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

#include <system_blast_tool.hpp>

Inheritance diagram for SystemBlastTool:

Collaboration diagram for SystemBlastTool:

Public Member Functions
	SystemBlastTool (BlastServiceJob service_job_p, const char name_s, const char factory_s, const BlastServiceData data_p, const char *blast_program_name_s)
	Create a SystemBlastTool for a given ServiceJob. More...

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

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

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

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

virtual OperationStatus	GetStatus (bool update_flag=true)
	Get the status of a BlastTool. 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	SetInputFilename (const char *const filename_s)
	Set the input filename for the BlastTool to use. More...

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

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...

bool	Init (const char *prog_s)
	Initialise the SystemBlastTool prior to it being run. More...

bool	SaveCommandLine (const char *command_line_s)

Protected Member Functions inherited from ExternalBlastTool
virtual bool	AddBlastArg (const char *const arg_s, const bool hyphen_flag)
	Add the argument to the command line arguments that this BlastTool will run with. More...

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...

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

Protected Attributes
ByteBufferArgsProcessor *	sbt_args_processor_p

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 system process.

Constructor & Destructor Documentation

◆ SystemBlastTool() [1/2]

SystemBlastTool	(	BlastServiceJob *	service_job_p,
		const char *	name_s,
		const char *	factory_s,
		const BlastServiceData *	data_p,
		const char *	blast_program_name_s
	)

Create a SystemBlastTool for a given ServiceJob.

Parameters

service_job_p	The ServiceJob to associate with this SystemBlastTool.
name_s	The name to give to this SystemBlastTool.
factory_s	The name of the DrmaaBlastFactory that is creating this DrmaaBlastTool.
data_p	The BlastServiceData for the Service that will run this SystemBlastTool.
blast_program_name_s	The name of blast command line executable that this SystemBlastTool will call to run its blast job.

◆ SystemBlastTool() [2/2]

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

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

Parameters

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

◆ ~SystemBlastTool()

virtual ~SystemBlastTool ( )

virtual

The SystemBlastTool destructor.

Member Function Documentation

◆ ParseParameters()

virtual bool ParseParameters	(	ParameterSet *	params_p,
		BlastAppParameters *	app_params_p
	)

virtual

Parse a ParameterSet to configure a BlastTool prior to it being ran.

Parameters

params_p	The ParameterSet to parse.
app_params_p	The BlastAppParameters to use process the values from the given ParameterSet.

Returns: true if the BlastTool was configured successfully and is ready to be ran, false otherwise.

See also: BlastTool::ParseParameters

Reimplemented from ExternalBlastTool.

◆ Run()

virtual OperationStatus Run ( )

virtual

Run this BlastTool.

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

Implements BlastTool.

Reimplemented in AsyncSystemBlastTool, and ThreadedBlastTool.

◆ GetStatus()

virtual OperationStatus GetStatus ( bool update_flag = true )

virtual

Get the status of a BlastTool.

Parameters

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

Returns: The OperationStatus of this BlastTool.

Reimplemented from BlastTool.

Reimplemented in AsyncSystemBlastTool, and ThreadedBlastTool.

◆ 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.

◆ Init()

bool Init ( const char * prog_s )

protected

Initialise the SystemBlastTool prior to it being run.

Parameters

prog_s The name of the BLAST program that this SystemBlastTool will run.

Returns: true if the SystemBlastTool was initialised successfully, false otherwise.

◆ SaveCommandLine()

bool SaveCommandLine ( const char * command_line_s )

protected

Field Documentation

◆ sbt_args_processor_p

ByteBufferArgsProcessor* sbt_args_processor_p

protected

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

system_blast_tool.hpp

Public Member Functions

Protected Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ SystemBlastTool() [1/2]

◆ SystemBlastTool() [2/2]

◆ ~SystemBlastTool()

Member Function Documentation

◆ ParseParameters()

◆ Run()

◆ GetStatus()

◆ GetArgsProcessor()

◆ Init()

◆ SaveCommandLine()

Field Documentation

◆ sbt_args_processor_p