Function reference • grunID

Adding data

These functions allow users to add information about samples being run to the database

add_agency(): Add Agency

add_assay(): Add Assay

add_enum_value(): Add Enumerated Type Value

add_genetic_identification(): Genetic Identification

add_genetic_method(): Add Genetic Method

add_laboratory(): Add Laboratory

add_new_plate_results(): Add New Plate Results

add_plate_run(): Create Plate Run

add_plate_thresholds(): Add Thresholds to Database

add_protocol(): Add Protocol

add_protocol_based_on(): Add Protocol Based on Existing Protocol

add_raw_assay_results(): Add Raw Results

add_run_type(): Add Run Type

add_sample_bins(): Create sample bins

add_sample_events(): Create sample events

add_sample_location(): Add Sample Location

add_sample_plan(): Add Sample Plan

add_sample_type(): Add Sample Type

add_samples(): Add samples

add_status_code(): Add Status Code

protocol_template: Templates

add_salvage_samples(): Seed Salvate Samples

add_sample(): Add single or many samples

Deleting data

These functions allow users to delete information about samples being run

delete_agency(): Delete Agency

delete_assay(): Delete Assay

delete_genetic_method(): Delete Genetic Method

delete_laboratory(): Delete Laboratory

delete_protocol(): Delete Protocol

delete_run_type(): Delete Run Type

delete_sample_location(): Delete Sample Location

delete_sample_type(): Delete Sample Type

delete_status_code(): Delete Status Code

Retrieving data

These functions allow users to retrieve information from the database

get_agencies(): Retrieve Agencies

get_assays(): Retrieve Assays

get_enum_values(): Get Enumerated Type Values

get_genetic_methods(): Retrieve Genetic Methods

get_laboratories(): Retrieve Laboratories

get_plate_run(): Query for plate run

get_protocols(): Retrieve Protocols

get_run_types(): Retrieve Run Types

get_sample_locations(): Retrieve Sample Locations

get_sample_status(): Get Sample Status

get_sample_types(): Retrieve Sample Types

get_samples(): Get Samples

get_samples_needing_action(): Samples needing further genetic analysis

get_status_codes(): Retrieve Status Codes

Processing data

These functions convert results into database-ready formats

process_plate_layout(): Process Plate Layout

process_raw_assay_results(): Process Raw Assay Results

process_raw_sample_plan(): Process Raw Sample Plan

process_sherlock(): Process Sherlock Results

process_well_sample_details(): Get Sample Details

Updating data

These functions update data in the database

activate_plate_run(): Activate Plate Run

deactivate_plate_run(): Deactivate Plate Run

set_sample_status(): Set Status Code

update_agency(): Update Agency

update_agency_status(): Update Agency Status

update_assay(): Update Assay

update_assay_detection(): Set detection for assay results

update_assay_status(): Update Assay Status

update_enum_value(): Update Enumerated Type Value

update_genetic_method(): Update Genetic Method

update_genetic_method_status(): Change Agency Status

update_laboratory(): Update Laboratory

update_laboratory_status(): Update Laboratory Status

update_protocol(): Update Protocol

update_protocol_status(): Update Protocol Status

update_run_type(): Update Run Type

update_run_type_status(): Update Run Type Status

update_sample_location(): Update Sample Location

update_sample_location_status(): Update Sample Location Status

update_sample_type(): Update Sample Type

update_sample_type_status(): Update Sample Type Status

update_status_code(): Update Status Code

update_status_code_status(): Update Status Code Status

Field sheet management

These functions relate to creating and processing field sheets

create_season_field_sheets(): Create Season Field Sheets

process_field_sheet_samples(): Process Sample Field Sheet Data

update_field_sheet_samples(): Update Sample Field Sheet Data

check_in_jpe_field_samples(): Check-in Samples from field

Helper functions

These functions are generally not used in standard workflow but are employed within functions.

excel_column_index: Excel Column Index

extract_previous_end_row(): Extract Previous End Row

extract_sherlock_protocol(): Extract Sherlock Protocol

generate_range(): Generate a cell range

generate_ranges(): Generate all cell ranges for tables containing assay results

generate_threshold(): Generate Thresholds

is_valid_sample_field_data(): Helper function - checks field sheet data format

is_valid_connection(): Check Database Connection is Valid

Connection functions

gr_db_connect(): Connect to Run ID Database

Genetic identification functions

ots_early_late_detection(): Determine Run identifcation after Early and Late Assays

ots_winter_spring_detection(): Determine Run identifcation after Spring and Winter Assays

run_genetic_identification(): Run genetic identification

Misc

fill_dual_assay_plate_map(): fill_dual_assay_plate_map

fill_single_assay_plate_map(): fill_single_assay_plate_map

generate_subsample(): Generate Subsample

generate_subsample_plate_map(): generate_subsample_plate_map

get_clean_dataset(): Query database for clean dataset

get_genetic_run_results(): Query Genetic Results

get_raw_dataset(): Query database for raw dataset

get_samples_by_season(): Get Samples by Season

get_unprocessed_dataset(): Query database for unprocessed dataset

make_salvage_ids(): Create salvage ids

parse_plate_flags(): Parse Comment for EBK Flags

process_field_sheet_samples2(): Process Field Sheets Version 2

sample_filter_to_season(): Filter dataset by season

update_genetic_run_id(): Update Genetic Run ID

validate_results(): Validate Results

view_genetic_id_audits(): View Results Table Audits

App functions

run_app(): Launch App