#====================================
USE `genomics`; # or change to `test`
#====================================
/* new lab-section */
INSERT INTO lab_sections(section_name, has_test_sign_out)
VALUES ('Consent update', 'yes'); /* all rest of cols default vals */
/* set lab-tests inactive */
UPDATE lab_tests SET is_active = 'no' WHERE test_name LIKE 'consent_q%'; /* consent_q1 .. consent_q14 */
UPDATE lab_tests SET is_active = 'no' WHERE test_name IN (
'edta1_qc_type','edta1_qc_result','tumour_qc_result',
'tumour_qc_type','number_of_biopsies','biopsy_gauge'
);
/* change lab-section parent of lab-tests to 'Specimens - FFPE' */
SELECT @section_id := id FROM lab_sections WHERE section_name = 'Specimens - FFPE';
UPDATE lab_tests SET lab_section_id = @section_id
WHERE test_name IN ('tumour_sample_type','number_of_sections','section_thickness','number_of_blocks' );
/* change lab-section parent of lab-tests to 'Specimens - tumour' */
SELECT @section_id := id FROM lab_sections WHERE section_name = 'Specimens - tumour';
UPDATE lab_tests SET lab_section_id = @section_id WHERE test_name = 'pre_invasive_elements';
/* new lab-tests */
SELECT @consent_id := id FROM lab_sections WHERE section_name = 'Consent';
INSERT INTO lab_tests (test_name, field_label, lab_section_id, test_type, has_results) VALUES
/* Consent section */
('health_related_additional', 'Health related additional', @consent_id, 'test', 'yes'),
('reproductive_additional', 'Reproductive additional', @consent_id, 'test', 'yes');
SELECT @consent_update_id := id FROM lab_sections WHERE section_name = 'Consent update';
INSERT INTO lab_tests (test_name, field_label, lab_section_id, test_type, has_results) VALUES
('consent_date_update', 'Consent date', @consent_update_id, 'test', 'yes'),
('consent_form_update', 'Consent form version', @consent_update_id, 'test', 'yes'),
('consent_given_update', 'Consent given', @consent_update_id, 'test', 'yes'),
('info_sheet_update', 'Info sheet version', @consent_update_id, 'test', 'yes'),
('update_health_related', 'Health related additional', @consent_update_id, 'test', 'yes'),
('update_reproductive_add', 'Reproductive additional', @consent_update_id, 'test', 'yes');
SELECT @dna_blood_id := id FROM lab_sections WHERE section_name = 'DNA - blood';
INSERT INTO lab_tests (test_name, field_label, lab_section_id, test_type, has_results) VALUES
('qubit_blood', 'Qubit', @dna_blood_id, 'test', 'yes'),
('blood_summary_qc', 'QC Summary', @dna_blood_id, 'test', 'yes');
SELECT @dna_tumour_id := id FROM lab_sections WHERE section_name = 'DNA - tumour';
INSERT INTO lab_tests (test_name, field_label, lab_section_id, test_type, has_results) VALUES
('cellularity', 'Cellularity', @dna_tumour_id, 'test', 'yes'),
('percent_necrosis', '% Necrosis', @dna_tumour_id, 'test', 'yes'),
('tumour_content', 'Tumour content', @dna_tumour_id, 'test', 'yes'),
('qubit_tumour', 'Qubit', @dna_tumour_id, 'test', 'yes'),
('tumour_summary_qc', 'QC Summary', @dna_tumour_id, 'test', 'yes');
/* new result data types */
INSERT INTO lab_test_result_data_types(description) VALUES
('info_sheet_update'),
('yes_no_irrelevant'),
('consent_update'),
('tumour_content'),
('cellularity'),
('pass_fail');
/* result data types for new lab-tests */
/* yes_no options */
SELECT @ltrdt_id := id FROM lab_test_result_data_types WHERE description = 'yes_no';
INSERT INTO lab_test_data_type(lab_test_id, data_type_id)
SELECT
(SELECT id FROM lab_tests WHERE test_name = 'health_related_additional'),
(@ltrdt_id);
INSERT INTO lab_test_data_type(lab_test_id, data_type_id)
SELECT
(SELECT id FROM lab_tests WHERE test_name = 'consent_given_update'),
(@ltrdt_id);
INSERT INTO lab_test_data_type(lab_test_id, data_type_id)
SELECT
(SELECT id FROM lab_tests WHERE test_name = 'update_health_related'),
(@ltrdt_id);
/* pass_fail options */
SELECT @ltrdt_id := id FROM lab_test_result_data_types WHERE description = 'pass_fail';
INSERT INTO lab_test_data_type(lab_test_id, data_type_id)
SELECT
(SELECT id FROM lab_tests WHERE test_name = 'blood_summary_qc'),
(@ltrdt_id);
INSERT INTO lab_test_data_type(lab_test_id, data_type_id)
SELECT
(SELECT id FROM lab_tests WHERE test_name = 'tumour_summary_qc'),
(@ltrdt_id);
/* free_text options */
SELECT @ltrdt_id := id FROM lab_test_result_data_types WHERE description = 'free_text';
INSERT INTO lab_test_data_type(lab_test_id, data_type_id)
SELECT
(SELECT id FROM lab_tests WHERE test_name = 'qubit_blood'),
(@ltrdt_id);
INSERT INTO lab_test_data_type(lab_test_id, data_type_id)
SELECT
(SELECT id FROM lab_tests WHERE test_name = 'qubit_tumour'),
(@ltrdt_id);
INSERT INTO lab_test_data_type(lab_test_id, data_type_id)
SELECT
(SELECT id FROM lab_tests WHERE test_name = 'percent_necrosis'),
(@ltrdt_id);
/* yes_no_irrelevant options */
SELECT @ltrdt_id := id FROM lab_test_result_data_types WHERE description = 'yes_no_irrelevant';
INSERT INTO lab_test_data_type(lab_test_id, data_type_id)
SELECT
(SELECT id FROM lab_tests WHERE test_name = 'reproductive_additional'),
(@ltrdt_id);
INSERT INTO lab_test_data_type(lab_test_id, data_type_id)
SELECT
(SELECT id FROM lab_tests WHERE test_name = 'update_reproductive_add'),
(@ltrdt_id);
/* other options */
INSERT INTO lab_test_data_type(lab_test_id, data_type_id)
SELECT
(SELECT id FROM lab_tests WHERE test_name = 'consent_date_update'),
(SELECT id FROM lab_test_result_data_types WHERE description = 'date');
INSERT INTO lab_test_data_type(lab_test_id, data_type_id)
SELECT
(SELECT id FROM lab_tests WHERE test_name = 'consent_form_update'),
(SELECT id FROM lab_test_result_data_types WHERE description = 'consent_update');
INSERT INTO lab_test_data_type(lab_test_id, data_type_id)
SELECT
(SELECT id FROM lab_tests WHERE test_name = 'info_sheet_update'),
(SELECT id FROM lab_test_result_data_types WHERE description = 'info_sheet_update');
INSERT INTO lab_test_data_type(lab_test_id, data_type_id)
SELECT
(SELECT id FROM lab_tests WHERE test_name = 'tumour_content'),
(SELECT id FROM lab_test_result_data_types WHERE description = 'tumour_content');
INSERT INTO lab_test_data_type(lab_test_id, data_type_id)
SELECT
(SELECT id FROM lab_tests WHERE test_name = 'cellularity'),
(SELECT id FROM lab_test_result_data_types WHERE description = 'cellularity');
/* new lab-test result menu options */
/* for existing data type 'info_sheet' (values R1 - R8 already exist )*/
SELECT @ltrdt_id := id FROM lab_test_result_data_types WHERE description = 'info_sheet';
INSERT INTO lab_test_result_options(data_type_id,`value`) VALUES
(@ltrdt_id, 'c1_pis'),
(@ltrdt_id, 'c2_pis'),
(@ltrdt_id, 'c3_pis'),
(@ltrdt_id, 'c4_pis'),
(@ltrdt_id, 'c5_pis');
/* for new data type 'consent_update' */
SELECT @ltrdt_id := id FROM lab_test_result_data_types WHERE description = 'consent_update';
INSERT INTO lab_test_result_options(data_type_id,`value`) VALUES
(@ltrdt_id, 'R1/R2'),
(@ltrdt_id, 'R3/R4'),
(@ltrdt_id, 'R5'),
(@ltrdt_id, 'R6'),
(@ltrdt_id, 'R7'),
(@ltrdt_id, 'R8'),
(@ltrdt_id, '7a_cf'),
(@ltrdt_id, '7b_cf'),
(@ltrdt_id, 'c1_cf'),
(@ltrdt_id, 'c2_cf'),
(@ltrdt_id, 'c5_cf');
/* for new data type 'info_sheet_update' */
SELECT @ltrdt_id := id FROM lab_test_result_data_types WHERE description = 'info_sheet_update';
INSERT INTO lab_test_result_options(data_type_id,`value`) VALUES
(@ltrdt_id, 'R1'),
(@ltrdt_id, 'R2'),
(@ltrdt_id, 'R3'),
(@ltrdt_id, 'R4'),
(@ltrdt_id, 'R5'),
(@ltrdt_id, 'R6'),
(@ltrdt_id, 'R7'),
(@ltrdt_id, 'R8'),
(@ltrdt_id, '7a_pis'),
(@ltrdt_id, '7b_pis'),
(@ltrdt_id, 'c1_pis'),
(@ltrdt_id, 'c2_pis'),
(@ltrdt_id, 'c3_pis'),
(@ltrdt_id, 'c4_pis'),
(@ltrdt_id, 'c5_pis');
/* for new data type 'tumour_content' */
SELECT @ltrdt_id := id FROM lab_test_result_data_types WHERE description = 'tumour_content';
INSERT INTO lab_test_result_options(data_type_id,`value`) VALUES
(@ltrdt_id, 'low'),
(@ltrdt_id, 'medium'),
(@ltrdt_id, 'high');
/* for new data type 'cellularity' */
SELECT @ltrdt_id := id FROM lab_test_result_data_types WHERE description = 'cellularity';
INSERT INTO lab_test_result_options(data_type_id,`value`) VALUES
(@ltrdt_id, 'verylow'),
(@ltrdt_id, 'low'),
(@ltrdt_id, 'medium'),
(@ltrdt_id, 'high'),
(@ltrdt_id, 'veryhigh');
/* for new data type 'pass_fail' */
SELECT @ltrdt_id := id FROM lab_test_result_data_types WHERE description = 'pass_fail';
INSERT INTO lab_test_result_options(data_type_id,`value`) VALUES
(@ltrdt_id, 'pass'),
(@ltrdt_id, 'fail');
/* for new data type 'yes_no_irrelevant' */
SELECT @ltrdt_id := id FROM lab_test_result_data_types WHERE description = 'yes_no_irrelevant';
INSERT INTO lab_test_result_options(data_type_id,`value`) VALUES
(@ltrdt_id, 'yes'),
(@ltrdt_id, 'no'),
(@ltrdt_id, 'not_relevant');
/* inactivate test result menu options */
UPDATE lab_test_result_options SET is_active = 'no' WHERE `value` IN ('C1','C2');
/* update lab-section names */
UPDATE lab_sections SET section_name = '1) Approach' WHERE section_name = 'Approach';
UPDATE lab_sections SET section_name = '2) Consent' WHERE section_name = 'Consent';
UPDATE lab_sections SET section_name = '2.1) Consent update' WHERE section_name = 'Consent update';
UPDATE lab_sections SET section_name = '2.2) Consent withdrawal' WHERE section_name = 'Consent withdrawal';
UPDATE lab_sections SET section_name = '3) Specimens - blood' WHERE section_name = 'Specimens - blood';
UPDATE lab_sections SET section_name = '4) DNA - blood' WHERE section_name = 'DNA - blood';
UPDATE lab_sections SET section_name = '5) Specimens - tumour' WHERE section_name = 'Specimens - tumour';
UPDATE lab_sections SET section_name = '5.1) Specimens - frozen' WHERE section_name = 'Specimens - frozen';
UPDATE lab_sections SET section_name = '5.2) Specimens - FFPE' WHERE section_name = 'Specimens - FFPE';
UPDATE lab_sections SET section_name = '6) Transfer to genetics' WHERE section_name = 'Transfer to genetics';
UPDATE lab_sections SET section_name = '7) DNA - tumour' WHERE section_name = 'DNA - tumour';
UPDATE lab_sections SET section_name = '8) Dispatch' WHERE section_name = 'Dispatch';
/* run genomics_v3_screen_lab_test.pl */
