#include "blast_app_parameters.h"
#include "blast_formatter.h"
#include "blast_service_api.h"
#include "parameter_set.h"
#include "temp_file.hpp"
#include "async_tasks_manager.h"

Include dependency graph for blast_service.h:

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Go to the source code of this file.

Data Structures
struct	DatabaseInfo
	A datatype describing the details of each database available to search against. More...

struct	BlastServiceData
	The configuration data for the Blast Service. More...

Macros
#define	BS_DEFAULT_OUTPUT_FORMAT (11)
	The default output format as a number to use. More...

#define	BS_GROUP_ALIAS_PREFIX_S "blast"
	The prefix to use for Blast Service aliases. More...

Typedefs
typedef bool(*	AddAdditionalParamsFn) (BlastServiceData data_p, ParameterSet param_set_p, ParameterGroup group_p, const void callback_data_p)
	A callback function used to amend a given ParameterSet. More...

Enumerations
enum	DatabaseType { DT_NUCLEOTIDE, DT_PROTEIN, DT_NUM_TYPES }
	An enumeration for differentiating between the different types of database that the BLAST algorithms can be used with. More...

enum	BlastServiceType { BST_BLASTN, BST_BLASTP, BST_BLASTX, BST_NUM_TYPES }
	An enumeration for differentiating between the differentBLAST algorithms that can be used. More...

Functions
ServicesArray *	GetServices (User user_p, GrassrootsServer grassroots_p)
	Get the Services available for running BLAST jobs. More...

void	ReleaseServices (ServicesArray *services_p)
	Free the ServicesArray and its associated BLAST Services. More...

ServiceJobSet *	RunBlastService (Service service_p, ParameterSet param_set_p, User user_p, ProvidersStateTable providers_p, BlastAppParameters *app_params_p)
	Run a Blast Service. More...

bool	CloseBlastService (Service *service_p)
	Close a Blast Service. More...

ParameterSet *	IsResourceForBlastService (Service service_p, DataResource resource_p, Handler *handler_p)
	Check whether a given Resource is suitable for running a Blast Service for and if so return the partially-completed ParameterSet. More...

bool	AddBaseBlastServiceParameters (Service blast_service_p, ParameterSet param_set_p, DataResource resource_p, const DatabaseType db_type, AddAdditionalParamsFn query_sequence_callback_fn, void callback_data_p)
	Add the common Blast Service parameters to a given ParameterSet. More...

bool	GetBaseBlastServiceParameterTypeForNamedParameter (const Service service_p, const char param_name_s, ParameterType *pt_p)

void	ReleaseBlastServiceParameters (Service service_p, ParameterSet params_p)
	Free a ParameterSet of Blast Service parameters. More...

bool	DetermineBlastResult (struct BlastServiceJob *job_p)
	Get the results of a given BlastServiceJob and store them within it. More...

OperationStatus	GetBlastServiceStatus (Service *service_p, const uuid_t service_id)
	Get the OperationStatus for a BlastServiceJob with the given job id. More...

TempFile *	GetInputTempFile (const ParameterSet params_p, const char working_directory_s, const uuid_t job_id)
	Get the TempFile detailing the query for a given BlastServiceJob UUID. More...

char *	GetBlastResultByUUID (const BlastServiceData data_p, const uuid_t job_id, const uint32 output_format_code, const char output_format_params_s)
	Get the result of a previously ran BlastServiceJob in a given output format. More...

char *	GetBlastResultByUUIDString (const BlastServiceData data_p, const char job_id_s, const uint32 output_format_code, const char *output_format_params_s)
	Get the result of a previously ran BlastServiceJob in a given output format. More...

ServiceJobSet *	GetPreviousJobResults (LinkedList ids_p, BlastServiceData blast_data_p, const uint32 output_format_code, const char *output_format_params_s)
	Get the results of previously ran BlastServiceJobs in a given output format. More...

ServiceJobSet *	CreateJobsForPreviousResults (ParameterSet params_p, const char ids_s, BlastServiceData *blast_data_p)
	Get the results of previously ran BlastServiceJobs in a given output format. More...

void	PrepareBlastServiceJobs (const DatabaseInfo db_p, const ParameterSet const param_set_p, Service service_p, BlastServiceData data_p)
	Prepare a ServiceJobSet of BlastServiceJobs prior to running them. More...

ServiceJob *	BuildBlastServiceJob (struct Service service_p, const json_t service_job_json_p)
	Create a BlastServiceJob from a JSON-based serialisation. More...

json_t *	BuildBlastServiceJobJSON (Service service_p, ServiceJob service_job_p, bool omit_results_flag)
	Get the JSON representation of a BlastServiceJob. More...

const char *	GetMatchingDatabaseFilename (const BlastServiceData data_p, const char name_s)
	For a given service-configured name, find the corresponding BLAST database filename. More...

const char *	GetMatchingDatabaseName (const BlastServiceData data_p, const char filename_s)
	For a given BLAST database filename, find the corresponding service-configured name. More...

ServiceMetadata *	GetGeneralBlastServiceMetadata (Service *service_p)

const DatabaseInfo *	GetMatchingDatabaseByFilename (const BlastServiceData data_p, const char filename_s)
	For a given BLAST database filename, find the corresponding DatabaseInfo object. More...

void	ReleaseBlastService (Service *service_p)

json_t *	GetBlastIndexingData (Service *service_p)

Variables
const char *	BS_INPUT_SUFFIX_S = ".input"
	The suffix to use for Blast Service input files. More...

const char *	BS_OUTPUT_SUFFIX_S = ".output"
	The suffix to use for Blast Service output files. More...

const char *	BS_LOG_SUFFIX_S = ".log"
	The suffix to use for Blast Service log files. More...

const char *	BS_DEFAULT_OUTPUT_FORMAT_S = "11"
	The default output format as a string to use. More...

const char *	BS_DATABASE_GROUP_NAME_S = "Available Databases"
	The prefix to use for the ParameterGroup names for available databases from all of the connected servers. More...

const char *	BS_DATABASES_S = "databases"

const char *	BS_TOOL_TYPE_NAME_S = "blast_tool"
	The configuration key used to declare which type of BlastTool to use. More...

const char *	BS_COMMAND_NAME_S = "blast_command"
	The configuration key used to declare the Blast executable file to use. More...

const char *	BS_APP_NAME_S = "blast_app_type"
	The configuration key used to declare the type of Blast application to use. More...

Macro Definition Documentation

◆ BS_DEFAULT_OUTPUT_FORMAT

#define BS_DEFAULT_OUTPUT_FORMAT (11)

The default output format as a number to use.

See also: BS_DEFAULT_OUTPUT_FORMAT_S

◆ BS_GROUP_ALIAS_PREFIX_S

#define BS_GROUP_ALIAS_PREFIX_S "blast"

The prefix to use for Blast Service aliases.

Typedef Documentation

◆ AddAdditionalParamsFn

typedef bool(* AddAdditionalParamsFn) (BlastServiceData *data_p, ParameterSet *param_set_p, ParameterGroup *group_p, const void *callback_data_p)

A callback function used to amend a given ParameterSet.

Parameters

data_p	The configuration data for the Blast Service.
param_set_p	The ParameterSet that the callback function's Parameters will be added to.
group_p	The optional ParameterGroup to add the generated Parameter to. This can be `NULL`.

Returns: true if the callback function's parameters were added successfully, false otherwise.

Function Documentation

◆ GetBaseBlastServiceParameterTypeForNamedParameter()

bool GetBaseBlastServiceParameterTypeForNamedParameter	(	const Service *	service_p,
		const char *	param_name_s,
		ParameterType *	pt_p
	)

◆ GetGeneralBlastServiceMetadata()

ServiceMetadata* GetGeneralBlastServiceMetadata ( Service * service_p )

◆ ReleaseBlastService()

void ReleaseBlastService ( Service * service_p )

◆ GetBlastIndexingData()

json_t* GetBlastIndexingData ( Service * service_p )

Variable Documentation

◆ BS_INPUT_SUFFIX_S

const char* BS_INPUT_SUFFIX_S = ".input"

The suffix to use for Blast Service input files.

◆ BS_OUTPUT_SUFFIX_S

const char* BS_OUTPUT_SUFFIX_S = ".output"

The suffix to use for Blast Service output files.

◆ BS_LOG_SUFFIX_S

const char* BS_LOG_SUFFIX_S = ".log"

The suffix to use for Blast Service log files.

◆ BS_DEFAULT_OUTPUT_FORMAT_S

const char* BS_DEFAULT_OUTPUT_FORMAT_S = "11"

The default output format as a string to use.

See also: BS_DEFAULT_OUTPUT_FORMAT

◆ BS_DATABASE_GROUP_NAME_S

const char* BS_DATABASE_GROUP_NAME_S = "Available Databases"

The prefix to use for the ParameterGroup names for available databases from all of the connected servers.

◆ BS_DATABASES_S

const char* BS_DATABASES_S = "databases"

◆ BS_TOOL_TYPE_NAME_S

const char* BS_TOOL_TYPE_NAME_S = "blast_tool"

The configuration key used to declare which type of BlastTool to use.

◆ BS_COMMAND_NAME_S

const char* BS_COMMAND_NAME_S = "blast_command"

The configuration key used to declare the Blast executable file to use.

◆ BS_APP_NAME_S

const char* BS_APP_NAME_S = "blast_app_type"

The configuration key used to declare the type of Blast application to use.

Data Structures

Macros

Typedefs

Enumerations

Functions

Variables