d5/d27/blast__service_8h_source.html

/*

** Copyright 2014-2016 The Earlham Institute

**

** Licensed under the Apache License, Version 2.0 (the "License");

** you may not use this file except in compliance with the License.

** You may obtain a copy of the License at

**

**     http://www.apache.org/licenses/LICENSE-2.0

**

** Unless required by applicable law or agreed to in writing, software

** distributed under the License is distributed on an "AS IS" BASIS,

** WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.

** See the License for the specific language governing permissions and

** limitations under the License.

*/


#ifndef BLAST_SERVICE_H

#define BLAST_SERVICE_H


#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"


typedef enum BLAST_SERVICE_LOCAL DatabaseType

{

  DT_NUCLEOTIDE,


  DT_PROTEIN,


  DT_NUM_TYPES

} DatabaseType;


typedef enum BLAST_SERVICE_LOCAL BlastServiceType

{

  BST_BLASTN,


  BST_BLASTP,


  BST_BLASTX,


  BST_NUM_TYPES

} BlastServiceType;


typedef struct BLAST_SERVICE_LOCAL DatabaseInfo

{

  const char *di_name_s;


  const char *di_filename_s;


  const char *di_description_s;


  const char *di_search_description_s;


  const char *di_download_uri_s;


  const char *di_info_uri_s;


  bool di_active_flag;


  DatabaseType di_type;


  const char *di_scaffold_key_s;


  const char *di_scaffold_regex_s;


} DatabaseInfo;


/* forward class declarations */

class BlastToolFactory;

struct BlastServiceJob;


typedef struct BLAST_SERVICE_LOCAL BlastServiceData

{

  ServiceData bsd_base_data;


  char *bsd_working_dir_s;


  BlastFormatter *bsd_formatter_p;


  DatabaseInfo *bsd_databases_p;


  BlastToolFactory *bsd_tool_factory_p;


  DatabaseType bsd_type;


  AsyncTasksManager *bsd_task_manager_p;


} BlastServiceData;


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


#ifndef DOXYGEN_SHOULD_SKIP_THIS


#ifdef ALLOCATE_BLAST_SERVICE_CONSTANTS

  #define BLAST_SERVICE_PREFIX BLAST_SERVICE_LOCAL

  #define BLAST_SERVICE_VAL(x)  = x

  #define BLAST_SERVICE_STRUCT_VAL(x,y) = { x, y}

#else

  #define BLAST_SERVICE_PREFIX extern

  #define BLAST_SERVICE_VAL(x)

  #define BLAST_SERVICE_STRUCT_VAL(x,y)

#endif


#endif    /* #ifndef DOXYGEN_SHOULD_SKIP_THIS */


#define BS_DEFAULT_OUTPUT_FORMAT (11)


BLAST_SERVICE_PREFIX const char *BS_INPUT_SUFFIX_S BLAST_SERVICE_VAL (".input");


BLAST_SERVICE_PREFIX const char *BS_OUTPUT_SUFFIX_S BLAST_SERVICE_VAL (".output");


BLAST_SERVICE_PREFIX const char *BS_LOG_SUFFIX_S BLAST_SERVICE_VAL (".log");


BLAST_SERVICE_PREFIX const char *BS_DEFAULT_OUTPUT_FORMAT_S BLAST_SERVICE_VAL ("11");


BLAST_SERVICE_PREFIX const char *BS_DATABASE_GROUP_NAME_S BLAST_SERVICE_VAL ("Available Databases");


BLAST_SERVICE_PREFIX const char *BS_DATABASES_S BLAST_SERVICE_VAL ("databases");


BLAST_SERVICE_PREFIX const char *BS_TOOL_TYPE_NAME_S BLAST_SERVICE_VAL ("blast_tool");


BLAST_SERVICE_PREFIX const char *BS_COMMAND_NAME_S BLAST_SERVICE_VAL ("blast_command");


BLAST_SERVICE_PREFIX const char *BS_APP_NAME_S BLAST_SERVICE_VAL ("blast_app_type");


#define BS_GROUP_ALIAS_PREFIX_S "blast"


#ifdef __cplusplus

extern "C"

{

#endif


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


BLAST_SERVICE_API void ReleaseServices (ServicesArray *services_p);


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


BLAST_SERVICE_LOCAL bool GetBlastServiceConfig (BlastServiceData *data_p);


BLAST_SERVICE_LOCAL BlastServiceData *AllocateBlastServiceData (Service *blast_service_p, DatabaseType database_type);


BLAST_SERVICE_LOCAL void FreeBlastServiceData (BlastServiceData *data_p);


BLAST_SERVICE_LOCAL bool CloseBlastService (Service *service_p);


BLAST_SERVICE_LOCAL ParameterSet *IsResourceForBlastService (Service *service_p, DataResource *resource_p, Handler *handler_p);


BLAST_SERVICE_LOCAL 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);


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


BLAST_SERVICE_LOCAL void ReleaseBlastServiceParameters (Service *service_p, ParameterSet *params_p);


BLAST_SERVICE_LOCAL bool DetermineBlastResult ( struct BlastServiceJob *job_p);


BLAST_SERVICE_LOCAL OperationStatus GetBlastServiceStatus (Service *service_p, const uuid_t service_id);


BLAST_SERVICE_LOCAL TempFile *GetInputTempFile (const ParameterSet *params_p, const char *working_directory_s, const uuid_t job_id);


BLAST_SERVICE_LOCAL char *GetBlastResultByUUID (const BlastServiceData *data_p, const uuid_t job_id, const uint32 output_format_code, const char *output_format_params_s);


BLAST_SERVICE_LOCAL char *GetBlastResultByUUIDString (const BlastServiceData *data_p, const char *job_id_s, const uint32 output_format_code, const char *output_format_params_s);


BLAST_SERVICE_LOCAL ServiceJobSet *GetPreviousJobResults (LinkedList *ids_p, BlastServiceData *blast_data_p, const uint32 output_format_code, const char *output_format_params_s);


BLAST_SERVICE_LOCAL ServiceJobSet *CreateJobsForPreviousResults (ParameterSet *params_p, const char *ids_s, BlastServiceData *blast_data_p);


BLAST_SERVICE_LOCAL void PrepareBlastServiceJobs (const DatabaseInfo *db_p, const ParameterSet * const param_set_p, Service *service_p, BlastServiceData *data_p);


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


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


BLAST_SERVICE_LOCAL void CustomiseBlastServiceJob (Service *service_p, ServiceJob *job_p);


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


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


BLAST_SERVICE_LOCAL ServiceMetadata *GetGeneralBlastServiceMetadata (Service *service_p);


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


BLAST_SERVICE_LOCAL void ReleaseBlastService (Service *service_p);


BLAST_SERVICE_LOCAL json_t *GetBlastIndexingData (Service *service_p);


#ifdef __cplusplus

}

#endif


#endif    /* #ifndef BLAST_SERVICE_H */