Services for the BLAST suite of tools. More...

Data Structures
class	ArgsProcessor
	An ArgsProcessor is a class to abstract out how a particular BlastTool stores a value when an argument is passed to it. More...

class	AsyncSystemBlastTool
	A class that will run Blast as an asynchronous system process. More...

struct	BlastAppParameters
	This datatype is used to parse a given ParameterSet in a method suitable for a particular BLAST configuration. More...

class	BlastFormatter
	This class is for converting the output of a blast job between the available different formats. More...

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...

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

struct	BlastTask
	This datatype is used for describing the algorithms that some of the BLAST tools allow the user to choose to optimise the search procedure. More...

class	BlastTool
	The base class for running Blast. More...

class	BlastToolFactory
	The base class for generating blast tools. More...

class	ByteBufferArgsProcessor
	An ArgsProcessor that adds all of its values to a given ByteBuffer. More...

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

class	DrmaaBlastToolFactory
	The base class for generating DrmaaBlastTools. More...

class	DrmaaToolArgsProcessor
	An ArgsProcessor that adds all of its values to a given DrmaaTool. More...

class	ExternalBlastTool
	A class that will run Blast using an external application such as blastn rather than calling Blast library routines directly. More...

class	ExternalBlastToolFactory
	The base class for running blast tools as a separate process. More...

class	StringsArgsProcessor
	An ArgsProcessor that adds all of its values to an array of strings. More...

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

class	SystemBlastToolFactory
	The base class for generating system blast tools. More...

class	ThreadedBlastTool
	A class that will run Blast within a pthread. 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...

enum	BlastOutputFormat { BOF_PAIRWISE, BOF_QUERY_ANCHORED_WITH_IDENTITIES, BOF_QUERY_ANCHORED_NO_IDENTITIES, BOF_FLAT_QUERY_ANCHORED_WITH_IDENTITIES, BOF_FLAT_QUERY_ANCHORED_NO_IDENTITIES, BOF_XML_BLAST, BOF_TABULAR, BOF_TABULAR_WITH_COMMENTS, BOF_TEXT_ASN1, BOF_BINARY_ASN1, BOF_CSV, BOF_BLAST_ASN1, BOF_JSON_SEQALIGN, BOF_MULTI_FILE_JSON_BLAST, BOF_MULTI_FILE_XML2_BLAST, BOF_SINGLE_FILE_JSON_BLAST, BOF_SINGLE_FILE_XML2_BLAST, BOF_SEQUENCE_ALIGNMENT, BOF_ORGANISM_REPORT, BOF_GRASSROOTS, BOF_NUM_TYPES }
	The different available output formats. 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...

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...

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

bool	AddQuerySequenceParams (BlastServiceData data_p, ParameterSet param_set_p, AddAdditionalParamsFn callback_fn, void *callback_data_p)
	Add the common query sequence parameters for a Blast Service. More...

bool	AddGeneralAlgorithmParams (BlastServiceData data_p, ParameterSet param_set_p, AddAdditionalParamsFn callback_fn, const void *callback_data_p)
	Add the common general algorithm parameters for a Blast Service. More...

bool	AddProgramSelectionParameters (BlastServiceData blast_data_p, ParameterSet param_set_p, const BlastTask tasks_p, const BlastTask default_task_p, const size_t task_mem_size, const size_t num_tasks)
	Add the program selection parameters for a Blast Service. More...

uint16	AddDatabaseParams (BlastServiceData data_p, ParameterSet param_set_p, DataResource *resource_p, const DatabaseType db_type)
	Add the database parameters for a Blast Service. More...

uint32	GetNumberOfDatabases (const BlastServiceData *data_p, const DatabaseType dt)
	Get the number of databases of a given type that this BlastService has. More...

Parameter *	SetUpPreviousJobUUIDParameter (const BlastServiceData service_data_p, ParameterSet param_set_p, ParameterGroup *group_p)
	Create the Parameter for specifying the UUIDs for any previous Blast searches. More...

Parameter *	SetUpOutputFormatParameters (const char *formats_ss, const uint32 num_formats, const uint32 default_format, const BlastServiceData service_data_p, ParameterSet param_set_p, ParameterGroup group_p)
	Create the Parameter for specifying the output format from a Blast search. More...

char *	CreateGroupName (const char *server_s)
	Create the group name to use for available databases from a given named Server. More...

int8	GetOutputFormatCodeForString (const char *output_format_s)
	Get the output format code corresponding to the given string representation. More...

Service *	GetBlastNService (GrassrootsServer *grassroots_p)
	Get a Service capable of running BlastN searches. More...

Service *	GetBlastPService (GrassrootsServer *grassroots_p)
	Get a Service capable of running BlastP searches. More...

Service *	GetBlastXService (GrassrootsServer *grassroots_p)
	Get a Service capable of running BlastX searches. More...

Service *	GetMagicBlastService (GrassrootsServer *grassroots_p)
	Get a Service capable of running Magic-Blast searches. More...

bool	AddPairedServiceParameters (Service service_p, ParameterSet internal_params_p)
	Add the parameters for all PairedServices of a given Service to given ParameterSet. More...

char *	GetPreviousRemoteBlastServiceJob (const char local_job_id_s, const uint32 output_format_code, const BlastServiceData blast_data_p)
	Try to get the results of a previously run BlastServiceJob on a remote server. More...

bool	SaveRemoteBlastJobDetails (RemoteServiceJob job_p, const ServiceData blast_data_p)
	Save the results of a RemoteServiceJob to a local file for ease of access. More...

bool	GetBlastServiceConfig (BlastServiceData *data_p)
	Check whether the required configuration details contain the required information for a Blast Service to be used. More...

bool	GetAndAddBlastArgs (const ParameterSet param_set_p, const char param_name_s, bool required_flag, ArgsProcessor *ap_p)
	Get the named Parameter from a ParameterSet and add it to an ArgsProcessor. More...

bool	AddBlastArgs (const Parameter param_p, ArgsProcessor ap_p)
	Add an argument derived from the current value of a Parameter to an ArgsProcessor. More...

bool	AddArgsPair (const char key_s, const char value_s, ArgsProcessor *ap_p)
	Add a pair of arguments to the command line arguments stored in a ByteBuffer. More...

bool	AddArgsPairFromIntegerParameter (const ParameterSet params_p, const char const param_name_s, const char key_s, ArgsProcessor ap_p, const bool unsigned_flag, const bool required_flag)
	Get the value of an integer-based Parameter and add it as key-value pair to the command line arguments accessed by an ArgsProcessor. More...

bool	AddArgsPairFromStringParameter (const ParameterSet params_p, const char const param_name_s, const char key_s, ArgsProcessor ap_p, const bool required_flag)
	Get the value of an string-based Parameter and add it as key-value pair to the command line arguments accessed by an ArgsProcessor. More...

Variables
NamedParameterType	BS_JOB_ID { .npt_name_s = "job_id" , .npt_type = PT_STRING }
	The Blast Service NamedParameterType for specifying previous job UUIDs. More...

NamedParameterType	BS_SUBRANGE_FROM { .npt_name_s = "subrange_from" , .npt_type = PT_UNSIGNED_INT }
	The Blast Service NamedParameterType for specifying the start of a subrange. More...

NamedParameterType	BS_SUBRANGE_TO { .npt_name_s = "subrange_to" , .npt_type = PT_UNSIGNED_INT }
	The Blast Service NamedParameterType for specifying the end of a subrange. More...

NamedParameterType	BS_TASK { .npt_name_s = "task" , .npt_type = PT_STRING }
	The Blast Service NamedParameterType for specifying the algorithm-specific task to use. More...

NamedParameterType	BS_INPUT_QUERY { .npt_name_s = "query" , .npt_type = PT_FASTA }
	The Blast Service NamedParameterType for specifying the input query. More...

NamedParameterType	BS_MAX_SEQUENCES { .npt_name_s = "max_target_seqs" , .npt_type = PT_UNSIGNED_INT }
	The Blast Service NamedParameterType for specifying the maximum number of sequences to return. More...

NamedParameterType	BS_EXPECT_THRESHOLD { .npt_name_s = "evalue" , .npt_type = PT_UNSIGNED_REAL }
	The Blast Service NamedParameterType for specifying the maximum number of e-value to use. More...

NamedParameterType	BS_OUTPUT_FORMAT { .npt_name_s = "outfmt" , .npt_type = PT_UNSIGNED_INT }
	The Blast Service NamedParameterType for specifying the output format to use. More...

NamedParameterType	BS_CUSTOM_OUTPUT_FORMAT { .npt_name_s = "custom_outfmt" , .npt_type = PT_STRING }
	The Blast Service NamedParameterType for specifying any custom output format options to use. More...

NamedParameterType	BS_WORD_SIZE { .npt_name_s = "word_size" , .npt_type = PT_UNSIGNED_INT }
	The Blast Service NamedParameterType for specifying the word size to use. More...

Detailed Description

Services for the BLAST suite of tools.

This Module performs BLAST searches on both nucleotide and protein databases. It currently offers the functionality given by blastn, blastp and blastx. The BLAST jobs can be run locally or also on a computing cluster using DRMAA. General information can be found in the blast_services_guide documentation.

Enumeration Type Documentation

◆ DatabaseType

enum DatabaseType

An enumeration for differentiating between the different types of database that the BLAST algorithms can be used with.

Enumerator
DT_NUCLEOTIDE	The database is a nucleotide sequence.
DT_PROTEIN	The database is a protein sequence.
DT_NUM_TYPES	The number of different database types.

◆ BlastServiceType

enum BlastServiceType

An enumeration for differentiating between the differentBLAST algorithms that can be used.

Enumerator
BST_BLASTN	A search using the BlastN program.
BST_BLASTP	A search using the BlastP program.
BST_BLASTX	A search using the BlastX program.
BST_NUM_TYPES	The number of different Blast service types.

◆ BlastOutputFormat

enum BlastOutputFormat

The different available output formats.

Enumerator
BOF_PAIRWISE	Pairwise.
BOF_QUERY_ANCHORED_WITH_IDENTITIES	Query-anchored showing identities.
BOF_QUERY_ANCHORED_NO_IDENTITIES	Query-anchored no identities.
BOF_FLAT_QUERY_ANCHORED_WITH_IDENTITIES	Flat query-anchored showing identities.
BOF_FLAT_QUERY_ANCHORED_NO_IDENTITIES	Flat query-anchored no identities.
BOF_XML_BLAST	BLAST XML.
BOF_TABULAR	Tabular.
BOF_TABULAR_WITH_COMMENTS	Tabular with comment lines.
BOF_TEXT_ASN1	Seqalign (Text ASN.1)
BOF_BINARY_ASN1	Seqalign (Binary ASN.1)
BOF_CSV	Comma-separated values.
BOF_BLAST_ASN1	BLAST archive (ASN.1)
BOF_JSON_SEQALIGN	Seqalign (JSON)
BOF_MULTI_FILE_JSON_BLAST	Multiple-file BLAST JSON.
BOF_MULTI_FILE_XML2_BLAST	Multiple-file BLAST XML2.
BOF_SINGLE_FILE_JSON_BLAST	Single-file BLAST JSON.
BOF_SINGLE_FILE_XML2_BLAST	Single-file BLAST XML2.
BOF_SEQUENCE_ALIGNMENT	Sequence Alignment/Map (SAM)
BOF_ORGANISM_REPORT	Organism Report.
BOF_GRASSROOTS	Grassroots JSON.
BOF_NUM_TYPES	The number of different output formats.

Function Documentation

◆ GetServices()

ServicesArray* GetServices	(	User *	user_p,
		GrassrootsServer *	grassroots_p
	)

Get the Services available for running BLAST jobs.

Parameters

user_p The details for the user accessing the BLAST Services.

Returns: The ServicesArray containing all of the BLAST Services or NULL upon error.

◆ ReleaseServices()

void ReleaseServices ( ServicesArray * services_p )

Free the ServicesArray and its associated BLAST Services.

Parameters

services_p The ServicesArray to free.

◆ RunBlastService()

ServiceJobSet* RunBlastService	(	Service *	service_p,
		ParameterSet *	param_set_p,
		User *	user_p,
		ProvidersStateTable *	providers_p,
		BlastAppParameters *	app_params_p
	)

Run a Blast Service.

Parameters

service_p	The Blast Service to run.
param_set_p	The ParameterSet specifying the Parameters to use.
user_p	The User of the user requesting to run the Service.
providers_p	The details of ExternalServers for any paired or external Blast Services.
app_params_p	The parser used for the current type of BlastTool.

Returns: The ServiceJobSet with the BlastServiceJobs or NULL upon error.

◆ CloseBlastService()

bool CloseBlastService ( Service * service_p )

Close a Blast Service.

Parameters

service_p The Blast Service to close.

Returns: true if the Blast Service was closed successfully, false otherwise.

◆ IsResourceForBlastService()

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.

Parameters

service_p	The Blast Service to check.
resource_p	The given Resource to check for.
handler_p	The appropriate Handler for accessing the given Resource.

Returns: The partially-completed ParameterSet if the Resource is an appropriate one or NULL if it is not valid for running a Blast search against.

◆ AddBaseBlastServiceParameters()

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.

Parameters

blast_service_p	The Blast Service to add the Parameters for.
param_set_p	The ParameterSet to add the common Parameters to.
resource_p	Any data passed by the user's request.
db_type	The type of databases that the given Blast Service will run against.
add_additional_params_fn	If a Blast Service wishes to add additional parameters this optional callback function can be used.

Returns: true if the Parameters were added successfully, false otherwise.

◆ ReleaseBlastServiceParameters()

void ReleaseBlastServiceParameters	(	Service *	service_p,
		ParameterSet *	params_p
	)

Free a ParameterSet of Blast Service parameters.

Parameters

service_p	The BlastService of the same type that allocated the given ParameterSet.
params_p	The ParameterSet to free.

◆ DetermineBlastResult()

bool DetermineBlastResult ( struct BlastServiceJob * job_p )

Get the results of a given BlastServiceJob and store them within it.

Parameters

job_p The BlastServiceJob to get the results for.

Returns: true if the results were added successfully, false otherwise.

◆ GetBlastServiceStatus()

OperationStatus GetBlastServiceStatus	(	Service *	service_p,
		const uuid_t	service_id
	)

Get the OperationStatus for a BlastServiceJob with the given job id.

Parameters

service_p	The Blast Service of the type which ran the BlastServiceJob.
service_id	The UUID for the given BlastServiceJob.

Returns: The OperationStatus for the given BlastServiceJob.

◆ GetInputTempFile()

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.

Parameters

params_p	The ParameterSet used to run the ServiceJob.
working_directory_s	The working directory specified in the Blast Service configuration.
job_id	The UUID of the BlastServiceJob to check.

Returns: A newly-allocated TempFile with the relevant values or NULL upon error.

◆ GetBlastResultByUUID()

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.

Parameters

data_p	The BlastServiceData of the Blast Service that ran the job.
job_id	The ServiceJob identifier to get the results for.
output_format_code	The required output format code.

Returns: A newly-allocated string containing the results in the requested format or NULL upon error.

See also: GetBlastResultByUUIDString

◆ GetBlastResultByUUIDString()

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.

Parameters

data_p	The BlastServiceData of the Blast Service that ran the job.
job_id_s	The ServiceJob identifier, as a string, to get the results for.
output_format_code	The required output format code.

Returns: A newly-allocated string containing the results in the requested format or NULL upon error.

See also: GetBlastResultByUUID

◆ GetPreviousJobResults()

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.

Parameters

ids_p	A LinkedList of StringListNodes each containing the UUIDs for the required ServiceJobs.
blast_data_p	The BlastServiceData of the Blast Service that ran the job.
output_format_code	The required output format code.

Returns: A newly-allocated ServiceJobSet containing the results in the requested format or NULL upon error.

See also: GetBlastResultByUUIDString; CreateJobsForPreviousResults

◆ CreateJobsForPreviousResults()

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.

Parameters

params_p	The ParameterSet to get the output format from.
ids_s	A string containing UUIDs separated by whitespace.
blast_data_p	The Blast Service configuration data.

Returns: The ServiceJobSet containing the results in the requested output format or NULL upon error.

See also: GetPreviousJobResults

◆ PrepareBlastServiceJobs()

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.

Parameters

db_p	The list of available databases terminated by `NULL`.
param_set_p	The ParameterSet for specifying the configuration of the BlastServiceJobs.
service_p	The BlastService.
data_p	The Blast Service configuration data.

◆ BuildBlastServiceJob()

ServiceJob* BuildBlastServiceJob	(	struct Service *	service_p,
		const json_t *	service_job_json_p
	)

Create a BlastServiceJob from a JSON-based serialisation.

Parameters

service_p	The type of Blast Service that previously created the BlastServiceJob.
service_job_json_p	The JSON fragment representing the BlastServiceJob.

Returns: The BlastServiceJob or NULL upon error.

◆ BuildBlastServiceJobJSON()

json_t* BuildBlastServiceJobJSON	(	Service *	service_p,
		ServiceJob *	service_job_p,
		bool	omit_results_flag
	)

Get the JSON representation of a BlastServiceJob.

Parameters

service_p	The Service that ran the BlastServiceJob.
service_job_p	The BlastServiceJob to serialise.
omit_results_flag	If this is `true` then just the minimal status information for the ServiceJob will be returned. If it is `false` then the job results will be included too if possible.

Returns: The JSON fragment representing the BlastServiceJob or NULL upon error.

◆ GetMatchingDatabaseFilename()

const char* GetMatchingDatabaseFilename	(	const BlastServiceData *	data_p,
		const char *	name_s
	)

For a given service-configured name, find the corresponding BLAST database filename.

Parameters

data_p	The BlastServiceData with the service configuration details.
name_s	The service-configured name.

Returns: The corresponding BLAST database filename or NULL if it could not be found.

◆ GetMatchingDatabaseName()

const char* GetMatchingDatabaseName	(	const BlastServiceData *	data_p,
		const char *	filename_s
	)

For a given BLAST database filename, find the corresponding service-configured name.

Parameters

data_p	The BlastServiceData with the service configuration details.
filename_s	The BLAST database filename.

Returns: The corresponding service-configured name or NULL if it could not be found.

◆ GetMatchingDatabaseByFilename()

const DatabaseInfo* GetMatchingDatabaseByFilename	(	const BlastServiceData *	data_p,
		const char *	filename_s
	)

For a given BLAST database filename, find the corresponding DatabaseInfo object.

Parameters

data_p	The BlastServiceData with the service configuration details.
filename_s	The BLAST database filename.

Returns: The corresponding DatabaseInfo object or NULL if it could not be found.

◆ AddQuerySequenceParams()

bool AddQuerySequenceParams	(	BlastServiceData *	data_p,
		ParameterSet *	param_set_p,
		AddAdditionalParamsFn	callback_fn,
		void *	callback_data_p
	)

Add the common query sequence parameters for a Blast Service.

Parameters

data_p	The configuration data for the Blast Service.
param_set_p	The ParameterSet that the query sequence parameters will be added to.
callback_fn	If the Blast Service wants to add extra Parameters to the query sequence group of Parameters, it can do so via this callback_fn. This can be `NULL`

Returns: true if the query sequence parameters were added successfully, false otherwise.

◆ AddGeneralAlgorithmParams()

bool AddGeneralAlgorithmParams	(	BlastServiceData *	data_p,
		ParameterSet *	param_set_p,
		AddAdditionalParamsFn	callback_fn,
		const void *	callback_data_p
	)

Add the common general algorithm parameters for a Blast Service.

Parameters

data_p	The configuration data for the Blast Service.
param_set_p	The ParameterSet that the general algorithm parameters will be added to.
callback_fn	If the Blast Service wants to add extra Parameters to the general algorithm group of Parameters, it can do so via this callback_fn. This can be `NULL`

Returns: true if the general algorithm parameters were added successfully, false otherwise.

◆ AddProgramSelectionParameters()

bool AddProgramSelectionParameters	(	BlastServiceData *	blast_data_p,
		ParameterSet *	param_set_p,
		const BlastTask *	tasks_p,
		const BlastTask *	default_task_p,
		const size_t	task_mem_size,
		const size_t	num_tasks
	)

Add the program selection parameters for a Blast Service.

Parameters

blast_data_p	The configuration data for the Blast Service.
param_set_p	The ParameterSet that the general algorithm parameters will be added to.
tasks_p	An optional array of BlastTasks that be can be chosen to alter the search.
num_tasks	The number of BlastTasks in the array pointed to by tasks_p.

Returns: true if the general algorithm parameters were added successfully, false otherwise.

◆ AddDatabaseParams()

uint16 AddDatabaseParams	(	BlastServiceData *	data_p,
		ParameterSet *	param_set_p,
		DataResource *	resource_p,
		const DatabaseType	db_type
	)

Add the database parameters for a Blast Service.

Parameters

data_p	The configuration data for the Blast Service.
param_set_p	The ParameterSet that the general algorithm parameters will be added to.
resource_p	The Resource detailing any data sent by the user's request.
db_type	The type of databases to add.

Returns: The number of database parameters added.

◆ GetNumberOfDatabases()

uint32 GetNumberOfDatabases	(	const BlastServiceData *	data_p,
		const DatabaseType	dt
	)

Get the number of databases of a given type that this BlastService has.

Parameters

data_p	The configuration data for the BlastService to check.
dt	The type of database to check.

Returns: The number of available databases of the given type.

◆ SetUpPreviousJobUUIDParameter()

Parameter* SetUpPreviousJobUUIDParameter	(	const BlastServiceData *	service_data_p,
		ParameterSet *	param_set_p,
		ParameterGroup *	group_p
	)

Create the Parameter for specifying the UUIDs for any previous Blast searches.

Parameters

service_data_p	The configuration data for the Blast Service.
param_set_p	The ParameterSet that the UUID Parameter will be added to.
group_p	The optional ParameterGroup to add the generated Parameter to. This can be `NULL`.

Returns: The UUID Parameter or NULL upon error.

◆ SetUpOutputFormatParameters()

Parameter* SetUpOutputFormatParameters	(	const char **	formats_ss,
		const uint32	num_formats,
		const uint32	default_format,
		const BlastServiceData *	service_data_p,
		ParameterSet *	param_set_p,
		ParameterGroup *	group_p
	)

Create the Parameter for specifying the output format from a Blast search.

Parameters

service_data_p	The configuration data for the Blast Service.
param_set_p	The ParameterSet that the output format Parameter will be added to.
group_p	The optional ParameterGroup to add the generated Parameter to. This can be `NULL`.

Returns: The output format Parameter or NULL upon error.

◆ CreateGroupName()

char* CreateGroupName ( const char * server_s )

Create the group name to use for available databases from a given named Server.

Parameters

server_s The name of the Server.

Returns: The newly-allocated group name that will need to be freed with FreeCopiedString to avoid a memory leak or NULL upon error.

◆ GetOutputFormatCodeForString()

int8 GetOutputFormatCodeForString ( const char * output_format_s )

Get the output format code corresponding to the given string representation.

Parameters

output_format_s The output format string.

Returns: Upon success the BlastOutputFormat cast to an int8. -1 if the string did not represent a valid output format string.

◆ GetBlastNService()

Service* GetBlastNService ( GrassrootsServer * grassroots_p )

Get a Service capable of running BlastN searches.

Returns: The BlastN Service or NULL upon error.

◆ GetBlastPService()

Service* GetBlastPService ( GrassrootsServer * grassroots_p )

Get a Service capable of running BlastP searches.

Returns: The BlastP Service or NULL upon error.

◆ GetBlastXService()

Service* GetBlastXService ( GrassrootsServer * grassroots_p )

Get a Service capable of running BlastX searches.

Returns: The BlastX Service or NULL upon error.

◆ GetMagicBlastService()

Service* GetMagicBlastService ( GrassrootsServer * grassroots_p )

Get a Service capable of running Magic-Blast searches.

Returns: The Magic-Blast Service or NULL upon error.

◆ AddPairedServiceParameters()

bool AddPairedServiceParameters	(	Service *	service_p,
		ParameterSet *	internal_params_p
	)

Add the parameters for all PairedServices of a given Service to given ParameterSet.

Parameters

service_p	The Blast Service whose PairedService Parameters will be added.
internal_params_p	The ParameterSet to add the PairedService Parameters to.

Returns: true if the PairedServices were added successfully, false otherwise.

◆ GetPreviousRemoteBlastServiceJob()

char* GetPreviousRemoteBlastServiceJob	(	const char *	local_job_id_s,
		const uint32	output_format_code,
		const BlastServiceData *	blast_data_p
	)

Try to get the results of a previously run BlastServiceJob on a remote server.

Parameters

local_job_id_s	The uuid as a c-style string on the local Server.
output_format_code	The output format to convert the result to.
blast_data_p	The configuration data for the local BlastService.

Returns: The previous result or NULL upon error.

◆ SaveRemoteBlastJobDetails()

bool SaveRemoteBlastJobDetails	(	RemoteServiceJob *	job_p,
		const ServiceData *	blast_data_p
	)

Save the results of a RemoteServiceJob to a local file for ease of access.

Parameters

job_p	The RemoteServiceJob whose results will be saved.
blast_data_p	The Service configuration data.

Returns: true if the results were saved successfully, false otherwise.

◆ GetBlastServiceConfig()

bool GetBlastServiceConfig ( BlastServiceData * data_p )

Check whether the required configuration details contain the required information for a Blast Service to be used.

Parameters

data_p The BlastServcieData to check.

Returns

true if the configuration details are sufficient, false otherwise.

◆ GetAndAddBlastArgs()

bool GetAndAddBlastArgs	(	const ParameterSet *	param_set_p,
		const char *	param_name_s,
		bool	required_flag,
		ArgsProcessor *	ap_p
	)

Get the named Parameter from a ParameterSet and add it to an ArgsProcessor.

Parameters

param_set_p	The ParameterSet to search for the named Parameter in.
param_name_s	The name of the Parameter to search for.
required_flag	`true` if the parameter refers to a required variable, `false` if it is optional.
ap_p	The ArgsProcessor to use.

Returns: true if the value was successfully added to the ArgsProcessor or if the value could not be found and the required_flag was false. false otherwise.

◆ AddBlastArgs()

bool AddBlastArgs	(	const Parameter *	param_p,
		ArgsProcessor *	ap_p
	)

Add an argument derived from the current value of a Parameter to an ArgsProcessor.

This will use the datatype of the current value (e.g. string, integer, etc.) when deciding how to add it to the ArgsProcessor

Parameters

param_p	The Parameter to get the current value from.
ap_p	The ArgsProcessor to use.

Returns: true if the value was successfully added to the ArgsProcessor, false otherwise.

◆ AddArgsPair()

bool AddArgsPair	(	const char *	key_s,
		const char *	value_s,
		ArgsProcessor *	ap_p
	)

Add a pair of arguments to the command line arguments stored in a ByteBuffer.

Parameters

ap_p	The ArgsProcessor to use to store the argument.
key_s	The first argument to add.
value_s	The second argument to add.

Returns: true if the arguments were added successfully, false otherwise.

◆ AddArgsPairFromIntegerParameter()

bool AddArgsPairFromIntegerParameter	(	const ParameterSet *	params_p,
		const char *const	param_name_s,
		const char *	key_s,
		ArgsProcessor *	ap_p,
		const bool	unsigned_flag,
		const bool	required_flag
	)

Get the value of an integer-based Parameter and add it as key-value pair to the command line arguments accessed by an ArgsProcessor.

Parameters

params_p	The ParameterSet to get the Parameter from.
param_name_s	The name of the desired Parameter.
key_s	The key to use when creating the command line arguments.
ap_p	The ArgsProcessor to use to store the argument.
unsigned_flag	Is the parameter value unsigned or not?
required_flag	If this is `true` then failure to find the Parameter will cause this function to return `false`. If the value is optional, then set this to `false`.

Returns: true if the arguments were added successfully, false otherwise.

◆ AddArgsPairFromStringParameter()

bool AddArgsPairFromStringParameter	(	const ParameterSet *	params_p,
		const char *const	param_name_s,
		const char *	key_s,
		ArgsProcessor *	ap_p,
		const bool	required_flag
	)

Get the value of an string-based Parameter and add it as key-value pair to the command line arguments accessed by an ArgsProcessor.

Parameters

params_p	The ParameterSet to get the Parameter from.
param_name_s	The name of the desired Parameter.
key_s	The key to use when creating the command line arguments.
ap_p	The ArgsProcessor to use to store the argument.
required_flag	If this is `true` then failure to find the Parameter will cause this function to return `false`. If the value is optional, then set this to `false`.

Returns: true if the arguments were added successfully, false otherwise.

Variable Documentation

◆ BS_JOB_ID

NamedParameterType BS_JOB_ID { .npt_name_s = "job_id" , .npt_type = PT_STRING }

The Blast Service NamedParameterType for specifying previous job UUIDs.

◆ BS_SUBRANGE_FROM

NamedParameterType BS_SUBRANGE_FROM { .npt_name_s = "subrange_from" , .npt_type = PT_UNSIGNED_INT }

The Blast Service NamedParameterType for specifying the start of a subrange.

◆ BS_SUBRANGE_TO

NamedParameterType BS_SUBRANGE_TO { .npt_name_s = "subrange_to" , .npt_type = PT_UNSIGNED_INT }

The Blast Service NamedParameterType for specifying the end of a subrange.

◆ BS_TASK

NamedParameterType BS_TASK { .npt_name_s = "task" , .npt_type = PT_STRING }

The Blast Service NamedParameterType for specifying the algorithm-specific task to use.

◆ BS_INPUT_QUERY

NamedParameterType BS_INPUT_QUERY { .npt_name_s = "query" , .npt_type = PT_FASTA }

The Blast Service NamedParameterType for specifying the input query.

◆ BS_MAX_SEQUENCES

NamedParameterType BS_MAX_SEQUENCES { .npt_name_s = "max_target_seqs" , .npt_type = PT_UNSIGNED_INT }

The Blast Service NamedParameterType for specifying the maximum number of sequences to return.

◆ BS_EXPECT_THRESHOLD

NamedParameterType BS_EXPECT_THRESHOLD { .npt_name_s = "evalue" , .npt_type = PT_UNSIGNED_REAL }

The Blast Service NamedParameterType for specifying the maximum number of e-value to use.

◆ BS_OUTPUT_FORMAT

NamedParameterType BS_OUTPUT_FORMAT { .npt_name_s = "outfmt" , .npt_type = PT_UNSIGNED_INT }

The Blast Service NamedParameterType for specifying the output format to use.

See also: BlastOutputFormat

◆ BS_CUSTOM_OUTPUT_FORMAT

NamedParameterType BS_CUSTOM_OUTPUT_FORMAT { .npt_name_s = "custom_outfmt" , .npt_type = PT_STRING }

The Blast Service NamedParameterType for specifying any custom output format options to use.

See also: BlastOutputFormat

◆ BS_WORD_SIZE

NamedParameterType BS_WORD_SIZE { .npt_name_s = "word_size" , .npt_type = PT_UNSIGNED_INT }

The Blast Service NamedParameterType for specifying the word size to use.

See also: BlastOutputFormat

Data Structures

Enumerations

Functions

Variables

Detailed Description

Enumeration Type Documentation

◆ DatabaseType

◆ BlastServiceType

◆ BlastOutputFormat

Function Documentation

◆ GetServices()

◆ ReleaseServices()

◆ RunBlastService()

◆ CloseBlastService()

◆ IsResourceForBlastService()

◆ AddBaseBlastServiceParameters()

◆ ReleaseBlastServiceParameters()

◆ DetermineBlastResult()

◆ GetBlastServiceStatus()

◆ GetInputTempFile()

◆ GetBlastResultByUUID()

◆ GetBlastResultByUUIDString()

◆ GetPreviousJobResults()

◆ CreateJobsForPreviousResults()

◆ PrepareBlastServiceJobs()

◆ BuildBlastServiceJob()

◆ BuildBlastServiceJobJSON()

◆ GetMatchingDatabaseFilename()

◆ GetMatchingDatabaseName()

◆ GetMatchingDatabaseByFilename()

◆ AddQuerySequenceParams()

◆ AddGeneralAlgorithmParams()

◆ AddProgramSelectionParameters()

◆ AddDatabaseParams()

◆ GetNumberOfDatabases()

◆ SetUpPreviousJobUUIDParameter()

◆ SetUpOutputFormatParameters()

◆ CreateGroupName()

◆ GetOutputFormatCodeForString()

◆ GetBlastNService()

◆ GetBlastPService()

◆ GetBlastXService()

◆ GetMagicBlastService()

◆ AddPairedServiceParameters()

◆ GetPreviousRemoteBlastServiceJob()

◆ SaveRemoteBlastJobDetails()

◆ GetBlastServiceConfig()

◆ GetAndAddBlastArgs()

◆ AddBlastArgs()

◆ AddArgsPair()

◆ AddArgsPairFromIntegerParameter()

◆ AddArgsPairFromStringParameter()

Variable Documentation

◆ BS_JOB_ID

◆ BS_SUBRANGE_FROM

◆ BS_SUBRANGE_TO

◆ BS_TASK

◆ BS_INPUT_QUERY

◆ BS_MAX_SEQUENCES

◆ BS_EXPECT_THRESHOLD

◆ BS_OUTPUT_FORMAT

◆ BS_CUSTOM_OUTPUT_FORMAT

◆ BS_WORD_SIZE