polymarker_service.h

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/*
** 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 POLYMARKER_SERVICE_H
#define POLYMARKER_SERVICE_H
 
#include "service.h"
#include "library.h"
 
#include "async_tasks_manager.h"
 
/*
** Now we use the generic helper definitions above to define LIB_API and LIB_LOCAL.
** LIB_API is used for the public API symbols. It either DLL imports or DLL exports
** (or does nothing for static build)
** LIB_LOCAL is used for non-api symbols.
*/
 
 
 
 
#ifdef SHARED_LIBRARY /* defined if LIB is compiled as a DLL */
  #ifdef POLYMARKER_LIBRARY_EXPORTS /* defined if we are building the LIB DLL (instead of using it) */
    #define POLYMARKER_SERVICE_API LIB_HELPER_SYMBOL_EXPORT
  #else
    #define POLYMARKER_SERVICE_API LIB_HELPER_SYMBOL_IMPORT
  #endif /* #ifdef POLYMARKER_LIBRARY_EXPORTS */
  #define POLYMARKER_SERVICE_LOCAL LIB_HELPER_SYMBOL_LOCAL
#else /* SHARED_LIBRARY is not defined: this means LIB is a static lib. */
  #define POLYMARKER_SERVICE_API
  #define POLYMARKER_SERVICE_LOCAL
#endif /* #ifdef SHARED_LIBRARY */
 
 
/*
 * The following preprocessor macros allow us to declare
 * and define the variables in the same place. By default,
 * they will expand to
 *
 *    extern const char *SERVICE_NAME_S;
 *
 * however if ALLOCATE_JSON_TAGS is defined then it will
 * become
 *
 *    const char *SERVICE_NAME_S = "path";
 *
 * ALLOCATE_POLYMARKER_TAGS must be defined only once prior to
 * including this header file. Currently this happens in
 * polymarker_service.c.
 */
#ifndef DOXYGEN_SHOULD_SKIP_THIS
 
#ifdef ALLOCATE_POLYMARKER_TAGS
  #define POLYMARKER_PREFIX POLYMARKER_SERVICE_API
  #define POLYMARKER_VAL(x) = x
  #define POLYMARKER_STRUCT_VAL(x,y)  = { x, y}
#else
  #define POLYMARKER_PREFIX extern
  #define POLYMARKER_VAL(x)
  #define POLYMARKER_STRUCT_VAL(x,y)
#endif
 
#endif    /* #ifndef DOXYGEN_SHOULD_SKIP_THIS */
 
typedef enum
{
  PTT_WEB,
 
  PTT_SYSTEM,
 
  PTT_NUM_TYPES
} PolymarkerToolType;
 
 
 
typedef struct PolymarkerSequence
{
  const char *ps_name_s;
 
  const char *ps_fasta_filename_s;
 
  const char *ps_description_s;
 
  bool ps_active_flag;
 
} PolymarkerSequence;
 
 
typedef struct PolymarkerServiceData
{
  ServiceData psd_base_data;
 
  PolymarkerToolType psd_tool_type;
 
  const char *psd_working_dir_s;
 
 
  const char *psd_executable_s;
 
 
  const char *psd_aligner_s;
 
 
  const char *psd_default_primer_config_file_s;
 
  const char *psd_thermodynamic_parameters_path_s;
 
  PolymarkerSequence *psd_index_data_p;
 
  size_t psd_index_data_size;
 
 
  AsyncTasksManager *psd_task_manager_p;
 
} PolymarkerServiceData;
 
 
POLYMARKER_PREFIX NamedParameterType PS_CONTIG_FILENAME POLYMARKER_STRUCT_VAL ("Contig filename", PT_STRING);
 
 
POLYMARKER_PREFIX NamedParameterType PS_GENE_ID POLYMARKER_STRUCT_VAL ("Gene", PT_STRING);
 
POLYMARKER_PREFIX NamedParameterType PS_TARGET_CHROMOSOME POLYMARKER_STRUCT_VAL ("Chromosome", PT_STRING);
 
 
POLYMARKER_PREFIX NamedParameterType PS_SEQUENCE POLYMARKER_STRUCT_VAL ("Sequence", PT_LARGE_STRING);
 
 
POLYMARKER_PREFIX NamedParameterType PS_JOB_IDS POLYMARKER_STRUCT_VAL ("Previous results", PT_LARGE_STRING);
 
 
POLYMARKER_PREFIX const char *PS_TOOL_S POLYMARKER_VAL ("tool");
 
POLYMARKER_PREFIX const char *PS_TOOL_SYSTEM_S POLYMARKER_VAL ("system");
 
POLYMARKER_PREFIX const char *PS_TOOL_WEB_S POLYMARKER_VAL ("web");
 
POLYMARKER_PREFIX const char *PS_ALIGNER_BLAST_S POLYMARKER_VAL ("blast");
 
POLYMARKER_PREFIX const char *PS_ALIGNER_EXONERATE_S POLYMARKER_VAL ("exonerate");
 
 
#ifdef __cplusplus
extern "C"
{
#endif
 
POLYMARKER_SERVICE_API ServicesArray *GetServices (UserDetails *user_p, GrassrootsServer *grassroots_p);
 
 
POLYMARKER_SERVICE_API void ReleaseServices (ServicesArray *services_p);
 
 
POLYMARKER_SERVICE_LOCAL void ReleasePolymarkerService (Service *service_p);
 
 
#ifdef __cplusplus
}
#endif
 
 
 
#endif    /* #ifndef POLYMARKER_SERVICE_H */