Move workflow-complete creation into a separate function. (1bb5c1e0) · Commits · research-computing-public / quake-bufferbox-workflow

bbox-log-lock-code.pl

+20 −0

Original line number	Diff line number	Diff line
		@@ -160,6 +160,26 @@ sub lock_release {
		return 1;
		}

		# workflow_complete: Create a file to avoid re-running workflow for a run.
		# $runfolder: The path to the directory where the marker file should be placed.
		sub workflow_complete {
		my ($runfolder) = @_;
		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 {
		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: $!
		EOF
		return 0;
		};
		print $complete_handle 'Workflow completed at ', localtime(time()), "\n";
		close($complete_handle);
		return 1;
		}


		# End on a true value.
		1;

bbox-workflow-miseq

+7 −13

Original line number	Diff line number	Diff line
		@@ -281,6 +281,7 @@ EOL
		# If we timed out, then exit.
		if ($TIMEOUT1 == 0) {
		dolog("Gave up waiting for $RUNFOLDER/RTAComplete.txt\n");
		workflow_complete($RUNFOLDER);
		log_failure("Gave up waiting for RTAComplete.txt to appear",
		'run', $RUNFOLDER, "$RealBin/email-recipients.txt",
		$LOGPATH, $LOG);
		@@ -297,6 +298,7 @@ Please make sure you are running this command with a valid run folder!
		The directory we are trying to open is: $basecalls_path
		The error we are getting is: $!
		EOF
		workflow_complete($RUNFOLDER);
		return;
		};
		while (readdir($basecalls_handle)) {
		@@ -345,6 +347,7 @@ There was a problem starting the analysis command.
		The command we tried to run was $runcommand_string
		The error we got was: $@
		EOF
		workflow_complete($RUNFOLDER);
		email_failure('Problem starting the analysis command',
		'run', $RUNFOLDER,
		"$RealBin/email-recipients.txt", $LOGPATH,
		@@ -369,6 +372,7 @@ EOF
		dolog("That's good! 8-)\n");
		email_analysis($RUNFOLDER, "$RealBin/email-recipients.txt",
		$LOGPATH, $RealBin, $RealScript) or do {
		workflow_complete($RUNFOLDER);
		email_failure('Problems sending the post-analysis mail',
		'run', $RUNFOLDER,
		"$RealBin/email-recipients.txt", $LOGPATH,
		@@ -376,25 +380,15 @@ EOF
		};
		} else {
		dolog("That's bad 8-(\n");
		workflow_complete($RUNFOLDER);
		email_failure('The analysis program had an error',
		'run', $RUNFOLDER,
		"$RealBin/email-recipients.txt", $LOGPATH, \$LOG,
		$RealBin, $RealScript);
		}

		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 {
		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: $!
		EOF
		return;
		};
		print $complete_handle 'Workflow completed at ', localtime(time()), "\n";
		close($complete_handle);
		# Create the completion marker
		workflow_complete($RUNFOLDER);
		};

bbox-workflow-nextseq

+14 −13

Original line number	Diff line number	Diff line
		@@ -298,6 +298,7 @@ EOL
		# If we timed out, then exit.
		if ($TIMEOUT2 == 0) {
		dolog("Gave up waiting for $RUNFOLDER/RTAComplete.txt\n");
		workflow_complete($RUNFOLDER);
		email_failure("Gave up waiting for RTAComplete.txt to appear",
		'run', $RUNFOLDER,
		"$RealBin/email-recipients.txt", $LOGPATH, \$LOG,
		@@ -321,6 +322,7 @@ EOL
		# If we timed out, then exit.
		if ($TIMEOUT2 == 0) {
		dolog("Gave up waiting for $RUNFOLDER/RunCompletionStatus.xml\n");
		workflow_complete($RUNFOLDER);
		email_failure("Gave up waiting for RunCompletionStatus.xml",
		'run', $RUNFOLDER,
		"$RealBin/email-recipients.txt", $LOGPATH, \$LOG,
		@@ -337,6 +339,7 @@ We got an error when trying to open RunCompletionStatus.xml.
		The full path we tried to open is: $RUNFOLDER/RunCompletionStatus.xml
		The error we got is: $!
		EOF
		workflow_complete($RUNFOLDER);
		email_failure("Could not open RunCompletionStatus.xml", 'run',
		$RUNFOLDER, "$RealBin/email-recipients.txt",
		$LOGPATH, \$LOG, $RealBin, $RealScript);
		@@ -356,6 +359,7 @@ EOF
		We have a completed run, but the CompletionStatus is not "CompletedAsPlanned".
		The completion status we found is: $1
		EOF
		workflow_complete($RUNFOLDER);
		email_failure("Un-good CompletionStatus", 'run',
		$RUNFOLDER,
		"$RealBin/email-recipients.txt", $LOGPATH,
		@@ -375,6 +379,7 @@ We got an error when trying to open RunParameters.xml.
		The full path we tried to open is: $RUNFOLDER/RunParameters.xml
		The error we got is: $!
		EOF
		workflow_complete($RUNFOLDER);
		email_failure("Could not open RunParameters.xml", 'run',
		$RUNFOLDER, "$RealBin/email-recipients.txt",
		$LOGPATH, \$LOG, $RealBin, $RealScript);
		@@ -394,6 +399,7 @@ EOF
		dolog(<<"EOF");
		We were unable to find a LibraryID inside RunParameters.xml.
		EOF
		workflow_complete($RUNFOLDER);
		email_failure("Could not find a LibraryID",
		'run', $RUNFOLDER,
		"$RealBin/email-recipients.txt", $LOGPATH, \$LOG,
		@@ -408,6 +414,7 @@ EOF
		Unable to access the Google Drive folder containing the samplesheets.
		The folder we are trying to access is: $DRIVEPATH
		EOF
		workflow_complete($RUNFOLDER);
		email_failure("Could not access gdrive folder", 'run', $RUNFOLDER, "$RealBin/email-recipients.txt",
		$LOGPATH, \$LOG, $RealBin, $RealScript);
		return;
		@@ -442,6 +449,7 @@ EOF
		my $samplesheet_path;
		if (scalar(@samplesheets) == 0) {
		dolog("No samplesheets found!\n");
		workflow_complete($RUNFOLDER);
		email_failure("No samplesheets found for $LIBRARYID", 'run',
		$RUNFOLDER, "$RealBin/email-recipients.txt",
		$LOGPATH, \$LOG, $RealBin, $RealScript);
		@@ -481,6 +489,7 @@ The file we tried to copy is: $samplesheet_path
		The destination was: $RUNFOLDER/SampleSheet.csv
		The error is: $!
		EOF
		workflow_complete($RUNFOLDER);
		email_failure('Unable to copy SampleSheet.csv into place', 'run',
		$RUNFOLDER, "$RealBin/email-recipients.txt",
		$LOGPATH, \$LOG, $RealBin, $RealScript);
		@@ -545,6 +554,7 @@ There was a problem starting the analysis command.
		The command we tried to run was $runcommand_string
		The error we got was: $@
		EOF
		workflow_complete($RUNFOLDER);
		email_failure('Problem starting the analysis command',
		'run', $RUNFOLDER,
		"$RealBin/email-recipients.txt", $LOGPATH,
		@@ -569,6 +579,7 @@ EOF
		dolog("That's good! 8-)\n");
		email_analysis($RUNFOLDER, "$RealBin/email-recipients.txt",
		$LOGPATH, $RealBin, $RealScript) or do {
		workflow_complete($RUNFOLDER);
		email_failure('Problems sending the post-analysis mail',
		'run', $RUNFOLDER,
		"$RealBin/email-recipients.txt", $LOGPATH,
		@@ -576,25 +587,15 @@ EOF
		};
		} else {
		dolog("That's bad 8-(\n");
		workflow_complete($RUNFOLDER);
		email_failure('The analysis program had an error',
		'run', $RUNFOLDER,
		"$RealBin/email-recipients.txt", $LOGPATH, \$LOG,
		$RealBin, $RealScript);
		}

		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 {
		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: $!
		EOF
		return;
		};
		print $complete_handle 'Workflow completed at ', localtime(time()), "\n";
		close($complete_handle);
		# Create the completion marker
		workflow_complete($RUNFOLDER);
		};

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