study.h File Reference

#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"

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Data Structures
struct	Study
struct	StudyNode

Macros
#define	ST_UNKNOWN_DIRECTION_S   "Unknown"
	The value to specify that the aspect parameter is not set. More...

Functions
const STUDY_PREFIX char *ST_NAME_S	STUDY_CONCAT_VAL (CONTEXT_PREFIX_SCHEMA_ORG_S, "name")
const STUDY_PREFIX char *ST_LOCATION_ID_S	STUDY_VAL ("address_id")
const STUDY_PREFIX char *ST_LOCATION_S	STUDY_VAL ("address")
const STUDY_PREFIX char *ST_CONTACT_S	STUDY_VAL ("contact")
const STUDY_PREFIX char *ST_CURATOR_S	STUDY_VAL ("curator")
const STUDY_PREFIX char *ST_CONTRIBUTORS_S	STUDY_VAL ("contributors")
const STUDY_PREFIX char *ST_ASPECT_S	STUDY_CONCAT_VAL (CONTEXT_PREFIX_NCI_THESAUSUS_ONTOLOGY_S, "C42677")
const STUDY_PREFIX char *ST_SLOPE_S	STUDY_CONCAT_VAL (CONTEXT_PREFIX_ENVIRONMENT_ONTOLOGY_S, "00002000")
const STUDY_PREFIX char *ST_PARENT_FIELD_TRIAL_S	STUDY_VAL ("parent_field_trial")
const STUDY_PREFIX char *ST_PLOTS_S	STUDY_VAL ("plots")
const STUDY_PREFIX char *ST_NUMBER_OF_PLOTS_S	STUDY_VAL ("number_of_plots")
const STUDY_PREFIX char *ST_DATA_LINK_S	STUDY_CONCAT_VAL (CONTEXT_PREFIX_SCHEMA_ORG_S, "url")
const STUDY_PREFIX char *ST_FRICTIONLESS_DATA_LINK_S	STUDY_CONCAT_VAL (CONTEXT_PREFIX_SCHEMA_ORG_S, "contentUrl")
const STUDY_PREFIX char *ST_HANDBOOK_DATA_LINK_S	STUDY_VAL ("handbook")
const STUDY_PREFIX char *ST_CURRENT_CROP_S	STUDY_VAL ("current_crop")
const STUDY_PREFIX char *ST_PREVIOUS_CROP_S	STUDY_VAL ("previous_crop")
const STUDY_PREFIX char *ST_DESCRIPTION_S	STUDY_CONCAT_VAL (CONTEXT_PREFIX_SCHEMA_ORG_S, "description")
const STUDY_PREFIX char *ST_DESIGN_S	STUDY_VAL ("study_design")
const STUDY_PREFIX char *ST_GROWING_CONDITIONS_S	STUDY_VAL ("growing_conditions")
const STUDY_PREFIX char *ST_PHENOTYPE_GATHERING_NOTES_S	STUDY_VAL ("phenotype_gathering_notes")
const STUDY_PREFIX char *ST_NUMBER_OF_PLOT_ROWS_S	STUDY_VAL ("num_rows")
const STUDY_PREFIX char *ST_NUMBER_OF_PLOT_COLUMN_S	STUDY_VAL ("num_columns")
const STUDY_PREFIX char *ST_NUMBER_OF_REPLICATES_S	STUDY_VAL ("num_replicates")
const STUDY_PREFIX char *ST_PLOT_LENGTH_S	STUDY_VAL ("plot_length")
const STUDY_PREFIX char *ST_PLOT_WIDTH_S	STUDY_VAL ("plot_width")
const STUDY_PREFIX char *ST_WEATHER_S	STUDY_VAL ("weather")
const STUDY_PREFIX char *ST_SHAPE_S	STUDY_VAL ("shape_data")
const STUDY_PREFIX char *ST_HAS_SHAPE_S	STUDY_VAL ("has_shape_data")
const STUDY_PREFIX char *ST_SHAPE_NOTES_S	STUDY_VAL ("shape_data_notes")
const STUDY_PREFIX char *ST_PLOT_H_GAP_S	STUDY_VAL ("plot_horizontal_gap")
const STUDY_PREFIX char *ST_PLOT_V_GAP_S	STUDY_VAL ("plot_vertical_gap")
const STUDY_PREFIX char *ST_PLOT_BLOCK_H_GAP_S	STUDY_VAL ("plot_block_horizontal_gap")
const STUDY_PREFIX char *ST_PLOT_BLOCK_V_GAP_S	STUDY_VAL ("plot_block_vertical_gap")
const STUDY_PREFIX char *ST_PLOT_ROWS_PER_BLOCK_S	STUDY_VAL ("plot_block_rows")
const STUDY_PREFIX char *ST_PLOT_COLS_PER_BLOCK_S	STUDY_VAL ("plot_block_columns")
const STUDY_PREFIX char *ST_TREATMENTS_S	STUDY_VAL ("treatment_factors")
const STUDY_PREFIX char *ST_PHENOTYPES_S	STUDY_VAL ("phenotypes")
const STUDY_PREFIX char *ST_ACCESSIONS_S	STUDY_VAL ("accessions")
const STUDY_PREFIX char *ST_PHENOTYPE_STATISTICS_S	STUDY_VAL ("statistics")
const STUDY_PREFIX char *ST_PHENOTYPE_DEFINITION_S	STUDY_VAL ("definition")
const STUDY_PREFIX char *ST_HARVEST_YEAR_S	STUDY_VAL ("harvest_year")
const STUDY_PREFIX char *ST_SOWING_YEAR_S	STUDY_VAL ("sowing_year")
const STUDY_PREFIX char *ST_PLAN_CHANGES_S	STUDY_VAL ("plan_changes")
const STUDY_PREFIX char *ST_PHYSICAL_SAMPLES_COLLECTED_S	STUDY_VAL ("physical_samples_collected")
const STUDY_PREFIX char *ST_DATA_NOT_INCLUDED_S	STUDY_VAL ("data_not_included")
const STUDY_PREFIX char *ST_PHOTO_URL_S	STUDY_CONCAT_VAL (CONTEXT_PREFIX_SCHEMA_ORG_S, "image")
const STUDY_PREFIX char *ST_IMAGE_COLLECTION_NOTE_S	STUDY_VAL ("image_collection_notes")
STUDY_PREFIX int32 ST_UNSET_PH	STUDY_VAL (-1)
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)
void	FreeStudy (Study *study_p)
StudyNode *	AllocateStudyNode (Study *study_p)
void	FreeStudyNode (ListItem *node_p)
json_t *	GetStudyAsJSON (Study *study_p, const ViewFormat format, JSONProcessor *processor_p, FieldTrialServiceData *data_p)
Study *	GetStudyFromJSON (const json_t *json_p, const ViewFormat format, const FieldTrialServiceData *data_p)
Study *	GetStudyWithParentTrialFromJSON (const json_t *json_p, FieldTrial *parent_trial_p, const ViewFormat format, const FieldTrialServiceData *data_p)
bool	GetStudyPlots (Study *study_p, const ViewFormat format, FieldTrialServiceData *data_p)
OperationStatus	SaveStudy (Study *study_p, ServiceJob *job_p, FieldTrialServiceData *data_p, const char *url_key_s)
Study *	GetStudyByIdString (const char *study_id_s, const ViewFormat format, const FieldTrialServiceData *data_p)
Study *	GetStudyById (bson_oid_t *st_id_p, const ViewFormat format, const FieldTrialServiceData *data_p)
bool	HasStudyGotPlotLayoutDetails (const Study *study_p)
bool	AddPhenotypesToJSON (const Study *study_p, json_t *study_json_p, const ViewFormat format, const FieldTrialServiceData *data_p)
bool	AddPlotToStudy (Study *study_p, struct Plot *plot_p)
int64	GetNumberOfPlotsInStudy (const Study *study_p, const FieldTrialServiceData *data_p)
OperationStatus	IndexStudy (Study *study_p, ServiceJob *job_p, const char *job_name_s, FieldTrialServiceData *data_p)
bool	AddStudyContributor (Study *study_p, Person *person_p, MEM_FLAG mf)
bool	IsMeasuredVariableOnStudy (const Study *const study_p, const char *mv_s)
bool	AddPhenotypeStatisticsToStudy (Study *const study_p, const char *mv_s, const Statistics *stats_p)

Macro Definition Documentation

ST_UNKNOWN_DIRECTION_S

#define ST_UNKNOWN_DIRECTION_S   "Unknown"

The value to specify that the aspect parameter is not set.

Function Documentation

STUDY_CONCAT_VAL() [1/7]

const STUDY_PREFIX char* ST_NAME_S STUDY_CONCAT_VAL	(	CONTEXT_PREFIX_SCHEMA_ORG_S	,
		"name"
	)

STUDY_VAL() [1/41]

const STUDY_PREFIX char* ST_LOCATION_ID_S STUDY_VAL

(

"address_id"

)

STUDY_VAL() [2/41]

const STUDY_PREFIX char* ST_LOCATION_S STUDY_VAL

(

"address"

)

STUDY_VAL() [3/41]

const STUDY_PREFIX char* ST_CONTACT_S STUDY_VAL

(

"contact"

)

STUDY_VAL() [4/41]

const STUDY_PREFIX char* ST_CURATOR_S STUDY_VAL

(

"curator"

)

STUDY_VAL() [5/41]

const STUDY_PREFIX char* ST_CONTRIBUTORS_S STUDY_VAL

(

"contributors"

)

STUDY_CONCAT_VAL() [2/7]

const STUDY_PREFIX char* ST_ASPECT_S STUDY_CONCAT_VAL	(	CONTEXT_PREFIX_NCI_THESAUSUS_ONTOLOGY_S	,
		"C42677"
	)

STUDY_CONCAT_VAL() [3/7]

const STUDY_PREFIX char* ST_SLOPE_S STUDY_CONCAT_VAL	(	CONTEXT_PREFIX_ENVIRONMENT_ONTOLOGY_S	,
		"00002000"
	)

STUDY_VAL() [6/41]

const STUDY_PREFIX char* ST_PARENT_FIELD_TRIAL_S STUDY_VAL

(

"parent_field_trial"

)

STUDY_VAL() [7/41]

const STUDY_PREFIX char* ST_PLOTS_S STUDY_VAL

(

"plots"

)

STUDY_VAL() [8/41]

const STUDY_PREFIX char* ST_NUMBER_OF_PLOTS_S STUDY_VAL

(

"number_of_plots"

)

STUDY_CONCAT_VAL() [4/7]

const STUDY_PREFIX char* ST_DATA_LINK_S STUDY_CONCAT_VAL	(	CONTEXT_PREFIX_SCHEMA_ORG_S	,
		"url"
	)

STUDY_CONCAT_VAL() [5/7]

const STUDY_PREFIX char* ST_FRICTIONLESS_DATA_LINK_S STUDY_CONCAT_VAL	(	CONTEXT_PREFIX_SCHEMA_ORG_S	,
		"contentUrl"
	)

STUDY_VAL() [9/41]

const STUDY_PREFIX char* ST_HANDBOOK_DATA_LINK_S STUDY_VAL

(

"handbook"

)

STUDY_VAL() [10/41]

const STUDY_PREFIX char* ST_CURRENT_CROP_S STUDY_VAL

(

"current_crop"

)

STUDY_VAL() [11/41]

const STUDY_PREFIX char* ST_PREVIOUS_CROP_S STUDY_VAL

(

"previous_crop"

)

STUDY_CONCAT_VAL() [6/7]

const STUDY_PREFIX char* ST_DESCRIPTION_S STUDY_CONCAT_VAL	(	CONTEXT_PREFIX_SCHEMA_ORG_S	,
		"description"
	)

STUDY_VAL() [12/41]

const STUDY_PREFIX char* ST_DESIGN_S STUDY_VAL

(

"study_design"

)

STUDY_VAL() [13/41]

const STUDY_PREFIX char* ST_GROWING_CONDITIONS_S STUDY_VAL

(

"growing_conditions"

)

STUDY_VAL() [14/41]

const STUDY_PREFIX char* ST_PHENOTYPE_GATHERING_NOTES_S STUDY_VAL

(

"phenotype_gathering_notes"

)

STUDY_VAL() [15/41]

const STUDY_PREFIX char* ST_NUMBER_OF_PLOT_ROWS_S STUDY_VAL

(

"num_rows"

)

STUDY_VAL() [16/41]

const STUDY_PREFIX char* ST_NUMBER_OF_PLOT_COLUMN_S STUDY_VAL

(

"num_columns"

)

STUDY_VAL() [17/41]

const STUDY_PREFIX char* ST_NUMBER_OF_REPLICATES_S STUDY_VAL

(

"num_replicates"

)

STUDY_VAL() [18/41]

const STUDY_PREFIX char* ST_PLOT_LENGTH_S STUDY_VAL

(

"plot_length"

)

STUDY_VAL() [19/41]

const STUDY_PREFIX char* ST_PLOT_WIDTH_S STUDY_VAL

(

"plot_width"

)

STUDY_VAL() [20/41]

const STUDY_PREFIX char* ST_WEATHER_S STUDY_VAL

(

"weather"

)

STUDY_VAL() [21/41]

const STUDY_PREFIX char* ST_SHAPE_S STUDY_VAL

(

"shape_data"

)

STUDY_VAL() [22/41]

const STUDY_PREFIX char* ST_HAS_SHAPE_S STUDY_VAL

(

"has_shape_data"

)

STUDY_VAL() [23/41]

const STUDY_PREFIX char* ST_SHAPE_NOTES_S STUDY_VAL

(

"shape_data_notes"

)

STUDY_VAL() [24/41]

const STUDY_PREFIX char* ST_PLOT_H_GAP_S STUDY_VAL

(

"plot_horizontal_gap"

)

STUDY_VAL() [25/41]

const STUDY_PREFIX char* ST_PLOT_V_GAP_S STUDY_VAL

(

"plot_vertical_gap"

)

STUDY_VAL() [26/41]

const STUDY_PREFIX char* ST_PLOT_BLOCK_H_GAP_S STUDY_VAL

(

"plot_block_horizontal_gap"

)

STUDY_VAL() [27/41]

const STUDY_PREFIX char* ST_PLOT_BLOCK_V_GAP_S STUDY_VAL

(

"plot_block_vertical_gap"

)

STUDY_VAL() [28/41]

const STUDY_PREFIX char* ST_PLOT_ROWS_PER_BLOCK_S STUDY_VAL

(

"plot_block_rows"

)

STUDY_VAL() [29/41]

const STUDY_PREFIX char* ST_PLOT_COLS_PER_BLOCK_S STUDY_VAL

(

"plot_block_columns"

)

STUDY_VAL() [30/41]

const STUDY_PREFIX char* ST_TREATMENTS_S STUDY_VAL

(

"treatment_factors"

)

STUDY_VAL() [31/41]

const STUDY_PREFIX char* ST_PHENOTYPES_S STUDY_VAL

(

"phenotypes"

)

STUDY_VAL() [32/41]

const STUDY_PREFIX char* ST_ACCESSIONS_S STUDY_VAL

(

"accessions"

)

STUDY_VAL() [33/41]

const STUDY_PREFIX char* ST_PHENOTYPE_STATISTICS_S STUDY_VAL

(

"statistics"

)

STUDY_VAL() [34/41]

const STUDY_PREFIX char* ST_PHENOTYPE_DEFINITION_S STUDY_VAL

(

"definition"

)

STUDY_VAL() [35/41]

const STUDY_PREFIX char* ST_HARVEST_YEAR_S STUDY_VAL

(

"harvest_year"

)

STUDY_VAL() [36/41]

const STUDY_PREFIX char* ST_SOWING_YEAR_S STUDY_VAL

(

"sowing_year"

)

STUDY_VAL() [37/41]

const STUDY_PREFIX char* ST_PLAN_CHANGES_S STUDY_VAL

(

"plan_changes"

)

STUDY_VAL() [38/41]

const STUDY_PREFIX char* ST_PHYSICAL_SAMPLES_COLLECTED_S STUDY_VAL

(

"physical_samples_collected"

)

STUDY_VAL() [39/41]

const STUDY_PREFIX char* ST_DATA_NOT_INCLUDED_S STUDY_VAL

(

"data_not_included"

)

STUDY_CONCAT_VAL() [7/7]

const STUDY_PREFIX char* ST_PHOTO_URL_S STUDY_CONCAT_VAL	(	CONTEXT_PREFIX_SCHEMA_ORG_S	,
		"image"
	)

STUDY_VAL() [40/41]

const STUDY_PREFIX char* ST_IMAGE_COLLECTION_NOTE_S STUDY_VAL

(

"image_collection_notes"

)

STUDY_VAL() [41/41]

STUDY_PREFIX int32 ST_UNSET_PH STUDY_VAL

(

-

1

)

AllocateStudy()

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
	)

FreeStudy()

void FreeStudy

(

Study *

study_p

)

AllocateStudyNode()

StudyNode* AllocateStudyNode

(

Study *

study_p

)

FreeStudyNode()

void FreeStudyNode

(

ListItem *

node_p

)

GetStudyAsJSON()

json_t* GetStudyAsJSON	(	Study *	study_p,
		const ViewFormat	format,
		JSONProcessor *	processor_p,
		FieldTrialServiceData *	data_p
	)

GetStudyFromJSON()

Study* GetStudyFromJSON	(	const json_t *	json_p,
		const ViewFormat	format,
		const FieldTrialServiceData *	data_p
	)

GetStudyWithParentTrialFromJSON()

Study* GetStudyWithParentTrialFromJSON	(	const json_t *	json_p,
		FieldTrial *	parent_trial_p,
		const ViewFormat	format,
		const FieldTrialServiceData *	data_p
	)

GetStudyPlots()

bool GetStudyPlots	(	Study *	study_p,
		const ViewFormat	format,
		FieldTrialServiceData *	data_p
	)

SaveStudy()

OperationStatus SaveStudy	(	Study *	study_p,
		ServiceJob *	job_p,
		FieldTrialServiceData *	data_p,
		const char *	url_key_s
	)

GetStudyByIdString()

Study* GetStudyByIdString	(	const char *	study_id_s,
		const ViewFormat	format,
		const FieldTrialServiceData *	data_p
	)

GetStudyById()

Study* GetStudyById	(	bson_oid_t *	st_id_p,
		const ViewFormat	format,
		const FieldTrialServiceData *	data_p
	)

HasStudyGotPlotLayoutDetails()

bool HasStudyGotPlotLayoutDetails

(

const Study *

study_p

)

AddPhenotypesToJSON()

bool AddPhenotypesToJSON	(	const Study *	study_p,
		json_t *	study_json_p,
		const ViewFormat	format,
		const FieldTrialServiceData *	data_p
	)

AddPlotToStudy()

bool AddPlotToStudy	(	Study *	study_p,
		struct Plot *	plot_p
	)

GetNumberOfPlotsInStudy()

int64 GetNumberOfPlotsInStudy	(	const Study *	study_p,
		const FieldTrialServiceData *	data_p
	)

IndexStudy()

OperationStatus IndexStudy	(	Study *	study_p,
		ServiceJob *	job_p,
		const char *	job_name_s,
		FieldTrialServiceData *	data_p
	)

AddStudyContributor()

bool AddStudyContributor	(	Study *	study_p,
		Person *	person_p,
		MEM_FLAG	mf
	)

IsMeasuredVariableOnStudy()

bool IsMeasuredVariableOnStudy	(	const Study *const	study_p,
		const char *	mv_s
	)

AddPhenotypeStatisticsToStudy()

bool AddPhenotypeStatisticsToStudy	(	Study *const	study_p,
		const char *	mv_s,
		const Statistics *	stats_p
	)