study.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.
*/
/*
 * experimental_area.h
 *
 *  Created on: 11 Sep 2018
 *      Author: billy
 */
 
#ifndef SERVICES_FIELD_TRIALS_INCLUDE_STUDY_H_
#define SERVICES_FIELD_TRIALS_INCLUDE_STUDY_H_
 
 
#include <time.h>
 
#include "dfw_field_trial_service_data.h"
#include "dfw_field_trial_service_library.h"
#include "field_trial.h"
#include "location.h"
#include "jansson.h"
#include "key_value_pair.h"
#include "crop.h"
#include "person.h"
 
#include "typedefs.h"
#include "address.h"
#include "json_processor.h"
#include "statistics.h"
 
 
#ifndef DOXYGEN_SHOULD_SKIP_THIS
 
#ifdef ALLOCATE_STUDY_TAGS
  #define STUDY_PREFIX DFW_FIELD_TRIAL_SERVICE_LOCAL
  #define STUDY_VAL(x)  = x
  #define STUDY_CONCAT_VAL(x,y) = x y
  #define STUDY_KEY_VALUE_PAIR_VAL(x,y) = {x, y}
#else
  #define STUDY_PREFIX extern
  #define STUDY_VAL(x)
  #define STUDY_CONCAT_VAL(x,y)
  #define STUDY_KEY_VALUE_PAIR_VAL(x,y)
#endif
 
#endif    /* #ifndef DOXYGEN_SHOULD_SKIP_THIS */
 
STUDY_PREFIX const char *ST_NAME_S STUDY_CONCAT_VAL (CONTEXT_PREFIX_SCHEMA_ORG_S, "name");
 
STUDY_PREFIX const char *ST_LOCATION_ID_S STUDY_VAL ("address_id");
 
STUDY_PREFIX const char *ST_LOCATION_S STUDY_VAL ("address");
 
 
STUDY_PREFIX const char *ST_CONTACT_S STUDY_VAL ("contact");
 
STUDY_PREFIX const char *ST_CURATOR_S STUDY_VAL ("curator");
 
 
STUDY_PREFIX const char *ST_CONTRIBUTORS_S STUDY_VAL ("contributors");
 
 
STUDY_PREFIX const char *ST_ASPECT_S STUDY_CONCAT_VAL (CONTEXT_PREFIX_NCI_THESAUSUS_ONTOLOGY_S, "C42677");
 
STUDY_PREFIX const char *ST_SLOPE_S STUDY_CONCAT_VAL (CONTEXT_PREFIX_ENVIRONMENT_ONTOLOGY_S, "00002000");
 
 
STUDY_PREFIX const char *ST_PARENT_FIELD_TRIAL_S STUDY_VAL ("parent_field_trial");
 
STUDY_PREFIX const char *ST_PLOTS_S STUDY_VAL ("plots");
 
STUDY_PREFIX const char *ST_NUMBER_OF_PLOTS_S STUDY_VAL ("number_of_plots");
 
 
STUDY_PREFIX const char *ST_DATA_LINK_S STUDY_CONCAT_VAL (CONTEXT_PREFIX_SCHEMA_ORG_S, "url");
 
STUDY_PREFIX const char *ST_FRICTIONLESS_DATA_LINK_S STUDY_CONCAT_VAL (CONTEXT_PREFIX_SCHEMA_ORG_S, "contentUrl");
 
 
STUDY_PREFIX const char *ST_HANDBOOK_DATA_LINK_S STUDY_VAL ("handbook");
 
 
STUDY_PREFIX const char *ST_CURRENT_CROP_S STUDY_VAL ("current_crop");
 
STUDY_PREFIX const char *ST_PREVIOUS_CROP_S STUDY_VAL ("previous_crop");
 
STUDY_PREFIX const char *ST_DESCRIPTION_S STUDY_CONCAT_VAL (CONTEXT_PREFIX_SCHEMA_ORG_S, "description");
 
 
STUDY_PREFIX const char *ST_DESIGN_S STUDY_VAL ("study_design");
 
STUDY_PREFIX const char *ST_GROWING_CONDITIONS_S STUDY_VAL ("growing_conditions");
 
STUDY_PREFIX const char *ST_PHENOTYPE_GATHERING_NOTES_S STUDY_VAL ("phenotype_gathering_notes");
 
 
STUDY_PREFIX const char *ST_NUMBER_OF_PLOT_ROWS_S STUDY_VAL ("num_rows");
 
STUDY_PREFIX const char *ST_NUMBER_OF_PLOT_COLUMN_S STUDY_VAL ("num_columns");
 
STUDY_PREFIX const char *ST_NUMBER_OF_REPLICATES_S STUDY_VAL ("num_replicates");
 
 
STUDY_PREFIX const char *ST_PLOT_LENGTH_S STUDY_VAL ("plot_length");
 
STUDY_PREFIX const char *ST_PLOT_WIDTH_S STUDY_VAL ("plot_width");
 
 
STUDY_PREFIX const char *ST_WEATHER_S STUDY_VAL ("weather");
 
STUDY_PREFIX const char *ST_SHAPE_S STUDY_VAL ("shape_data");
 
STUDY_PREFIX const char *ST_HAS_SHAPE_S STUDY_VAL ("has_shape_data");
 
STUDY_PREFIX const char *ST_SHAPE_NOTES_S STUDY_VAL ("shape_data_notes");
 
 
STUDY_PREFIX const char *ST_PLOT_H_GAP_S STUDY_VAL ("plot_horizontal_gap");
 
STUDY_PREFIX const char *ST_PLOT_V_GAP_S STUDY_VAL ("plot_vertical_gap");
 
STUDY_PREFIX const char *ST_PLOT_BLOCK_H_GAP_S STUDY_VAL ("plot_block_horizontal_gap");
 
STUDY_PREFIX const char *ST_PLOT_BLOCK_V_GAP_S STUDY_VAL ("plot_block_vertical_gap");
 
STUDY_PREFIX const char *ST_PLOT_ROWS_PER_BLOCK_S STUDY_VAL ("plot_block_rows");
 
STUDY_PREFIX const char *ST_PLOT_COLS_PER_BLOCK_S STUDY_VAL ("plot_block_columns");
 
 
STUDY_PREFIX const char *ST_TREATMENTS_S STUDY_VAL ("treatment_factors");
 
 
STUDY_PREFIX const char *ST_PHENOTYPES_S STUDY_VAL ("phenotypes");
 
STUDY_PREFIX const char *ST_ACCESSIONS_S STUDY_VAL ("accessions");
 
 
STUDY_PREFIX const char *ST_PHENOTYPE_STATISTICS_S STUDY_VAL ("statistics");
 
STUDY_PREFIX const char *ST_PHENOTYPE_DEFINITION_S STUDY_VAL ("definition");
 
 
STUDY_PREFIX const char *ST_HARVEST_YEAR_S STUDY_VAL ("harvest_year");
 
STUDY_PREFIX const char *ST_SOWING_YEAR_S STUDY_VAL ("sowing_year");
 
 
STUDY_PREFIX const char *ST_PLAN_CHANGES_S STUDY_VAL ("plan_changes");
 
STUDY_PREFIX const char *ST_PHYSICAL_SAMPLES_COLLECTED_S STUDY_VAL ("physical_samples_collected");
 
STUDY_PREFIX const char *ST_DATA_NOT_INCLUDED_S STUDY_VAL ("data_not_included");
 
STUDY_PREFIX const char *ST_PHOTO_URL_S STUDY_CONCAT_VAL (CONTEXT_PREFIX_SCHEMA_ORG_S, "image");
 
STUDY_PREFIX const char *ST_IMAGE_COLLECTION_NOTE_S STUDY_VAL ("image_collection_notes");
 
STUDY_PREFIX int32 ST_UNSET_PH STUDY_VAL (-1);
 
 
#define ST_UNKNOWN_DIRECTION_S "Unknown"
 
 
 
 
typedef struct Study
{
  bson_oid_t *st_id_p;
 
  char *st_timestamp_s;
 
  FieldTrial *st_parent_p;
 
  MEM_FLAG st_parent_field_trial_mem;
 
  struct Location *st_location_p;
 
  char *st_name_s;
 
  char *st_data_url_s;
 
  char *st_aspect_s;
 
  char *st_slope_s;
 
  LinkedList *st_plots_p;
 
  Crop *st_current_crop_p;
 
  Crop *st_previous_crop_p;
 
  char *st_description_s;
 
  char *st_design_s;
 
  char *st_plan_changes_s;
 
  char *st_physical_samples_collected_s;
 
  char *st_data_not_included_s;
 
  char *st_growing_conditions_s;
 
  char *st_phenotype_gathering_notes_s;
 
  double64 *st_default_plot_width_p;
 
  double64 *st_default_plot_length_p;
 
  uint32 *st_num_rows_p;
 
  uint32 *st_num_columns_p;
 
  uint32 *st_num_replicates_p;
 
  char *st_weather_link_s;
 
  json_t *st_shape_p;
 
  char *st_shape_notes_s;
 
  double64 *st_plot_horizontal_gap_p;
 
  double64 *st_plot_vertical_gap_p;
 
 
  uint32 *st_plots_rows_per_block_p;
 
  uint32 *st_plots_columns_per_block_p;
 
  double64 *st_plot_block_horizontal_gap_p;
 
  double64 *st_plot_block_vertical_gap_p;
 
  LinkedList *st_treatments_p;
 
  Person *st_curator_p;
 
  Person *st_contact_p;
 
  uint32 *st_predicted_sowing_year_p;
 
  uint32 *st_predicted_harvest_year_p;
 
  char *st_photo_url_s;
 
  char *st_image_collection_notes_s;
 
  LinkedList *st_phenotypes_p;
 
  LinkedList *st_contributors_p;
 
} Study;
 
 
 
typedef struct StudyNode
{
  ListItem stn_node;
 
  Study *stn_study_p;
 
} StudyNode;
 
 
 
/* forward declarations */
struct Plot;
 
#ifdef __cplusplus
extern "C"
{
#endif
 
 
 
 
DFW_FIELD_TRIAL_SERVICE_LOCAL Study *AllocateStudy (bson_oid_t *id_p, const char *name_s, const char *data_url_s, const char *aspect_s, const char *slope_s,
                                                    struct Location *location_p, FieldTrial *parent_field_trial_p,
                                                    MEM_FLAG parent_field_trial_mem, Crop *current_crop_p, Crop *previous_crop_p, const char *description_s,
                                                    const char *design_s, const char *growing_conditions_s, const char *phenotype_gathering_notes_s,
                                                    const uint32 *num_rows_p, const uint32 *num_cols_p, const uint32 *num_replicates_p, const double64 *plot_width_p, const double64 *plot_length_p,
                                                    const char *weather_s, const json_t *shape_p, const double64 *plot_horizontal_gap_p, const double64 *plot_vertical_gap_p,
                                                    const uint32 *plot_rows_per_block_p, const uint32 *plot_columns_per_block_p, const double64 *plot_block_horizontal_gap_p,
                                                    const double64 *plot_block_vertical_gap_p,
                                                    Person *curator_p, Person *contact_p,
                                                    const uint32 *sowing_year_p, const uint32 *harvest_year_p,
                                                    const char *plan_changes_s, const char *physical_samples_collected_s, const char *data_not_included_s,
                                                    const char *photo_url_s, const char *image_collection_notes_s,
                                                    const char *gps_notes_s,
                                                    const FieldTrialServiceData *data_p);
 
 
DFW_FIELD_TRIAL_SERVICE_LOCAL void FreeStudy (Study *study_p);
 
DFW_FIELD_TRIAL_SERVICE_LOCAL StudyNode *AllocateStudyNode (Study *study_p);
 
DFW_FIELD_TRIAL_SERVICE_LOCAL void FreeStudyNode (ListItem *node_p);
 
DFW_FIELD_TRIAL_SERVICE_LOCAL json_t *GetStudyAsJSON (Study *study_p, const ViewFormat format, JSONProcessor *processor_p, FieldTrialServiceData *data_p);
 
DFW_FIELD_TRIAL_SERVICE_LOCAL Study *GetStudyFromJSON (const json_t *json_p, const ViewFormat format, const FieldTrialServiceData *data_p);
 
DFW_FIELD_TRIAL_SERVICE_LOCAL Study *GetStudyWithParentTrialFromJSON (const json_t *json_p, FieldTrial *parent_trial_p, const ViewFormat format, const FieldTrialServiceData *data_p);
 
DFW_FIELD_TRIAL_SERVICE_LOCAL bool GetStudyPlots (Study *study_p, const ViewFormat format, FieldTrialServiceData *data_p);
 
DFW_FIELD_TRIAL_SERVICE_LOCAL OperationStatus SaveStudy (Study *study_p, ServiceJob *job_p, FieldTrialServiceData *data_p, const char *url_key_s);
 
DFW_FIELD_TRIAL_SERVICE_LOCAL Study *GetStudyByIdString (const char *study_id_s, const ViewFormat format, const FieldTrialServiceData *data_p);
 
DFW_FIELD_TRIAL_SERVICE_LOCAL Study *GetStudyById (bson_oid_t *st_id_p, const ViewFormat format, const FieldTrialServiceData *data_p);
 
DFW_FIELD_TRIAL_SERVICE_LOCAL bool HasStudyGotPlotLayoutDetails (const Study *study_p);
 
DFW_FIELD_TRIAL_SERVICE_LOCAL bool AddPhenotypesToJSON (const Study *study_p, json_t *study_json_p, const ViewFormat format, const FieldTrialServiceData *data_p);
 
 
DFW_FIELD_TRIAL_SERVICE_LOCAL bool AddPlotToStudy (Study *study_p, struct Plot *plot_p);
 
 
DFW_FIELD_TRIAL_SERVICE_LOCAL int64 GetNumberOfPlotsInStudy (const Study *study_p, const FieldTrialServiceData *data_p);
 
DFW_FIELD_TRIAL_SERVICE_LOCAL OperationStatus IndexStudy (Study *study_p, ServiceJob *job_p, const char *job_name_s, FieldTrialServiceData *data_p);
 
 
DFW_FIELD_TRIAL_SERVICE_LOCAL bool AddStudyContributor (Study *study_p, Person *person_p, MEM_FLAG mf);
 
 
DFW_FIELD_TRIAL_SERVICE_LOCAL bool IsMeasuredVariableOnStudy (const Study * const study_p, const char *mv_s);
 
 
DFW_FIELD_TRIAL_SERVICE_LOCAL bool AddPhenotypeStatisticsToStudy (Study * const study_p, const char *mv_s, const Statistics *stats_p);
 
#ifdef __cplusplus
}
#endif
 
 
#endif /* SERVICES_FIELD_TRIALS_INCLUDE_STUDY_H_ */