This datatype stores the ServiceJob and its associated BlastTool. More...

#include <blast_service_job.h>

Inheritance diagram for BlastServiceJob:

Collaboration diagram for BlastServiceJob:

Public Member Functions
void	CustomiseBlastServiceJob (Service service_p, ServiceJob job_p)
	Initialise a BlastServiceJob with its required functions for updating and freeing itself. More...

BlastServiceJob *	AllocateBlastServiceJobForDatabase (Service service_p, const DatabaseInfo db_p, struct BlastServiceData *data_p)
	Create a BlastServiceJob. More...

BlastServiceJob *	AllocateBlastServiceJob (Service service_p, const char job_name_s, const char job_description_s, const char tool_name_s, BlastServiceData *data_p)
	Create a BlastServiceJob. More...

void	FreeBlastServiceJob (ServiceJob *job_p)
	Free the BlastServiceJob. More...

char *	GetPreviousJobFilename (const BlastServiceData data_p, const char job_id_s, const char *suffix_s)
	Get the filename with the data for a previously-ran BlastServiceJob. More...

BlastServiceJob *	GetBlastServiceJobFromJSON (const json_t blast_job_json_p, BlastServiceData config_p)
	Deserialise a BlastServiceJob from a JSON fragment. More...

json_t *	ConvertBlastServiceJobToJSON (BlastServiceJob *job_p, bool omit_results_flag)
	Serialise a BlastServiceJob into a JSON fragment. More...

bool	AddErrorToBlastServiceJob (BlastServiceJob *job_p)
	Add the logged information from a failed BlastServiceJob to its list of stored errors. More...

bool	UpdateBlastServiceJob (ServiceJob *job_p)
	Update the running status of BlastServiceJob if needed. More...

bool	ProcessLinkedServiceForBlastServiceJobOutput (Service service_p, ServiceJob job_p, LinkedService *linked_service_p)
	Process a LinkedService for a given BlastServiceJob. More...

void	BlastServiceJobCompleted (ServiceJob *job_p)
	This is the callback function used by an AsyncTask that is called when a BlastServiceJob has completed running. More...

bool	AddHsp (json_t marked_up_hit_p, const json_t hsp_p)
	Add the marked-up data for a High-scoring Segment Pair (HSP) to a marked-up hit. More...

bool	GetAndAddDatabaseMappedParameter (LinkedService linked_service_p, const json_t report_p, ParameterSet output_params_p, const char *database_ss)
	After the blast job has ran, get the database that it ran against from a hit from within SINGLE_JSON_FILE output formatted result. More...

const json_t *	GetScaffoldsForDatabaseHit (const json_t *hit_p)
	After the blast job has ran, get the scaffolds that it ran against from a hit from within SINGLE_JSON_FILE output formatted result. More...

json_t *	MarkUpBlastResult (BlastServiceJob *job_p)
	Get the Grassroots marked-up data from a BlastServiceJob. More...

Public Member Functions inherited from ServiceJob
void	FreeServiceJob (ServiceJob *job_p)
	Free a ServiceJob. More...

void	FreeBaseServiceJob (ServiceJob *job_p)
	Free a ServiceJob ignoring if it is a subclass. More...

ServiceJob *	AllocateServiceJob (struct Service service_p, const char job_name_s, const char job_description_s, bool(update_fn)(struct ServiceJob job_p), bool(calculate_results_fn)(struct ServiceJob job_p), void(free_job_fn)(struct ServiceJob job_p), const char job_type_s)
	Allocate a ServiceJob. More...

ServiceJob *	CreateAndAddServiceJobToService (struct Service service_p, const char job_name_s, const char job_description_s, bool(update_fn)(struct ServiceJob job_p), bool(calculate_results_fn)(struct ServiceJob job_p), void(free_job_fn)(struct ServiceJob *job_p))
	Allocate a ServiceJob and add it to a ServiceJobSet. More...

bool	InitServiceJob (ServiceJob job_p, struct Service service_p, const char job_name_s, const char job_description_s, bool(update_fn)(struct ServiceJob job_p), bool(calculate_results_fn)(struct ServiceJob job_p), void(free_job_fn)(struct ServiceJob job_p), uuid_t id_p, const char job_type_s)
	Initialise a ServiceJob. More...

void	ClearServiceJob (ServiceJob *job_p)
	Clear a Service Job ready for reuse. More...

ServiceJob *	CloneServiceJob (const ServiceJob *src_p)
	Create a deep copy of a ServiceJob. More...

bool	CopyServiceJob (const ServiceJob src_p, ServiceJob dest_p)
	Make a deep copy of one ServiceJob to another. More...

struct Service *	GetServiceFromServiceJob (ServiceJob *job_p)
	Get the owning Service for a given ServiceJob. More...

bool	SetServiceJobDescription (ServiceJob job_p, const char const description_s)
	Set the description of ServiceJob. More...

bool	SetServiceJobURL (ServiceJob job_p, const char const url_s)
	Set the description of ServiceJob. More...

bool	SetServiceJobName (ServiceJob job_p, const char const name_s)
	Set the name of ServiceJob. More...

json_t *	GetServiceJobAsJSON (ServiceJob *const job_p, bool omit_results_flag)
	Get a ServiceJob as JSON. More...

json_t *	GetServiceJobStatusAsJSON (ServiceJob *job_p, bool omit_results_flag)
	Get the Current OperationStatus of a ServiceJob as JSON. More...

ServiceJob *	CreateServiceJobFromJSON (const json_t job_json_p, GrassrootsServer grassroots_p)
	Create a ServiceJob from a json_t object. More...

bool	InitServiceJobFromJSON (ServiceJob job_p, const json_t json_p, struct Service service_p, GrassrootsServer grassroots_p)
	Get a ServiceJob from a json_t object. More...

OperationStatus	GetServiceJobStatus (ServiceJob *job_p)
	Get the Current OperationStatus of a ServiceJob. More...

OperationStatus	GetCachedServiceJobStatus (const ServiceJob *job_p)
	Get the last retrieved OperationStatus of a ServiceJob. More...

const char *	GetServiceJobName (const ServiceJob *job_p)
	Get the name of ServiceJob. More...

bool	CloseServiceJob (ServiceJob *job_p)
	Close a ServiceJob. More...

void	ClearServiceJobResults (ServiceJob *job_p, bool free_memory_flag)
	Clear the results associated with a ServiceJob. More...

char *	SerialiseServiceJobToJSON (ServiceJob *const job_p, bool omit_results_flag)
	Save the ServiceJob to a persistent format that allows the ServiceJob to be recreated in a potentially different thread and/or process. More...

ServiceJob *	CreateServiceJobFromResultsJSON (const json_t results_p, struct Service service_p, const char name_s, const char description_s, OperationStatus status, const char *job_type_s)
	Create a ServiceJob from a JSON Resource fragment. More...

bool	InitServiceJobFromResultsJSON (ServiceJob job_p, const json_t results_p, struct Service service_p, const char name_s, const char description_s, OperationStatus status, const char job_type_s)
	Fill in the data for a ServiceJob from a given JSON fragement. More...

bool	AddParameterErrorMessageToServiceJob (ServiceJob job_p, const char const param_s, const ParameterType param_type, const char *const value_s)
	Add a key-value pair error statement to a ServiceJob. More...

bool	AddGeneralErrorMessageToServiceJob (ServiceJob job_p, const char const value_s)
	Add a key-value pair error statement to a ServiceJob. More...

bool	AddCompoundErrorToServiceJob (ServiceJob job_p, const char param_s, const ParameterType param_type, json_t *error_details_p)
	Add a key-value pair error statement to a ServiceJob. More...

bool	AddResultToServiceJob (ServiceJob job_p, json_t result_p)
	Add a result to ServiceJob. More...

void	SetServiceJobStatus (ServiceJob *job_p, OperationStatus status)
	Set the current OperationStatus for a given ServiceJob. More...

void	SetServiceJobUpdateFunction (ServiceJob job_p, bool(update_fn)(ServiceJob *job_p))
	Set the function that a ServiceJob will use to update itself. More...

void	SetServiceJobFreeFunction (ServiceJob job_p, void(free_fn)(ServiceJob *job_p))
	Set the function that a ServiceJob will use to free itself. More...

void	SetServiceJobCalculateResultFunction (ServiceJob job_p, bool(calculate_fn)(ServiceJob *job_p))
	Set the function that a ServiceJob will use to calculate its results. More...

bool	UpdateServiceJob (ServiceJob *job_p)
	Update, if appropriate, a given ServiceJob. More...

uint32	GetNumberOfServiceJobResults (const ServiceJob *job_p)
	Get the number of results stored on a ServiceJob. More...

bool	ReplaceServiceJobResults (ServiceJob job_p, json_t results_p)
	Replace the set of results for a given ServiceJob. More...

bool	AddLinkedServiceToServiceJob (ServiceJob job_p, struct LinkedService linked_service_p)
	Add a LinkedService to ServiceJob. More...

void	ProcessLinkedServices (ServiceJob *job_p)
	Attempt to extract the relevant data for all LinkedServices that the ServiceJob's Service has and store them in the ServiceJob. More...

bool	CalculateServiceJobResult (ServiceJob *job_p)
	Calculate the results for the given ServiceJob. More...

void	SetServiceJobUUID (ServiceJob *job_p, const uuid_t new_job_id)
	Replace the uuid for a given ServiceJob. More...

Data Fields
const char *	BSJ_TYPE_S = "blast_service_job"
	The type for BlastServiceJobs. More...

ServiceJob	bsj_job
	The ServiceJob. More...

BlastTool *	bsj_tool_p
	The BlastTool. More...

Data Fields inherited from ServiceJob
struct Service *	sj_service_p
	The Service that is running this job. More...

uuid_t	sj_id
	The unique identifier for this job. More...

enum OperationStatus	sj_status
	Is the service currently in an open state? More...

char *	sj_service_name_s
	The name of the Service that this ServiceJob is for. More...

char *	sj_name_s
	The name of the ServiceJob. More...

char *	sj_description_s
	The description of the ServiceJob. More...

char *	sj_url_s
	Any user-facing URL for showing results of running this ServiceJob. More...

json_t *	sj_result_p
	The JSON fragment for the results of this ServiceJob. More...

json_t *	sj_metadata_p
	The JSON fragment for any extra information for this ServiceJob. More...

json_t *	sj_errors_p
	The JSON fragment for any errors that have occurred whilst running this ServiceJob. More...

json_t *	sj_linked_services_p
	A JSON array where each object contains the details of running a different Service based upon the results of this ServiceJob. More...

bool(*	sj_update_fn )(struct ServiceJob *job_p)
	The callback function to use when checking the status of this ServiceJob. More...

void(*	sj_free_fn )(struct ServiceJob *job_p)
	The callback function to use when freeing this ServiceJob. More...

bool(*	sj_calculate_result_fn )(struct ServiceJob *job_p)
	The callback function to use when a ServiceJob needs to generate its results This is useful for subclasses of ServiceJob that need custom behaviour. More...

bool	sj_is_updating_flag
	Is this ServiceJob in the process of updating itself? More...

char *	sj_type_s
	The type of ServiceJob. More...

Detailed Description

This datatype stores the ServiceJob and its associated BlastTool.

Member Function Documentation

◆ CustomiseBlastServiceJob()

void CustomiseBlastServiceJob	(	Service *	service_p,
		ServiceJob *	job_p
	)

Initialise a BlastServiceJob with its required functions for updating and freeing itself.

Parameters

service_p	The BlastService that has created the BlastServiceJob.
job_p	The BlastServiceJob.

◆ AllocateBlastServiceJobForDatabase()

BlastServiceJob * AllocateBlastServiceJobForDatabase	(	Service *	service_p,
		const DatabaseInfo *	db_p,
		struct BlastServiceData *	data_p
	)

Create a BlastServiceJob.

Parameters

service_p	The Blast service.
db_p	The DatabaseInfo details that the BlastServiceJob will run against.
data_p	The BlastServiceData.

Returns: The newly-allocated BlastServiceJob or NULL upon error.

◆ AllocateBlastServiceJob()

BlastServiceJob * AllocateBlastServiceJob	(	Service *	service_p,
		const char *	job_name_s,
		const char *	job_description_s,
		const char *	tool_name_s,
		BlastServiceData *	data_p
	)

Create a BlastServiceJob.

Parameters

service_p	The Blast service.
job_name_s	The name of the BlastServiceJob.
job_description_s	The description of the BlastServiceJob. This can be `NULL`.
tool_name_s	The name to give to the underlying BlastTool for this BlastServiceJob. This value will be deep-copied.
data_p	The BlastServiceData.

Returns: The newly-allocated BlastServiceJob or NULL upon error.

◆ FreeBlastServiceJob()

void FreeBlastServiceJob ( ServiceJob * job_p )

Free the BlastServiceJob.

Parameters

job_p The BlastServiceJob to free.

◆ GetPreviousJobFilename()

char * GetPreviousJobFilename	(	const BlastServiceData *	data_p,
		const char *	job_id_s,
		const char *	suffix_s
	)

Get the filename with the data for a previously-ran BlastServiceJob.

Parameters

data_p	The configuration data for the BlastService that ran the BlastServiceJob.
job_id_s	A string containing the UUID for the BlastServiceJob.
suffix_s	The file suffix to append.

Returns: The appropriate filename or NULL upon error.

See also: BS_INPUT_SUFFIX_S; BS_OUTPUT_SUFFIX_S; BS_LOG_SUFFIX_S

◆ GetBlastServiceJobFromJSON()

BlastServiceJob * GetBlastServiceJobFromJSON	(	const json_t *	blast_job_json_p,
		BlastServiceData *	config_p
	)

Deserialise a BlastServiceJob from a JSON fragment.

Parameters

blast_job_json_p	The JSON fragment to generate the BlastServiceJob from .
config_p	The configuration data for the Blast Service.

Returns: The newly-created BlastServiceJob or NULL upon error.

◆ ConvertBlastServiceJobToJSON()

json_t * ConvertBlastServiceJobToJSON	(	BlastServiceJob *	job_p,
		bool	omit_results_flag
	)

Serialise a BlastServiceJob into a JSON fragment.

Parameters

job_p	The BlastServiceJob to serialise
omit_results_flag	`true` if the BlastServiceJob is to exclude any results from the created JSON fragment, `false` to include them.

Returns: The newly-created JSON fragment or NULL upon error.

◆ AddErrorToBlastServiceJob()

bool AddErrorToBlastServiceJob ( BlastServiceJob * job_p )

Add the logged information from a failed BlastServiceJob to its list of stored errors.

Parameters

job_p The BlastServiceJob to update

Returns: true if the BlastServiceJob had its errors updated successfully, false otherwise.

◆ UpdateBlastServiceJob()

bool UpdateBlastServiceJob ( ServiceJob * job_p )

Update the running status of BlastServiceJob if needed.

Parameters

job_p The BlastServiceJob to check.

Returns: true if the BlastServiceJob was updated successfully, false otherwise.

◆ ProcessLinkedServiceForBlastServiceJobOutput()

bool ProcessLinkedServiceForBlastServiceJobOutput	(	Service *	service_p,
		ServiceJob *	job_p,
		LinkedService *	linked_service_p
	)

Process a LinkedService for a given BlastServiceJob.

Parameters

service_p	The BlastService that generated the BlastServiceJob.
job_p	The BlastServiceJob to process for LinkedSrevice results.
linked_service_p	The LinkedService definition to produce the values for.

Returns: true if the BlastServiceJob was processed successfully, false otherwise.

◆ BlastServiceJobCompleted()

void BlastServiceJobCompleted ( ServiceJob * job_p )

This is the callback function used by an AsyncTask that is called when a BlastServiceJob has completed running.

This is used when by AsyncSystemBlastTool objects.

Parameters

job_p The BlastServiceJob that has completed running.

◆ AddHsp()

bool AddHsp	(	json_t *	marked_up_hit_p,
		const json_t *	hsp_p
	)

Add the marked-up data for a High-scoring Segment Pair (HSP) to a marked-up hit.

Parameters

marked_up_hit_p	The marked-up hit that the HSP will be added to.
hsp_p	The HSP to add.

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

◆ GetAndAddDatabaseMappedParameter()

bool GetAndAddDatabaseMappedParameter	(	LinkedService *	linked_service_p,
		const json_t *	report_p,
		ParameterSet *	output_params_p,
		const char **	database_ss
	)

After the blast job has ran, get the database that it ran against from a hit from within SINGLE_JSON_FILE output formatted result.

Parameters

report_p The JSON fragment for the report.

◆ GetScaffoldsForDatabaseHit()

const json_t * GetScaffoldsForDatabaseHit ( const json_t * hit_p )

After the blast job has ran, get the scaffolds that it ran against from a hit from within SINGLE_JSON_FILE output formatted result.

Parameters

hit_p The JSON fragment for the hit.

Returns: A JSON array where each element is an object with "scaffold" as the key and the scaffold name as the value or NULL upon error.

◆ MarkUpBlastResult()

json_t * MarkUpBlastResult ( BlastServiceJob * job_p )

Get the Grassroots marked-up data from a BlastServiceJob.

Parameters

job_p The BlastServiceJob to get the marked-up result for.

Returns: The JSON fragment containing the marked-up data or NULL upon error.

Field Documentation

◆ BSJ_TYPE_S

const char* BSJ_TYPE_S = "blast_service_job"

The type for BlastServiceJobs.

◆ bsj_job

ServiceJob bsj_job

The ServiceJob.

◆ bsj_tool_p

BlastTool* bsj_tool_p

The BlastTool.

The documentation for this struct was generated from the following files:

Public Member Functions

Data Fields

Detailed Description

Member Function Documentation

◆ CustomiseBlastServiceJob()

◆ AllocateBlastServiceJobForDatabase()

◆ AllocateBlastServiceJob()

◆ FreeBlastServiceJob()

◆ GetPreviousJobFilename()

◆ GetBlastServiceJobFromJSON()

◆ ConvertBlastServiceJobToJSON()

◆ AddErrorToBlastServiceJob()

◆ UpdateBlastServiceJob()

◆ ProcessLinkedServiceForBlastServiceJobOutput()

◆ BlastServiceJobCompleted()

◆ AddHsp()

◆ GetAndAddDatabaseMappedParameter()

◆ GetScaffoldsForDatabaseHit()

◆ MarkUpBlastResult()

Field Documentation

◆ BSJ_TYPE_S

◆ bsj_job

◆ bsj_tool_p