file\n");

	my $complete_path = "$RUNFOLDER/workflow-complete.txt";

	my $complete_handle;

	open($complete_handle, '>', $complete_path) or do {

		log_msg(<<"EOF");

		dolog(<<"EOF");

Unable to open the workflow-complete.txt file for writing!

Tried to open this file: $complete_path

Here is the error we received: $!
@@ -373,7 +374,7 @@ $possible_actions{deliver} = sub { 
	# Get the run folder from the command line

	# (Same as with the `run` action)

	if (scalar(@ARGV) < 1) {

		log_msg(<<"EOL");

		dolog(<<"EOL");

When using the `run` action, please provide the path to the run folder.

For example: $RealScript run 160804-NS500126-0555-ABCDEFG

EOL
@@ -385,7 +386,7 @@ EOL 
	# (Same as with the `run` action)

	$RUNFOLDER = validate_path($candidate_runfolder);

	if (!defined($RUNFOLDER)) {

		log_msg(<<"EOL");

		dolog(<<"EOL");

The run folder you provided does not exist, is not a directory, or cannot be

read.  Please re-run your command with a valid folder path.

The path you provided is: $candidate_runfolder
@@ -411,9 +412,9 @@ EOL 
	my $basecalls_path = "$RUNFOLDER/Data/Intensities/BaseCalls";

	my $basecalls_handle;

	my @candidate_projects;

	log_msg("Searching for Project directories...\n");

	dolog("Searching for Project directories...\n");

	opendir($basecalls_handle, $basecalls_path) or do {

		log_msg(<<"EOF");

		dolog(<<"EOF");

We had a problem accessing the BaseCalls directory.

The path we tried to access is: $basecalls_path

The error we got is: $!
@@ -422,18 +423,18 @@ EOF 
	};

	while (my $project_name = readdir($basecalls_handle)) {

		if ($project_name !~ m{\AProject_[a-z0-9]+\z}xims) {

			log_msg("$project_name doesn't look like a Project.  ");

			log_msg("Skipping...\n");

			dolog("$project_name doesn't look like a Project.  ");

			dolog("Skipping...\n");

			next;

		}



		log_msg("Found Project directory $project_name\n");

		dolog("Found Project directory $project_name\n");

		push @candidate_projects, $project_name;

	}



	# Exit if we don't find any Project directories

	if (!scalar(@candidate_projects)) {

		log_msg(<<"EOF");

		dolog(<<"EOF");

We could not find any Project directories.

The run folder we were searching is: $RUNFOLDER

Please make sure that an analysis was completed, and try your command again.
@@ -448,7 +449,7 @@ EOF 
			$RealScript);

	}



	log_msg("Delivery complete!\n");

	dolog("Delivery complete!\n");

	return;

};
@@ -459,7 +460,7 @@ if (exists($possible_actions{$ACTION})) { 
	&{$possible_actions{$ACTION}};

}

else {

	log_msg(<<"EOL");

	dolog(<<"EOL");

The action you specified, $ACTION, is not a known action.

You have three possible actions:

* scan: Scan a given directory for unprocessed work folders.
@@ -469,147 +470,27 @@ EOL 
}



# That's it!  Let's exit

log_close();

lock_release();

exit 0;





#

# Logging and Locking Subroutines Go Here

# 





# Open our log file

sub log_open {

	# If our log file exists, then rename it by appending ".old".

	if (-r $LOGPATH) {

		log_rename($LOGPATH);

	}



	# Try opening our log file, and set autoflush

	# autoflush, in particular, is important: If we don't do that, and we

	# have to send the log file somewhere, it might not all be written to

	# disk.

	open($LOGHANDLE, '>', $LOGPATH) or do {

		log_msg(<<"EOL");

We are having trouble opening the log file.

The file we tried to create is: $LOGPATH

The error we got is: $!

EOL

		return 0;

	};

	my $old_handle = select($LOGHANDLE);

	$| = 1;

	select($old_handle);



	# Put a header into the log file.

	# Also, if we have anything in our holding variable, output it.

	my $start_time = localtime(time());

	$LOG = <<"EOL";

This is the log of the bbox-workflow program!

This log file was started on: $start_time

If you need help, please email research-computing-support\@stanford.edu

$LOG

EOL

	print $LOGHANDLE $LOG;

	$LOG = '';



	# The log is ready to go!

	return 1;

}



# Rename a log file, by appending .old

# We make this a separate subroutine because we might recurse.

sub log_rename {

	my ($file) = @_;

	if (-r "$file.old") {

		log_rename("$file.old");

	}

	rename($file, "$file.old");

	return 1;

}



# Close the log

sub log_close {

	return unless defined($LOGHANDLE);

	my $end_time = localtime(time());

	print $LOGHANDLE <<"EOL";

The time is now $end_time.

Logging complete!

EOL



	close($LOGHANDLE);

log_close($LOGHANDLE);

undef $LOGHANDLE;

	return 1;

}

	

# Log stuff

sub log_msg {

	my ($message) = @_;



	# First, print the log entry to standard output

	print $message;



	# Next, if the log file is open, output it there.

	# If the log file isn't open, then write to our holding variable.

	if (defined($LOGHANDLE)) {

		print $LOGHANDLE $message;

	} else {

		$LOG .= $message;

	}

}



# Create and lock our lock file

sub lock_get {

	# We already have $LOCKPATH set globally, so we'll use that.



	# First, open the lock file, in append mode.

	# We open in append mode because we don't want to change anything

	# immediately.  We'll wait for the lock first.

	open ($LOCKHANDLE, '>>', $LOCKPATH) or do {

		log_msg(<<"EOL");

We have just tried to create/open the following file:

$LOCKPATH

However, we got this error: $!

This should not happen.  Please contact Support!

EOL

		return 0;

	};



	# Actually take the lock.  If already locked, fail immediately.

	flock($LOCKHANDLE, LOCK_EX | LOCK_NB) or do {

		log_msg(<<"EOL");

It appears that the run folder you specified is already being actively worked

on by another instance of the workflow program.  You should wait for that other

instance to complete.  To see what it's doing, you can look at the log file,

which should be here: $LOGPATH

EOL

		return 0;

	};



	# We are locked!  Write in our process ID, and return.

	truncate($LOCKHANDLE, 0);

	print $LOCKHANDLE "$$\n";

	log_msg("Lock file $LOCKPATH locked.\n");

	return 1;

}



# Release our lock

sub lock_release {

	# We already have everything set globally

	return unless defined($LOCKHANDLE);

	unlink($LOCKPATH);

	flock($LOCKHANDLE, LOCK_UN);

	close($LOCKHANDLE);

lock_release($LOCKPATH, $LOCKHANDLE);

undef $LOCKPATH;

undef $LOCKHANDLE;

	return 1;

}

exit 0;





#

# Other Subroutines Go Here

# 



# dolog: This is a convenience subroutine to log something.  The logging code

# needs a handle and scalar ref passed in, which would be annoying if needed on

# every call.

# $msg: The message to log.

sub dolog {

	my ($msg) = @_;

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

}





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

sub barcode_path {
@@ -622,7 +503,7 @@ sub barcode_path { 
	my $html_handle;

	my $html_dir;

	opendir($html_handle, $html_path) or do {

		log_msg(<<"EOF");

		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: $!