material.h

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/*
** Copyright 2014-2018 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.
*/
/*
 * material.h
 *
 *  Created on: 11 Sep 2018
 *      Author: billy
 */
 
#ifndef SERVICES_FIELD_TRIALS_INCLUDE_MATERIAL_H_
#define SERVICES_FIELD_TRIALS_INCLUDE_MATERIAL_H_
 
 
 
 
 
#include "dfw_field_trial_service_data.h"
#include "dfw_field_trial_service_library.h"
#include "jansson.h"
#include "typedefs.h"
#include "study.h"
#include "gene_bank.h"
 
/*
 *
 * Species name
 * Germplasm ID
 * Type of Material
 * Reason for selection
 * Generation
 * Seed Supplier
 * Source of Seed
 * Germplasm Origin
 * In GRU?
 * GRU Accession
 * TGW
 * Seed Treatment
 * Cleaned
      keyword list  F2, F3 etc  Organisation  Trial or Organisation Organisation  Y/N ID  Number  Treatment   Y/N
Triticum aestivum BT1604  Synthetic Derived yield, drought tolerance    Rothamsted  17/18 Trial NIAB
Triticum aestivum Skyfall Elite control   RAGT  Commercial  RAGT      150 Azole fungicide X
 
 *
 */
 
 
typedef struct MaterialStudyDetails
{
  char *ma_germplasm_id_s;
 
  const Study *ma_parent_area_p;
 
  char *ma_species_name_s;
 
  char *ma_type_s;
 
  char *ma_selection_reason_s;
 
  char *ma_generation_s;
 
  char *ma_seed_supplier_s;
 
  char *ma_seed_source_s;
 
  char *ma_germplasm_origin_s;
 
  bool ma_in_gru_flag;
 
  uint32 ma_tgw;
 
  char *ma_seed_treatment_s;
 
  bool ma_cleaned_flag;
 
  char *ma_primary_name_s;
 
 
  char *ma_secondary_name_s;
 
  char *ma_tertiary_name_s;
 
  char *ma_store_code_s;
 
 
}  MaterialStudyDetails;
 
 
typedef struct MaterialStudyDetailsNode
{
  ListItem msdn_node;
 
  MaterialStudyDetails *msdn_details_p;
} MaterialStudyDetailsNode;
 
 
typedef struct Material
{
  bson_oid_t *ma_id_p;
 
  bson_oid_t *ma_gene_bank_id_p;
 
  char *ma_accession_s;
 
} Material;
 
 
 
 
 
#ifndef DOXYGEN_SHOULD_SKIP_THIS
 
#ifdef ALLOCATE_MATERIAL_TAGS
  #define MATERIAL_PREFIX DFW_FIELD_TRIAL_SERVICE_LOCAL
  #define MATERIAL_VAL(x) = x
  #define MATERIAL_CONCAT_VAL(x,y)  = x y
#else
  #define MATERIAL_PREFIX extern
  #define MATERIAL_VAL(x)
  #define MATERIAL_CONCAT_VAL(x,y)
#endif
 
#endif    /* #ifndef DOXYGEN_SHOULD_SKIP_THIS */
 
 
 
MATERIAL_PREFIX const char *MA_ID_S MATERIAL_VAL ("id");
 
MATERIAL_PREFIX const char *MA_ACCESSION_S MATERIAL_VAL ("accession");
 
MATERIAL_PREFIX const char *MA_BARCODE_S MATERIAL_VAL ("barcode");
 
MATERIAL_PREFIX const char *MA_PEDIGREE_S MATERIAL_VAL ("pedigree");
 
MATERIAL_PREFIX const char *MA_GENE_BANK_ID_S MATERIAL_VAL ("gene_bank_id");
 
MATERIAL_PREFIX const char *MA_GENE_BANK_S MATERIAL_VAL ("gene_bank");
 
MATERIAL_PREFIX const char *MA_EXPERIMENTAL_AREA_ID_S MATERIAL_VAL ("area_id");
 
MATERIAL_PREFIX const char *MA_GERMPLASM_ID_S MATERIAL_VAL ("germplasm_id");
 
 
 
 
MATERIAL_PREFIX const char *MA_SPECIES_S MATERIAL_VAL ("http://purl.obolibrary.org/obo/NCIT_C45293");
 
MATERIAL_PREFIX const char *MA_TYPE_S MATERIAL_VAL ("type");
MATERIAL_PREFIX const char *MA_SELECTION_REASON_S MATERIAL_VAL ("selection_reason");
MATERIAL_PREFIX const char *MA_GENERATION_S MATERIAL_VAL ("generation");
MATERIAL_PREFIX const char *MA_SEED_SUPPLIER_S MATERIAL_VAL ("seed_supplier");
MATERIAL_PREFIX const char *MA_SEED_SOURCE_S MATERIAL_VAL ("seed_source");
MATERIAL_PREFIX const char *MA_GERMPLASM_ORIGIN_S MATERIAL_VAL ("germplasm_origin");
MATERIAL_PREFIX const char *MA_IN_GRU_S MATERIAL_VAL ("in_gru");
MATERIAL_PREFIX const char *MA_TGW_S MATERIAL_VAL ("tgw");
MATERIAL_PREFIX const char *MA_SEED_TREATMENT_S MATERIAL_VAL ("seed_treatment");
 
MATERIAL_PREFIX const char *MA_PRIMARY_NAME_S MATERIAL_VAL("primary_name");
MATERIAL_PREFIX const char *MA_SECONDARY_NAME_S MATERIAL_VAL("secondary_name");
MATERIAL_PREFIX const char *MA_TERTIARY_NAME_S MATERIAL_VAL("tertiary_name");
MATERIAL_PREFIX const char *MA_STODE_CODE_S MATERIAL_VAL("store_code");
 
MATERIAL_PREFIX const char *MA_CLEANED_NAME_S MATERIAL_VAL ("cleaned");
 
 
 
 
#ifdef __cplusplus
extern "C"
{
#endif
 
 
DFW_FIELD_TRIAL_SERVICE_LOCAL Material *AllocateMaterial (bson_oid_t *id_p, const char *accession_s, const char *species_s, const char *type_s, const char *selection_reason_s, const char *generation_s, const char *supplier_s, const char *source_s, const char *germplasm_origin_s, const char *treatment_s, bool gru_flag, bool cleaned_flag, uint32 tgw, const Study *area_p, const bson_oid_t *gene_bank_id_p, const FieldTrialServiceData *data_p);
 
 
DFW_FIELD_TRIAL_SERVICE_LOCAL Material *AllocateMaterialByGermplasmID (bson_oid_t *id_p, const char *germplasm_id_s, const Study *area_p, const FieldTrialServiceData *data_p);
 
 
DFW_FIELD_TRIAL_SERVICE_LOCAL Material *AllocateMaterialByAccession (bson_oid_t *id_p, const char *accession_s, bson_oid_t *gene_bank_id_p, const FieldTrialServiceData *data_p);
 
 
 
DFW_FIELD_TRIAL_SERVICE_LOCAL bool SetMaterialAccession (Material *material_p, const char * const accession_s);
 
/*
DFW_FIELD_TRIAL_SERVICE_LOCAL bool SetMaterialPedigree (Material *material_p, const char * const pedigree_s);
 
DFW_FIELD_TRIAL_SERVICE_LOCAL bool SetMaterialBarcode (Material *material_p, const char * const barcode_s);
 
DFW_FIELD_TRIAL_SERVICE_LOCAL bool SetMaterialInternalName (Material *material_p, const char * const internal_name_s);
*/
 
DFW_FIELD_TRIAL_SERVICE_LOCAL void FreeMaterial (Material *material_p);
 
DFW_FIELD_TRIAL_SERVICE_LOCAL json_t *GetMaterialAsJSON (const Material *material_p, const ViewFormat format, const FieldTrialServiceData *data_p);
 
DFW_FIELD_TRIAL_SERVICE_LOCAL Material *GetMaterialFromJSON (const json_t *json_p, const ViewFormat format, const FieldTrialServiceData *data_p);
 
 
DFW_FIELD_TRIAL_SERVICE_LOCAL bool SaveMaterial (Material *material_p, const FieldTrialServiceData *data_p);
 
DFW_FIELD_TRIAL_SERVICE_LOCAL Material *LoadMaterial (const int32 material_id, FieldTrialServiceData *data_p);
 
 
DFW_FIELD_TRIAL_SERVICE_LOCAL Material*GetOrCreateMaterialByInternalName (const char *material_s, Study *area_p, const FieldTrialServiceData *data_p);
 
DFW_FIELD_TRIAL_SERVICE_LOCAL Material *GetOrCreateMaterialByAccession (const char *accession_s, GeneBank *gene_bank_p, const FieldTrialServiceData *data_p);
 
 
DFW_FIELD_TRIAL_SERVICE_LOCAL Material *GetMaterialByGermplasmID (const char *material_s, Study *area_p, const FieldTrialServiceData *data_p);
 
DFW_FIELD_TRIAL_SERVICE_LOCAL Material *GetMaterialById (const bson_oid_t *material_id_p, const FieldTrialServiceData *data_p);
 
 
DFW_FIELD_TRIAL_SERVICE_LOCAL Material *GetMaterialByAccession (const char *accession_s, GeneBank *gene_bank_p, const bool case_sensitive_flag, const FieldTrialServiceData *data_p);
 
 
DFW_FIELD_TRIAL_SERVICE_LOCAL bool IsMaterialComplete (const Material * const material_p);
 
 
#ifdef __cplusplus
}
#endif
 
 
#endif /* SERVICES_FIELD_TRIALS_INCLUDE_MATERIAL_H_ */