#====================================
USE `genomics`; # or change to `test`
#====================================
/* to test, clone these tables & data from `genomics` to `test`:
* lab_sections
* lab_tests
* lab_test_result_data_types
* lab_test_data_type
* lab_test_result_options
* screen_category
* screens
*/
INSERT INTO lab_sections(section_name, has_test_sign_out)
/* new v3.1.2 lab-section */
VALUES ('Consent update', 'yes'), /* all rest of cols default vals */
/* new v3.2 lab-sections */
('Specimens - saliva', 'yes'),
('DNA - saliva', 'yes'),
('Specimens - bone marrow', 'yes'),
('DNA - bone marrow', 'yes');
/* map lab_section_sample_type lab-section => sample_type */
SELECT @sample_id := id FROM specimens WHERE sample_code = 'GEN'; /* only have 1 */
INSERT INTO lab_section_sample_type(lab_section_id, sample_type_id)
SELECT
(SELECT id FROM lab_sections WHERE section_name = 'Specimens - saliva'),
(@sample_id);
INSERT INTO lab_section_sample_type(lab_section_id, sample_type_id)
SELECT
(SELECT id FROM lab_sections WHERE section_name = 'DNA - saliva'),
(@sample_id);
INSERT INTO lab_section_sample_type(lab_section_id, sample_type_id)
SELECT
(SELECT id FROM lab_sections WHERE section_name = 'Specimens - bone marrow'),
(@sample_id);
INSERT INTO lab_section_sample_type(lab_section_id, sample_type_id)
SELECT
(SELECT id FROM lab_sections WHERE section_name = 'DNA - bone marrow'),
(@sample_id);
/* 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','tumour_qc_date'
);
/* 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'),
('cellularity_datetime', 'Cellularity datetime', @dna_tumour_id, 'test', 'yes'),
('percent_necrosis', '% Necrosis', @dna_tumour_id, 'test', 'yes'),
('percent_necrosis_datetime', '% Necrosis datetime', @dna_tumour_id, 'test', 'yes'),
('tumour_content', 'Tumour content', @dna_tumour_id, 'test', 'yes'),
('tumour_content_datetime', 'Tumour content datetime', @dna_tumour_id, 'test', 'yes'),
('qubit_tumour', 'Qubit', @dna_tumour_id, 'test', 'yes'),
('qubit_tumour_datetime', 'Qubit datetime', @dna_tumour_id, 'test', 'yes'),
('tumour_summary_qc', 'QC Summary', @dna_tumour_id, 'test', 'yes');
SELECT @saliva_id := id FROM lab_sections WHERE section_name = 'Specimens - saliva';
INSERT INTO lab_tests (test_name, field_label, lab_section_id, test_type, has_results) VALUES
('saliva_sample_taken', 'Sample taken', @saliva_id, 'test', 'yes'),
('saliva_handling_protocol', 'Handling protocol', @saliva_id, 'test', 'yes'),
('oragene_tube_1', 'Oragene tube #1', @saliva_id, 'test', 'yes'),
('oragene_tube_2', 'Oragene tube #2', @saliva_id, 'test', 'yes');
SELECT @bm_id := id FROM lab_sections WHERE section_name = 'Specimens - bone marrow';
INSERT INTO lab_tests (test_name, field_label, lab_section_id, test_type, has_results) VALUES
('bm_sample_taken', 'Sample taken', @bm_id, 'test', 'yes'),
('bm_clinic_sample_type', 'Clinic sample type', @bm_id, 'test', 'yes'),
('bm_unsent_sample_reason', 'Unsent sample reason', @bm_id, 'test', 'yes'),
('bm_tumour_size', 'Trephine length (mm)', @bm_id, 'test', 'yes'),
('bm_sample_id', 'Sample ID', @bm_id, 'test', 'yes'),
('bm_lab_identifier', 'Lab number', @bm_id, 'test', 'yes');
SELECT @dna_saliva_id := id FROM lab_sections WHERE section_name = 'DNA - saliva';
INSERT INTO lab_tests (test_name, field_label, lab_section_id, test_type, has_results) VALUES
('saliva_dna_lab_number', 'DNA lab number', @dna_saliva_id, 'test', 'yes'),
('saliva_dna_fluidx', 'Fluidx vial ID', @dna_saliva_id, 'test', 'yes'),
('saliva_dna_fluidx_rack_id', 'Rack ID', @dna_saliva_id, 'test', 'yes'),
('saliva_dna_fluidx_vol', 'Fluidx vol', @dna_saliva_id, 'test', 'yes'),
('saliva_dna_fluidx_well', 'Fluidx well pos', @dna_saliva_id, 'test', 'yes'),
('saliva_dna_qc_datetime', 'QC datetime', @dna_saliva_id, 'test', 'yes'),
('saliva_dna_summary_qc', 'QC summary', @dna_saliva_id, 'test', 'yes'),
('saliva_dna_qubit', 'Qubit', @dna_saliva_id, 'test', 'yes'),
('saliva_dna_volume_stored', 'Volume stored', @dna_saliva_id, 'test', 'yes');
SELECT @dna_bm_id := id FROM lab_sections WHERE section_name = 'DNA - bone marrow';
INSERT INTO lab_tests (test_name, field_label, lab_section_id, test_type, has_results) VALUES
('bm_dna_lab_number', 'DNA lab number', @dna_bm_id, 'test', 'yes'),
('bm_dna_fluidx', 'Fluidx vial ID', @dna_bm_id, 'test', 'yes'),
('bm_dna_fluidx_rack_id', 'Rack ID', @dna_bm_id, 'test', 'yes'),
('bm_dna_fluidx_vol', 'Fluidx vol', @dna_bm_id, 'test', 'yes'),
('bm_dna_fluidx_rack_well', 'Fluidx well pos', @dna_bm_id, 'test', 'yes'),
('bm_dna_qc_datetime', 'QC datetime', @dna_bm_id, 'test', 'yes'),
('bm_dna_summary_qc', 'QC summary', @dna_bm_id, 'test', 'yes'),
('bm_dna_qubit', 'Qubit', @dna_bm_id, 'test', 'yes'),
('bm_dna_volume_stored', 'Volume stored', @dna_bm_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);
INSERT INTO lab_test_data_type(lab_test_id, data_type_id)
SELECT
(SELECT id FROM lab_tests WHERE test_name = 'bm_dna_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 = 'saliva_dna_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 = 'bm_dna_qubit'),
(@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);
INSERT INTO lab_test_data_type(lab_test_id, data_type_id)
SELECT
(SELECT id FROM lab_tests WHERE test_name = 'bm_dna_lab_number'),
(@ltrdt_id);
INSERT INTO lab_test_data_type(lab_test_id, data_type_id)
SELECT
(SELECT id FROM lab_tests WHERE test_name = 'bm_dna_fluidx'),
(@ltrdt_id);
INSERT INTO lab_test_data_type(lab_test_id, data_type_id)
SELECT
(SELECT id FROM lab_tests WHERE test_name = 'bm_dna_fluidx_rack_id'),
(@ltrdt_id);
INSERT INTO lab_test_data_type(lab_test_id, data_type_id)
SELECT
(SELECT id FROM lab_tests WHERE test_name = 'bm_dna_fluidx_rack_well'),
(@ltrdt_id);
INSERT INTO lab_test_data_type(lab_test_id, data_type_id)
SELECT
(SELECT id FROM lab_tests WHERE test_name = 'bm_dna_fluidx_vol'),
(@ltrdt_id);
INSERT INTO lab_test_data_type(lab_test_id, data_type_id)
SELECT
(SELECT id FROM lab_tests WHERE test_name = 'bm_dna_volume_stored'),
(@ltrdt_id);
INSERT INTO lab_test_data_type(lab_test_id, data_type_id)
SELECT
(SELECT id FROM lab_tests WHERE test_name = 'bm_tumour_size'),
(@ltrdt_id);
INSERT INTO lab_test_data_type(lab_test_id, data_type_id)
SELECT
(SELECT id FROM lab_tests WHERE test_name = 'bm_sample_id'),
(@ltrdt_id);
INSERT INTO lab_test_data_type(lab_test_id, data_type_id)
SELECT
(SELECT id FROM lab_tests WHERE test_name = 'bm_lab_identifier'),
(@ltrdt_id);
INSERT INTO lab_test_data_type(lab_test_id, data_type_id)
SELECT
(SELECT id FROM lab_tests WHERE test_name = 'oragene_tube_1'),
(@ltrdt_id);
INSERT INTO lab_test_data_type(lab_test_id, data_type_id)
SELECT
(SELECT id FROM lab_tests WHERE test_name = 'oragene_tube_2'),
(@ltrdt_id);
INSERT INTO lab_test_data_type(lab_test_id, data_type_id)
SELECT
(SELECT id FROM lab_tests WHERE test_name = 'saliva_dna_lab_number'),
(@ltrdt_id);
INSERT INTO lab_test_data_type(lab_test_id, data_type_id)
SELECT
(SELECT id FROM lab_tests WHERE test_name = 'saliva_dna_volume_stored'),
(@ltrdt_id);
INSERT INTO lab_test_data_type(lab_test_id, data_type_id)
SELECT
(SELECT id FROM lab_tests WHERE test_name = 'saliva_dna_fluidx'),
(@ltrdt_id);
INSERT INTO lab_test_data_type(lab_test_id, data_type_id)
SELECT
(SELECT id FROM lab_tests WHERE test_name = 'saliva_dna_fluidx_rack_id'),
(@ltrdt_id);
INSERT INTO lab_test_data_type(lab_test_id, data_type_id)
SELECT
(SELECT id FROM lab_tests WHERE test_name = 'saliva_dna_fluidx_well'),
(@ltrdt_id);
INSERT INTO lab_test_data_type(lab_test_id, data_type_id)
SELECT
(SELECT id FROM lab_tests WHERE test_name = 'saliva_dna_fluidx_vol'),
(@ltrdt_id);
INSERT INTO lab_test_data_type(lab_test_id, data_type_id)
SELECT
(SELECT id FROM lab_tests WHERE test_name = 'saliva_dna_qubit'),
(@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);
/* datetime options */
SELECT @ltrdt_id := id FROM lab_test_result_data_types WHERE description = 'datetime';
INSERT INTO lab_test_data_type(lab_test_id, data_type_id)
SELECT
(SELECT id FROM lab_tests WHERE test_name = 'percent_necrosis_datetime'),
(@ltrdt_id);
INSERT INTO lab_test_data_type(lab_test_id, data_type_id)
SELECT
(SELECT id FROM lab_tests WHERE test_name = 'cellularity_datetime'),
(@ltrdt_id);
INSERT INTO lab_test_data_type(lab_test_id, data_type_id)
SELECT
(SELECT id FROM lab_tests WHERE test_name = 'tumour_content_datetime'),
(@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_datetime'),
(@ltrdt_id);
INSERT INTO lab_test_data_type(lab_test_id, data_type_id)
SELECT
(SELECT id FROM lab_tests WHERE test_name = 'bm_dna_qc_datetime'),
(@ltrdt_id);
INSERT INTO lab_test_data_type(lab_test_id, data_type_id)
SELECT
(SELECT id FROM lab_tests WHERE test_name = 'bm_sample_taken'),
(@ltrdt_id);
INSERT INTO lab_test_data_type(lab_test_id, data_type_id)
SELECT
(SELECT id FROM lab_tests WHERE test_name = 'saliva_sample_taken'),
(@ltrdt_id);
INSERT INTO lab_test_data_type(lab_test_id, data_type_id)
SELECT
(SELECT id FROM lab_tests WHERE test_name = 'saliva_dna_qc_datetime'),
(@ltrdt_id);
/* date options */
SELECT @ltrdt_id := 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_date_update'),
(@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_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');
INSERT INTO lab_test_data_type(lab_test_id, data_type_id)
SELECT
(SELECT id FROM lab_tests WHERE test_name = 'bm_clinic_sample_type'),
(SELECT id FROM lab_test_result_data_types WHERE description = 'clinic_sample_type');
INSERT INTO lab_test_data_type(lab_test_id, data_type_id)
SELECT
(SELECT id FROM lab_tests WHERE test_name = 'bm_unsent_sample_reason'),
(SELECT id FROM lab_test_result_data_types WHERE description = 'unsent_sample_reason');
INSERT INTO lab_test_data_type(lab_test_id, data_type_id)
SELECT
(SELECT id FROM lab_tests WHERE test_name = 'saliva_handling_protocol'),
(SELECT id FROM lab_test_result_data_types WHERE description = 'handling_protocol');
/* 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');
/* additional unsent_sample_reason options */
SELECT @ltrdt_id := id FROM lab_test_result_data_types WHERE description = 'unsent_sample_reason';
INSERT INTO lab_test_result_options(data_type_id,`value`) VALUES
(@ltrdt_id, 'FFPE not optimally fixed'),
(@ltrdt_id, 'FFPE not optimally processed'),
(@ltrdt_id, 'High necrosis (over 20%)');
/* update some additional tissue_source options */
SELECT @ltrdt_id := id FROM lab_test_result_data_types WHERE description = 'tissue_source';
UPDATE lab_test_result_options SET `value` = 'Endoscopic biopsy'
WHERE `value` = 'endoscopic biopsy';
UPDATE lab_test_result_options SET `value` = 'Non-guided biopsy'
WHERE `value` = 'non-guided biopsy';
UPDATE lab_test_result_options SET `value` = 'Stereotactically guided biopsy'
WHERE `value` = 'stereotactically guided biopsy';
UPDATE lab_test_result_options SET `value` = 'Surgical resection'
WHERE `value` = 'surgical resection';
/* additional tissue_source options */
INSERT INTO lab_test_result_options(data_type_id,`value`) VALUES
(@ltrdt_id, 'Endoscopic USS-guided biopsy'),
(@ltrdt_id, 'Endoscopic USS-guided FNA'),
(@ltrdt_id, 'Laparoscopic biopsy'),
(@ltrdt_id, 'Laparoscopic excision');
/* set all tissue_source lab_test_result_options active; should be 11 total */
UPDATE lab_test_result_options SET is_active = 'yes' WHERE data_type_id = @ltrdt_id;
/*
lab_test_result_data_types:
13 = sample_type (not used)
19 = clinic_sample_type (new name for sample_type)
20 = tumour_sample_type (has 2 options, sections & blocks)
need to move all lab_test_result_options where data_type_id = 13 to 19, except
'DNA FFPE Tumour' & 'DNA FF Tumour' which are already in both sections
*/
SELECT @st_id := id FROM lab_test_result_data_types WHERE description = 'sample_type';
SELECT @cst_id := id FROM lab_test_result_data_types WHERE description = 'clinic_sample_type';
/* need a double-select to avoid error: "can't specify target table
`lab_test_result_options` for update in FROM clause" */
UPDATE lab_test_result_options t1 SET t1.data_type_id = @cst_id
WHERE t1.data_type_id = @st_id AND t1.`value` NOT IN
( SELECT duplicate FROM ( SELECT t2.`value` as duplicate
FROM lab_test_result_options t2 WHERE t2.data_type_id = @cst_id) as t3 );
/* switch off lab_test_result_data_types 'sample_type' & its remaining lab_test_result_options */
UPDATE lab_test_result_data_types SET is_active = 'no' WHERE id = @st_id;
UPDATE lab_test_result_options SET is_active = 'no' WHERE data_type_id = @st_id;
/* rename some existing clinic_sample_type options */
UPDATE lab_test_result_options SET `value` = 'Additional Research Material'
WHERE `value` = 'Additional Tumour Material';
UPDATE lab_test_result_options SET `value` = 'FFPE Scrapings/Slides'
WHERE `value` = 'Tumour Scrapings';
UPDATE lab_test_result_options SET `value` = 'EDTA Plasma (for ctDNA)'
WHERE `value` = 'EDTA Plasma';
UPDATE lab_test_result_options SET `value` = 'DNA HaemOnc Blood'
WHERE `value` = 'DNA Blood Tumour';
UPDATE lab_test_result_options SET `value` = 'Deparaffinised Lysed Cells'
WHERE `value` = 'Lysed Tumour Cells';
/* additional clinic_sample_type options */
INSERT INTO lab_test_result_options(data_type_id,`value`) VALUES
(@cst_id, 'DNA Bone Marrow Aspirate'),
(@cst_id, 'DNA BMA Sorted Cells'),
(@cst_id, 'Tumour Tissue FFPE'),
(@cst_id, 'Lysate FFPE'),
(@cst_id, 'Lysate FF'),
(@cst_id, 'Buffy Coat'),
(@cst_id, 'Streck Plasma'); /* check 21 lab_test_result_options for data_type_id = 19 */
/* 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) Specimens - bone marrow'
WHERE section_name = 'Specimens - bone marrow';
UPDATE lab_sections SET section_name = '5) Specimens - saliva'
WHERE section_name = 'Specimens - saliva';
UPDATE lab_sections SET section_name = '6) Specimens - tumour'
WHERE section_name = 'Specimens - tumour';
UPDATE lab_sections SET section_name = '6.1) Specimens - frozen'
WHERE section_name = 'Specimens - frozen';
UPDATE lab_sections SET section_name = '6.2) Specimens - FFPE'
WHERE section_name = 'Specimens - FFPE';
UPDATE lab_sections SET section_name = '7) DNA - blood'
WHERE section_name = 'DNA - blood';
UPDATE lab_sections SET section_name = '8) DNA - bone marrow'
WHERE section_name = 'DNA - bone marrow';
UPDATE lab_sections SET section_name = '9) DNA - saliva'
WHERE section_name = 'DNA - saliva';
UPDATE lab_sections SET section_name = '10) DNA - tumour'
WHERE section_name = 'DNA - tumour';
UPDATE lab_sections SET section_name = '11) Transfer to genetics'
WHERE section_name = 'Transfer to genetics';
UPDATE lab_sections SET section_name = '12) Dispatch'
WHERE section_name = 'Dispatch';
/* new HaemOnc category: */
INSERT INTO screen_category (`name`) VALUES ('HaemOnc');
INSERT INTO screens (`description`, `category_id`, `active`) VALUES
('Acute Lymphoblastic Leukaemia', 3, 'yes'),
('Acute Myeloid Leukaemia', 3, 'yes'),
('Chronic Lymphocytic Leukaemia', 3, 'yes'),
('Burkitt Lymphoma', 3, 'yes'),
('Chronic Myeloid Leukaemia', 3, 'yes'),
('Diffuse Large B-cell Lymphoma', 3, 'yes'),
('High Grade Lymphoma NOS', 3, 'yes'),
('Mediastinal B-cell Lymphoma', 3, 'yes'),
('Multiple Myeloma', 3, 'yes'),
('Myelodysplastic Syndrome (high risk)', 3, 'yes'),
('Non-Hodgkins B-cell Lymphoma (low/moderate grade)', 3, 'yes'),
('Classical Hodgkins Lymphoma', 3, 'yes'),
('Nodular Lymphocyte Predominant Hodgkins Lymphoma', 3, 'yes'),
('T-cell Lymphoma', 3, 'yes'),
/* 3 new cancers */
('Nasopharyngeal', 2, 'yes'),
('Sinonasal', 2, 'yes'),
('Oral or Oropharyngeal', 2, 'yes');
/* run genomics_v3_screen_lab_test.pl */
/* set genomics.xsd symlink to <current>.xsd */
/* run scripts/xml_validate.pl */
