A class that will run Blast as a drmaa process. More...

#include <drmaa_blast_tool.hpp>

Inheritance diagram for DrmaaBlastTool:

Collaboration diagram for DrmaaBlastTool:

Public Member Functions
	DrmaaBlastTool (BlastServiceJob job_p, const char name_s, const char factory_s, const BlastServiceData data_p, const char blast_program_name_s, const char queue_name_s, const char *const output_path_s, bool async_flag)
	Create a DrmaaBlastTool for a given ServiceJob. More...

	DrmaaBlastTool (BlastServiceJob job_p, const BlastServiceData data_p, const json_t *json_p)
	Create a DrmaaBlastTool for a given ServiceJob using the configuration details from a serialised JSON fragment. More...

void	SetDrmaaOptions (DrmaaTool *drmaa_p, bool async_flag)
	Set the Drmaa settings for this DrmaaBlastTool. More...

virtual	~DrmaaBlastTool ()
	The DrmaaBlastTool destructor. More...

virtual OperationStatus	Run ()
	Run this DrmaaBlastTool. More...

virtual OperationStatus	GetStatus (bool update_flag=true)
	Get the status of a DrmaaBlastTool. More...

void	SetCoresPerSearch (uint32 cores)
	Set the number of cores that this DrmaaBlastTool that will try to use when it runs. More...

bool	SetEmailNotifications (const char **email_addresses_ss)
	This sets up notification emails for each Blast job via DRMAA. More...

virtual bool	SetUpOutputFile ()
	Set the output file parameter. More...

Public Member Functions inherited from ExternalBlastTool
	ExternalBlastTool (BlastServiceJob job_p, const char name_s, const char factory_s, const BlastServiceData data_p, const char *blast_program_name_s, const bool async_flag)
	Create a ExternalBlastTool for a given ServiceJob. More...

	ExternalBlastTool (BlastServiceJob job_p, const BlastServiceData data_p, const json_t *json_p)
	Create a ExternalBlastTool for a given ServiceJob using the configuration details from a serialised JSON fragment. More...

virtual	~ExternalBlastTool ()
	The ExternalBlastTool destructor. More...

virtual bool	ParseParameters (ParameterSet param_set_p, BlastAppParameters app_params_p)
	Parse a ParameterSet to configure a ExternalBlastTool prior to it being ran. More...

virtual bool	SetInputFilename (const char *const filename_s)
	Set the input filename for the BlastTool to use. More...

virtual char *	GetResults (BlastFormatter *formatter_p)
	Get the results after the ExternalBlastTool has finished running. More...

virtual char *	GetLog ()
	Get a copy of the log data from the run of this ExternalBlastTool's run. More...

Public Member Functions inherited from BlastTool
	BlastTool (BlastServiceJob job_p, const char name_s, const char factory_s, const BlastServiceData data_p, const uint32 output_format, const char *custom_output_s)
	Create a BlastTool for a given ServiceJob. More...

	BlastTool (BlastServiceJob job_p, const BlastServiceData data_p, const json_t *json_p)
	Create a BlastTool for a given ServiceJob. More...

virtual	~BlastTool ()
	The BlastTool destructor,. More...

uint32	GetOutputFormat () const
	Get the output format code that this BlastTool will produce its results in. More...

virtual bool	PreRun ()
	Any custom functionality required before running a BlastTool. More...

virtual void	PostRun ()
	Any custom functionality required after running a BlastTool. More...

virtual bool	AddErrorDetails ()

const uuid_t &	GetUUID () const
	Get the uuid for the ServiceJob that this BlastTool is linked with. More...

const char *	GetName () const
	Get the name asssociated with this BlastTool. More...

json_t *	GetAsJSON ()
	Get the JSON-based persistent description of this BlastTool. More...

const char *	GetFactoryName () const
	Get the name of the BlastToolFactory that created this BlastTool. More...

bool	SetCustomOutputColumns (const char *custom_columns_s)

void	FreeBlastTool (BlastTool *tool_p)
	Free a BlastTool. More...

OperationStatus	RunBlast (BlastTool *tool_p)
	Run Blast using the parameters that have been previously using ConvertArguments. More...

OperationStatus	GetBlastStatus (BlastTool *tool_p)
	Get the current OperationStatus of a BlastTool. More...

bool	IsBlastToolSynchronous (BlastTool *tool_p)
	Is the BlastTool going to run asynchronously? More...

Static Public Member Functions
static DrmaaBlastTool *	GetFromJSON (const json_t json_p, const char name_s, const char program_name_s, ServiceJob job_p, BlastServiceData *service_data_p)
	Create a DrmaaBlastTool for a given ServiceJob using the configuration details from a serialised JSON fragment. More...

Protected Member Functions
virtual ArgsProcessor *	GetArgsProcessor ()
	Get the ArgsProcessor that this BlastTool will use to parse the input ParameterSet prior to running its job. More...

virtual bool	AddBlastArg (const char *const arg_s, const bool hyphen_flag)
	Add the argument to the command line arguments that this DrmaaBlastTool will run with. More...

virtual bool	AddToJSON (json_t *root_p)
	This method is used to serialise this DrmaaBlastTool so that it can be recreated from another calling process when required. More...

Protected Member Functions inherited from ExternalBlastTool
virtual bool	AddBlastArgsPair (const char key_s, const char value_s)
	Add a pair of arguments to the command line arguments that this BlastTool will run with. More...

char *	GetJobFilename (const char const prefix_s, const char const suffix_s)
	Create the filename to use for a ServiceJob. More...

Protected Attributes
DrmaaToolArgsProcessor *	dbt_args_processor_p
	The DrmaaToolArgsProcessor that this DrmaaBlastTool will use. More...

Protected Attributes inherited from ExternalBlastTool
char *	ebt_results_filename_s
	The filename which the Blast results will be written to if the job runs successfully. More...

char *	ebt_working_directory_s
	The working directory where all of the input, output and log files will be created. More...

char *	ebt_blast_s
	The name of the blast command line executable to use. More...

bool	ebt_async_flag
	If this is `true`, then the ExternalBlastTool will run asynchronously. More...

Protected Attributes inherited from BlastTool
uint32	bt_output_format
	The output format code to use. More...

char *	bt_custom_output_columns_s
	Any custom columns for tabular output formats. More...

Additional Inherited Members
Static Public Attributes inherited from ExternalBlastTool
static const char *const	EBT_INPUT_SUFFIX_S
	This is the string that will get appended to each input file used by the ExternalBlastTool. More...

static const char *const	EBT_ASYNC_S
	This is the string that will get appended to each log file created when an ExternalBlastTool is ran. More...

Detailed Description

A class that will run Blast as a drmaa process.

Constructor & Destructor Documentation

◆ DrmaaBlastTool() [1/2]

DrmaaBlastTool	(	BlastServiceJob *	job_p,
		const char *	name_s,
		const char *	factory_s,
		const BlastServiceData *	data_p,
		const char *	blast_program_name_s,
		const char *	queue_name_s,
		const char *const	output_path_s,
		bool	async_flag
	)

Create a DrmaaBlastTool for a given ServiceJob.

Parameters

job_p	The ServiceJob to associate with this DrmaaBlastTool.
name_s	The name to give to this DrmaaBlastTool.
factory_s	The name of the DrmaaBlastFactory that is creating this DrmaaBlastTool.
data_p	The BlastServiceData for the Service that will run this DrmaaBlastTool.
blast_program_name_s	The name of blast command line executable that this DrmaaBlastTool. will call to run its blast job.
queue_name_s	The name of the queue that this DrmaaBlastTool will use.
output_path_s	The folder where all of the Blast output and log files will be written to.
async_flag	Should the DrmaaBlastTool run in asynchronous mode.

◆ DrmaaBlastTool() [2/2]

DrmaaBlastTool	(	BlastServiceJob *	job_p,
		const BlastServiceData *	data_p,
		const json_t *	json_p
	)

Create a DrmaaBlastTool for a given ServiceJob using the configuration details from a serialised JSON fragment.

Parameters

job_p	The ServiceJob to associate with this DrmaaBlastTool.
data_p	The BlastServiceData for the Service that will run this DrmaaBlastTool.
json_p	The JSON fragment to fill in the serialised values such as factory, queue_name, etc. with.

◆ ~DrmaaBlastTool()

virtual ~DrmaaBlastTool ( )

virtual

The DrmaaBlastTool destructor.

Member Function Documentation

◆ GetFromJSON()

static DrmaaBlastTool* GetFromJSON	(	const json_t *	json_p,
		const char *	name_s,
		const char *	program_name_s,
		ServiceJob *	job_p,
		BlastServiceData *	service_data_p
	)

static

Create a DrmaaBlastTool for a given ServiceJob using the configuration details from a serialised JSON fragment.

Parameters

json_p	The JSON fragment to fill in the serialised values such as factory, queue_name, etc. with.
name_s	The name to give to the DrmaaBlastTool.
program_name_s	The path of the BLAST program to run.
job_p	The ServiceJob to attach to the DrmaaBlastTool.
service_data_p	The BlastServiceData for the Service that will run this DrmaaBlastTool.

Returns: The newly-created DrmaaBlastTool or 0 upon error.

◆ SetDrmaaOptions()

void SetDrmaaOptions	(	DrmaaTool *	drmaa_p,
		bool	async_flag
	)

Set the Drmaa settings for this DrmaaBlastTool.

Parameters

drmaa_p	The DrmaaTool that will be used to rub the Blast job.
async_flag	If this is `true` then the call to run the Blast job will return immediately and can be polled for results as required. If this is `false` then the call to Run will not return until the Blast job has finished running.

◆ Run()

virtual OperationStatus Run ( )

virtual

Run this DrmaaBlastTool.

If this is set to run asynchronously, then the call to run the Blast job will return immediately and can be polled for results as required. If not, then this will not return until the Blast job has finished running.

Returns: The OperationStatus of this DrmaaBlastTool after it has started running.

Implements BlastTool.

◆ GetStatus()

virtual OperationStatus GetStatus ( bool update_flag = true )

virtual

Get the status of a DrmaaBlastTool.

Returns: The OperationStatus of this DrmaaBlastTool.

Parameters

update_flag if this is true then the DrmaaBlastTool will check the status of its running jobs if necessary, if this is false it will return the last cached value.

See also: BlastTool::GetStatus

Reimplemented from BlastTool.

◆ SetCoresPerSearch()

void SetCoresPerSearch ( uint32 cores )

Set the number of cores that this DrmaaBlastTool that will try to use when it runs.

Parameters

cores The number of cores.

See also: SetDrmaaToolCores

◆ SetEmailNotifications()

bool SetEmailNotifications ( const char ** email_addresses_ss )

This sets up notification emails for each Blast job via DRMAA.

Parameters

email_addresses_ss A NULL-terminated array of email addresses to send notification emails to

Returns: true if the notifications were set successfully, false otherwise.

See also: SetDrmaaToolEmailNotifications

◆ SetUpOutputFile()

virtual bool SetUpOutputFile ( )

virtual

Set the output file parameter.

Returns: true if the input filename was set successfully, false otherwise.

Reimplemented from ExternalBlastTool.

◆ GetArgsProcessor()

virtual ArgsProcessor* GetArgsProcessor ( )

protectedvirtual

Get the ArgsProcessor that this BlastTool will use to parse the input ParameterSet prior to running its job.

Returns: The ArgsProcessor for this BlastTool or 0 upon error.

Implements ExternalBlastTool.

◆ AddBlastArg()

virtual bool AddBlastArg	(	const char *const	arg_s,
		const bool	hyphen_flag
	)

protectedvirtual

Add the argument to the command line arguments that this DrmaaBlastTool will run with.

Parameters

arg_s	The argument to add.
hyphen_flag	If this is `true` then a hyphen will be prefixed the given value e.g. turning "foo" into "-foo" before being added, if this is `false` then the argument is added unaltered.

Returns: true if the argument was added successfully, false otherwise.

Reimplemented from ExternalBlastTool.

◆ AddToJSON()

virtual bool AddToJSON ( json_t * root_p )

protectedvirtual

This method is used to serialise this DrmaaBlastTool so that it can be recreated from another calling process when required.

This is used to store the DrmaaBlastTool in the JobsManager.

Parameters

root_p The json object to add the serialisation of this DrmaaBlastTool to.

Returns: true if the DrmaaBlastTool was serialised successfully, false otherwise.

Reimplemented from ExternalBlastTool.

Field Documentation

◆ dbt_args_processor_p

DrmaaToolArgsProcessor* dbt_args_processor_p

protected

The DrmaaToolArgsProcessor that this DrmaaBlastTool will use.

See also: GetArgsProcessor

The documentation for this class was generated from the following file:

drmaa_blast_tool.hpp

Public Member Functions

Static Public Member Functions

Protected Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ DrmaaBlastTool() [1/2]

◆ DrmaaBlastTool() [2/2]

◆ ~DrmaaBlastTool()

Member Function Documentation

◆ GetFromJSON()

◆ SetDrmaaOptions()

◆ Run()

◆ GetStatus()

◆ SetCoresPerSearch()

◆ SetEmailNotifications()

◆ SetUpOutputFile()

◆ GetArgsProcessor()

◆ AddBlastArg()

◆ AddToJSON()

Field Documentation

◆ dbt_args_processor_p