From 8d844ead1ed9dd0ce0e5718bccfd0a8d458425f8 Mon Sep 17 00:00:00 2001 From: Dennis Kigen Date: Mon, 16 Aug 2021 10:10:28 +0300 Subject: [PATCH] POCONC-213: Fix patient summary snapshots This PR tweaks the stored procedure to get it to work within the constraints of other modifications to the breast and cervical cancer screening procedures. More specifically, these changes include: - Renaming indicators: - `breast_exam_findings` to `breast_exam_findings_this_visit`. Also changes the way the value of this indicator is determined using a subtle hack (necessitated by a bug in the form's design where past_breast_exam_findings and breast_exam_findings_this_visit reuse the same concept ID). - `via_test_result` to `via_or_via_vili_test_result`. Also changes to the way the value of this indicator is determined. This changes are necessitated by earlier modifications to the cervical cancer screening form. - Linting (sorry, not sorry). --- ...generate_flat_onc_patient_history_v1_0.sql | 1187 ++++++++--------- 1 file changed, 593 insertions(+), 594 deletions(-) diff --git a/etl-scripts/stored-procedures/generate_flat_onc_patient_history_v1_0.sql b/etl-scripts/stored-procedures/generate_flat_onc_patient_history_v1_0.sql index a0e567a..3fb3884 100644 --- a/etl-scripts/stored-procedures/generate_flat_onc_patient_history_v1_0.sql +++ b/etl-scripts/stored-procedures/generate_flat_onc_patient_history_v1_0.sql @@ -1,628 +1,627 @@ -DELIMITER $$ CREATE PROCEDURE `generate_flat_onc_patient_history_v1_0`(IN query_type varchar(50), IN queue_number int, IN queue_size int, IN cycle_size int) BEGIN - SET @primary_table := "flat_onc_patient_history"; - SET @query_type := query_type; - - SET @total_rows_written := 0; + SET @primary_table := "flat_onc_patient_history"; + SET @query_type := query_type; + + SET @total_rows_written := 0; - SET @encounter_types := "(69,70,86,145,146,147,160,38,39,40,41,42,45,130,141,148,149,150,151,175,142,143,169,170,177,91,92,89,90,93,94,184)"; - SET @clinical_encounter_types := "(69,70,86,145,146,147,160,38,39,40,41,42,45,130,141,148,149,150,151,175,142,143,169,170,177,91,92,89,90,93,94,184)"; - SET @non_clinical_encounter_types := "(-1)"; - SET @other_encounter_types := "(-1)"; - - SET @start := now(); - SET @table_version := "flat_onc_patient_history_v1.0"; + SET @encounter_types := "(69,70,86,145,146,147,160,38,39,40,41,42,45,130,141,148,149,150,151,175,142,143,169,170,177,91,92,89,90,93,94,184)"; + SET @clinical_encounter_types := "(69,70,86,145,146,147,160,38,39,40,41,42,45,130,141,148,149,150,151,175,142,143,169,170,177,91,92,89,90,93,94,184)"; + SET @non_clinical_encounter_types := "(-1)"; + SET @other_encounter_types := "(-1)"; + + SET @start := now(); + SET @table_version := "flat_onc_patient_history_v1.0"; - SET session sort_buffer_size := 512000000; + SET session sort_buffer_size := 512000000; - SET @sep := " ## "; - SET @boundary := "!!"; - SET @last_date_created := (SELECT MAX(max_date_created) FROM etl.flat_obs); + SET @sep := " ## "; + SET @boundary := "!!"; + SET @last_date_created := (SELECT MAX(max_date_created) FROM etl.flat_obs); - CREATE TABLE IF NOT EXISTS flat_onc_patient_history ( - date_created TIMESTAMP DEFAULT CURRENT_TIMESTAMP ON UPDATE CURRENT_TIMESTAMP, - person_id INT, - uuid VARCHAR(100), - encounter_id INT, - encounter_datetime DATETIME, - encounter_type INT, - encounter_type_name VARCHAR(100), - visit_id INT, - visit_type_id SMALLINT, - visit_start_datetime DATETIME, - location_id SMALLINT, - program_id SMALLINT, - is_clinical INT, - enrollment_date DATETIME, - prev_rtc_date DATETIME, - rtc_date DATETIME, - diagnosis INT, - diagnosis_method INT, - result_of_diagnosis INT, - diagnosis_date DATETIME, - breast_exam_findings INT, - prior_via_test_result INT, - prior_via_test_result_date DATETIME, - via_test_result INT, - hiv_status INT, - cancer_type INT, - cancer_subtype INT, - breast_cancer_type INT, - non_cancer_diagnosis INT, - cancer_stage INT, - overall_cancer_stage_group INT, - cur_onc_meds VARCHAR(500), - cur_onc_meds_dose VARCHAR(500), - cur_onc_meds_frequency VARCHAR(500), - cur_onc_meds_start_date DATETIME, - cur_onc_meds_end_date DATETIME, - oncology_treatment_plan INT, - chemotherapy INT, - current_chemo_cycle INT, - total_chemo_cycles_planned INT, - therapeutic_notes VARCHAR(1000), - cancer_diagnosis_status INT, - reasons_for_surgery INT, - chemotherapy_intent INT, - chemotherapy_plan INT, - chemotherapy_regimen VARCHAR(50), - drug_route VARCHAR(500), - medication_history INT, - other_meds_added INT, - sickle_cell_drugs INT, - PRIMARY KEY encounter_id (encounter_id), - INDEX person_date (person_id, encounter_datetime), - INDEX location_id_enc_date (location_id, encounter_datetime), - INDEX enc_date_location_id (encounter_datetime, location_id), - INDEX location_id_rtc_date (location_id, rtc_date), - INDEX encounter_type (encounter_type), - INDEX date_created (date_created) - ); + CREATE TABLE IF NOT EXISTS flat_onc_patient_history ( + date_created TIMESTAMP DEFAULT CURRENT_TIMESTAMP ON UPDATE CURRENT_TIMESTAMP, + person_id INT, + uuid VARCHAR(100), + encounter_id INT, + encounter_datetime DATETIME, + encounter_type INT, + encounter_type_name VARCHAR(100), + visit_id INT, + visit_type_id SMALLINT, + visit_start_datetime DATETIME, + location_id SMALLINT, + program_id SMALLINT, + is_clinical INT, + enrollment_date DATETIME, + prev_rtc_date DATETIME, + rtc_date DATETIME, + diagnosis INT, + diagnosis_method INT, + result_of_diagnosis INT, + diagnosis_date DATETIME, + breast_exam_findings_this_visit VARCHAR(5), + via_or_via_vili_test_result INT, + prior_via_result INT, + prior_via_date DATETIME, + hiv_status INT, + cancer_type INT, + cancer_subtype INT, + breast_cancer_type INT, + non_cancer_diagnosis INT, + cancer_stage INT, + overall_cancer_stage_group INT, + cur_onc_meds VARCHAR(500), + cur_onc_meds_dose VARCHAR(500), + cur_onc_meds_frequency VARCHAR(500), + cur_onc_meds_start_date DATETIME, + cur_onc_meds_end_date DATETIME, + oncology_treatment_plan INT, + chemotherapy INT, + current_chemo_cycle INT, + total_chemo_cycles_planned INT, + therapeutic_notes VARCHAR(1000), + cancer_diagnosis_status INT, + reasons_for_surgery INT, + chemotherapy_intent INT, + chemotherapy_plan INT, + chemotherapy_regimen VARCHAR(50), + drug_route VARCHAR(500), + medication_history INT, + other_meds_added INT, + sickle_cell_drugs INT, + PRIMARY KEY encounter_id (encounter_id), + INDEX person_date (person_id, encounter_datetime), + INDEX location_id_enc_date (location_id, encounter_datetime), + INDEX enc_date_location_id (encounter_datetime, location_id), + INDEX location_id_rtc_date (location_id, rtc_date), + INDEX encounter_type (encounter_type), + INDEX date_created (date_created) + ); - IF (@query_type = "build") THEN - SELECT 'BUILDING..........................................'; + IF (@query_type = "build") THEN + SELECT 'BUILDING..........................................'; - SET @write_table := CONCAT("flat_onc_patient_history_temp_", queue_number); - SET @queue_table := CONCAT("flat_onc_patient_history_build_queue_", queue_number); - SET @primary_queue_table := "flat_onc_patient_history_build_queue"; - - SET @dyn_sql=CONCAT('CREATE TABLE IF NOT EXISTS ',@write_table,' like ',@primary_table); - PREPARE s1 FROM @dyn_sql; - EXECUTE s1; - DEALLOCATE PREPARE s1; + SET @write_table := CONCAT("flat_onc_patient_history_temp_", queue_number); + SET @queue_table := CONCAT("flat_onc_patient_history_build_queue_", queue_number); + SET @primary_queue_table := "flat_onc_patient_history_build_queue"; + + SET @dyn_sql=CONCAT('CREATE TABLE IF NOT EXISTS ',@write_table,' like ',@primary_table); + PREPARE s1 FROM @dyn_sql; + EXECUTE s1; + DEALLOCATE PREPARE s1; - SET @dyn_sql=CONCAT('CREATE TABLE IF NOT EXISTS ',@queue_table,' (SELECT * FROM ', @primary_queue_table, ' limit ', queue_size, ');'); - PREPARE s1 FROM @dyn_sql; - EXECUTE s1; - DEALLOCATE PREPARE s1; - - SET @dyn_sql=CONCAT('DELETE t1 FROM ', @primary_queue_table, ' t1 JOIN ',@queue_table, ' t2 using (person_id);'); - PREPARE s1 FROM @dyn_sql; - EXECUTE s1; - DEALLOCATE PREPARE s1; - END IF; + SET @dyn_sql=CONCAT('CREATE TABLE IF NOT EXISTS ',@queue_table,' (SELECT * FROM ', @primary_queue_table, ' limit ', queue_size, ');'); + PREPARE s1 FROM @dyn_sql; + EXECUTE s1; + DEALLOCATE PREPARE s1; + + SET @dyn_sql=CONCAT('DELETE t1 FROM ', @primary_queue_table, ' t1 JOIN ',@queue_table, ' t2 using (person_id);'); + PREPARE s1 FROM @dyn_sql; + EXECUTE s1; + DEALLOCATE PREPARE s1; + END IF; - IF (@query_type = "sync") THEN - SELECT 'SYNCING..........................................'; - SET @write_table := "flat_onc_patient_history"; - SET @queue_table := "flat_onc_patient_history_sync_queue"; - - CREATE TABLE IF NOT EXISTS flat_onc_patient_history_sync_queue ( - person_id INT PRIMARY KEY - ); - - SET @last_update := NULL; + IF (@query_type = "sync") THEN + SELECT 'SYNCING..........................................'; + SET @write_table := "flat_onc_patient_history"; + SET @queue_table := "flat_onc_patient_history_sync_queue"; + + CREATE TABLE IF NOT EXISTS flat_onc_patient_history_sync_queue ( + person_id INT PRIMARY KEY + ); + + SET @last_update := NULL; - SELECT - MAX(date_updated) - INTO @last_update FROM - etl.flat_log - WHERE - table_name = @table_version; + SELECT + MAX(date_updated) + INTO @last_update FROM + etl.flat_log + WHERE + table_name = @table_version; - REPLACE INTO flat_onc_patient_history_sync_queue - (SELECT DISTINCT patient_id - from amrs.encounter - where date_changed > @last_update - ); + REPLACE INTO flat_onc_patient_history_sync_queue + (SELECT DISTINCT patient_id + from amrs.encounter + where date_changed > @last_update + ); - REPLACE INTO flat_onc_patient_history_sync_queue - (SELECT DISTINCT person_id - from etl.flat_obs - where max_date_created > @last_update - ); + REPLACE INTO flat_onc_patient_history_sync_queue + (SELECT DISTINCT person_id + from etl.flat_obs + where max_date_created > @last_update + ); - REPLACE INTO flat_onc_patient_history_sync_queue - (SELECT DISTINCT person_id - from etl.flat_lab_obs - where max_date_created > @last_update - ); + REPLACE INTO flat_onc_patient_history_sync_queue + (SELECT DISTINCT person_id + from etl.flat_lab_obs + where max_date_created > @last_update + ); - REPLACE INTO flat_onc_patient_history_sync_queue - (SELECT DISTINCT person_id - from etl.flat_orders - where max_date_created > @last_update - ); - - REPLACE INTO flat_onc_patient_history_sync_queue - (SELECT person_id FROM - amrs.person - where date_voided > @last_update); + REPLACE INTO flat_onc_patient_history_sync_queue + (SELECT DISTINCT person_id + from etl.flat_orders + where max_date_created > @last_update + ); + + REPLACE INTO flat_onc_patient_history_sync_queue + (SELECT person_id FROM + amrs.person + where date_voided > @last_update); - REPLACE INTO flat_onc_patient_history_sync_queue - (SELECT person_id FROM - amrs.person - where date_changed > @last_update); - END IF; + REPLACE INTO flat_onc_patient_history_sync_queue + (SELECT person_id FROM + amrs.person + where date_changed > @last_update); + END IF; - -- Remove test patients - SET @dyn_sql := CONCAT('DELETE t1 FROM ',@queue_table,' t1 - JOIN amrs.person_attribute t2 using (person_id) - where t2.person_attribute_type_id=28 and value="true" and voided=0'); - PREPARE s1 FROM @dyn_sql; - EXECUTE s1; - DEALLOCATE PREPARE s1; + -- Remove test patients + SET @dyn_sql := CONCAT('DELETE t1 FROM ',@queue_table,' t1 + JOIN amrs.person_attribute t2 using (person_id) + where t2.person_attribute_type_id=28 and value="true" and voided=0'); + PREPARE s1 FROM @dyn_sql; + EXECUTE s1; + DEALLOCATE PREPARE s1; - SET @person_ids_count := 0; - SET @dyn_sql := CONCAT('SELECT count(*) into @person_ids_count FROM ',@queue_table); - PREPARE s1 FROM @dyn_sql; - EXECUTE s1; - DEALLOCATE PREPARE s1; + SET @person_ids_count := 0; + SET @dyn_sql := CONCAT('SELECT count(*) into @person_ids_count FROM ',@queue_table); + PREPARE s1 FROM @dyn_sql; + EXECUTE s1; + DEALLOCATE PREPARE s1; - SELECT @person_ids_count AS 'num patients to update'; + SELECT @person_ids_count AS 'num patients to update'; - SET @dyn_sql := CONCAT('DELETE t1 FROM ',@primary_table, ' t1 JOIN ',@queue_table,' t2 using (person_id);'); - PREPARE s1 FROM @dyn_sql; - EXECUTE s1; - DEALLOCATE PREPARE s1; - - SET @total_time := 0; - SET @cycle_number := 0; - - WHILE @person_ids_count > 0 DO - SET @loop_start_time := now(); - - DROP TEMPORARY TABLE IF EXISTS flat_onc_patient_history_build_queue__0; - SET @dyn_sql := CONCAT('CREATE TEMPORARY TABLE flat_onc_patient_history_build_queue__0 (person_id int primary key) (SELECT * FROM ',@queue_table,' limit ',cycle_size,');'); - PREPARE s1 FROM @dyn_sql; - EXECUTE s1; - DEALLOCATE PREPARE s1; - - DROP TEMPORARY TABLE IF EXISTS flat_onc_patient_history_0a; - - SET @dyn_sql := CONCAT( - 'CREATE TEMPORARY TABLE flat_onc_patient_history_0a - (select - t1.person_id, - t4.uuid, - t1.encounter_id, - t1.encounter_datetime, - t1.encounter_type, - t1.obs, - t1.obs_datetimes, - t1.visit_id, - v.visit_type_id, - v.date_started AS visit_start_datetime, - t1.location_id, - t5.program_id, - et.name, - CASE - when t1.encounter_type in ',@clinical_encounter_types,' then 1 - else NULL - END AS is_clinical_encounter, - CASE - when t1.encounter_type in ',@non_clinical_encounter_types,' then 20 - when t1.encounter_type in ',@clinical_encounter_types,' then 10 - when t1.encounter_type in', @other_encounter_types, ' then 5 - else 1 - END AS encounter_type_sort_index, - t2.orders - FROM etl.flat_obs t1 - JOIN flat_onc_patient_history_build_queue__0 t0 on t0.person_id = t1.person_id - LEFT JOIN etl.flat_orders t2 using(encounter_id) - LEFT JOIN amrs.visit v on (v.visit_id = t1.visit_id) - JOIN amrs.person t4 on t4.person_id = t1.person_id - LEFT JOIN etl.clinical_encounter_type_map t5 on (t5.encounter_type = t1.encounter_type) - LEFT JOIN amrs.encounter_type et on (et.encounter_type_id = t1.encounter_type) - where t1.encounter_type in ',@encounter_types,');'); - - PREPARE s1 FROM @dyn_sql; - EXECUTE s1; - DEALLOCATE PREPARE s1; + SET @dyn_sql := CONCAT('DELETE t1 FROM ',@primary_table, ' t1 JOIN ',@queue_table,' t2 using (person_id);'); + PREPARE s1 FROM @dyn_sql; + EXECUTE s1; + DEALLOCATE PREPARE s1; + + SET @total_time := 0; + SET @cycle_number := 0; + + WHILE @person_ids_count > 0 DO + SET @loop_start_time := now(); + + DROP TEMPORARY TABLE IF EXISTS flat_onc_patient_history_build_queue__0; + SET @dyn_sql := CONCAT('CREATE TEMPORARY TABLE flat_onc_patient_history_build_queue__0 (person_id int primary key) (SELECT * FROM ',@queue_table,' limit ',cycle_size,');'); + PREPARE s1 FROM @dyn_sql; + EXECUTE s1; + DEALLOCATE PREPARE s1; + + DROP TEMPORARY TABLE IF EXISTS flat_onc_patient_history_0a; + + SET @dyn_sql := CONCAT( + 'CREATE TEMPORARY TABLE flat_onc_patient_history_0a + (select + t1.person_id, + t4.uuid, + t1.encounter_id, + t1.encounter_datetime, + t1.encounter_type, + t1.obs, + t1.obs_datetimes, + t1.visit_id, + v.visit_type_id, + v.date_started AS visit_start_datetime, + t1.location_id, + t5.program_id, + et.name, + CASE + when t1.encounter_type in ',@clinical_encounter_types,' then 1 + else NULL + END AS is_clinical_encounter, + CASE + when t1.encounter_type in ',@non_clinical_encounter_types,' then 20 + when t1.encounter_type in ',@clinical_encounter_types,' then 10 + when t1.encounter_type in', @other_encounter_types, ' then 5 + else 1 + END AS encounter_type_sort_index, + t2.orders + FROM etl.flat_obs t1 + JOIN flat_onc_patient_history_build_queue__0 t0 on t0.person_id = t1.person_id + LEFT JOIN etl.flat_orders t2 using(encounter_id) + LEFT JOIN amrs.visit v on (v.visit_id = t1.visit_id) + JOIN amrs.person t4 on t4.person_id = t1.person_id + LEFT JOIN etl.clinical_encounter_type_map t5 on (t5.encounter_type = t1.encounter_type) + LEFT JOIN amrs.encounter_type et on (et.encounter_type_id = t1.encounter_type) + where t1.encounter_type in ',@encounter_types,');'); + + PREPARE s1 FROM @dyn_sql; + EXECUTE s1; + DEALLOCATE PREPARE s1; - INSERT INTO flat_onc_patient_history_0a - (SELECT - t1.person_id, - p.uuid, - t1.encounter_id, - t1.test_datetime, - t1.encounter_type, - t1.obs, - NULL, - NULL, - t3.visit_type_id, - t3.date_started AS visit_start_datetime, - t1.location_id, - t5.program_id, - et.name, - 0 AS is_clinical_encounter, - 1 AS encounter_type_sort_index, - NULL AS orders - from etl.flat_lab_obs t1 - JOIN - amrs.person p on p.person_id = t1.person_id - JOIN - amrs.visit t3 on t1.person_id = t3.patient_id - JOIN - flat_onc_patient_history_build_queue__0 t0 on t0.person_id = t1.person_id - JOIN - etl.clinical_encounter_type_map t5 on t5.encounter_type = t1.encounter_type - JOIN - amrs.encounter_type et on et.encounter_type_id = t1.encounter_type - ); + INSERT INTO flat_onc_patient_history_0a + (SELECT + t1.person_id, + p.uuid, + t1.encounter_id, + t1.test_datetime, + t1.encounter_type, + t1.obs, + NULL, + NULL, + t3.visit_type_id, + t3.date_started AS visit_start_datetime, + t1.location_id, + t5.program_id, + et.name, + 0 AS is_clinical_encounter, + 1 AS encounter_type_sort_index, + NULL AS orders + from etl.flat_lab_obs t1 + JOIN + amrs.person p on p.person_id = t1.person_id + JOIN + amrs.visit t3 on t1.person_id = t3.patient_id + JOIN + flat_onc_patient_history_build_queue__0 t0 on t0.person_id = t1.person_id + JOIN + etl.clinical_encounter_type_map t5 on t5.encounter_type = t1.encounter_type + JOIN + amrs.encounter_type et on et.encounter_type_id = t1.encounter_type + ); - DROP TEMPORARY TABLE IF EXISTS flat_onc_patient_history_0; - CREATE TEMPORARY TABLE flat_onc_patient_history_0(index encounter_id (encounter_id), index person_enc (person_id,encounter_datetime)) - (SELECT * FROM flat_onc_patient_history_0a - ORDER BY person_id, date(encounter_datetime), encounter_type_sort_index - ); + DROP TEMPORARY TABLE IF EXISTS flat_onc_patient_history_0; + CREATE TEMPORARY TABLE flat_onc_patient_history_0(index encounter_id (encounter_id), index person_enc (person_id,encounter_datetime)) + (SELECT * FROM flat_onc_patient_history_0a + ORDER BY person_id, date(encounter_datetime), encounter_type_sort_index + ); - SET @prev_rtc_date := NULL; - SET @rtc_date := NULL; - SET @diagnosis := NULL; - SET @diagnosis_method := NULL; - SET @result_of_diagnosis := NULL; - SET @diagnosis_date := NULL; - SET @breast_exam_findings := NULL; - SET @prior_via_test_result := NULL; - SET @prior_via_test_result_date := NULL; - SET @via_test_result := NULL; - SET @hiv_status := NULL; - SET @cancer_type := NULL; - SET @cancer_subtype := NULL; - SET @breast_cancer_type := NULL; - SET @non_cancer_diagnosis := NULL; - SET @cancer_stage := NULL; - SET @overall_cancer_stage_group := NULL; - SET @cur_onc_meds_start_date := NULL; - SET @cur_onc_meds_end_date := NULL; - SET @cur_onc_meds := NULL; - SET @cur_onc_meds_dose := NULL; - SET @cur_onc_meds_frequency := NULL; - SET @oncology_treatment_plan := NULL; - SET @chemotherapy := NULL; - SET @current_chemo_cycle := NULL; - SET @total_chemo_cycles_planned := NULL; - SET @therapeutic_notes := NULL; - SET @cancer_diagnosis_status := NULL; - SET @reasons_for_surgery := NULL; - SET @chemotherapy_intent := NULL; - SET @chemotherapy_plan := NULL; - SET @chemotherapy_regimen := NULL; - SET @drug_route := NULL; - SET @medication_history := NULL; - SET @other_meds_added := NULL; - SET @sickle_cell_drugs := NULL; - SET @lab_encounter_type := 99999; - SET @prev_id := NULL; - SET @cur_id := NULL; - SET @enrollment_date := NULL; - SET @cur_rtc_date := NULL; - SET @prev_rtc_date := NULL; - - DROP TEMPORARY TABLE IF EXISTS flat_onc_patient_history_1; - CREATE TEMPORARY TABLE flat_onc_patient_history_1 #(index encounter_id (encounter_id)) - (SELECT - @prev_id := @cur_id AS prev_id, - @cur_id := t1.person_id AS cur_id, - t1.person_id, - t1.uuid, - t1.encounter_id, - t1.encounter_datetime, - t1.encounter_type, - t1.name as `encounter_type_name`, - t1.visit_id, - t1.visit_type_id, - t1.visit_start_datetime, - t1.location_id, - t1.program_id, - t1.is_clinical_encounter, - CASE - WHEN @prev_id != @cur_id AND t1.encounter_type IN (21, @lab_encounter_type) THEN @enrollment_date := NULL - WHEN @prev_id != @cur_id THEN @enrollment_date := encounter_datetime - WHEN t1.encounter_type NOT IN (21, @lab_encounter_type) AND @enrollment_date IS NULL THEN @enrollment_date := encounter_datetime - ELSE @enrollment_date - END AS enrollment_date, - CASE - WHEN @prev_id = @cur_id THEN @prev_rtc_date := @cur_rtc_date - ELSE @prev_rtc_date := NULL - END AS prev_rtc_date, - CASE - WHEN obs regexp "!!5096=" THEN @cur_rtc_date := REPLACE(REPLACE((substring_index(substring(obs,locate("!!5096=", obs)), @sep, 1)),"!!5096=",""),"!!","") - WHEN @prev_id = @cur_id THEN IF (@cur_rtc_date > encounter_datetime, @cur_rtc_date, NULL) - ELSE @cur_rtc_date := NULL - END AS rtc_date, - CASE - WHEN obs regexp "!!7179=" THEN @diagnosis := REPLACE(REPLACE((substring_index(substring(obs,locate("!!7179=",obs)),@sep,1)),"!!7179=",""),"!!","") - ELSE @diagnosis := NULL - END AS diagnosis, - @diagnosis_method := GetValues(obs, 6504) AS diagnosis_method, - @result_of_diagnosis := CAST(REPLACE(REPLACE((substring_index(substring(obs,locate("!!7191=",obs)),@sep,1)),"!!7191=",""),"!!","") AS unsigned) AS result_of_diagnosis, - CASE - WHEN obs regexp "!!9728=" THEN @diagnosis_date := REPLACE(REPLACE((substring_index(substring(obs,locate("!!9728=",obs)),@sep,1)),"!!9728=",""),"!!","") - ELSE @diagnosis_date := NULL - END AS diagnosis_date, - CASE - WHEN obs regexp "!!6251=" THEN @breast_exam_findings := GetValues(obs, 6251) - ELSE @breast_exam_findings := NULL - END AS breast_exam_findings, - CASE - WHEN obs regexp "!!7381=" THEN @prior_via_test_result := GetValues(obs, 7381) - ELSE @prior_via_test_result := NULL - END AS prior_via_test_result, - CASE - WHEN obs regexp "!!7381=" THEN @prior_via_test_result_date := GetValues(obs_datetimes, 7381) - ELSE @prior_via_test_result_date := NULL - END AS prior_via_test_result_date, - CASE - WHEN obs regexp "!!9590=" THEN @via_test_result := GetValues(obs, 9590) - ELSE @via_test_result := NULL - END AS via_test_result, - CASE - WHEN obs regexp "!!6709=" THEN @hiv_status := GetValues(obs, 6709) - ELSE @hiv_status := NULL - END AS hiv_status, - CASE - WHEN obs regexp "!!6042=6555!!" THEN @cancer_type := 6555 - WHEN obs regexp "!!7176=" THEN @cancer_type := GetValues(obs, 7176) - ELSE @cancer_type := NULL - END AS cancer_type, - CASE - WHEN obs REGEXP "!!9841=" THEN @cancer_subtype := GetValues(obs, 9841) -- Breast cancer type - WHEN obs REGEXP "!!6536=" THEN @cancer_subtype := GetValues(obs, 6536) -- Gynecologic cancer type - WHEN obs REGEXP "!!9843=" THEN @cancer_subtype := GetValues(obs, 9843) -- Sarcoma cancer type - WHEN obs REGEXP "!!9844=" THEN @cancer_subtype := GetValues(obs, 9844) -- Leukemia cancer type - WHEN obs REGEXP "!!6551=" THEN @cancer_subtype := GetValues(obs, 6551) -- Lymphoma cancer type - WHEN obs REGEXP "!!9846=" THEN @cancer_subtype := GetValues(obs, 9846) -- Other solid cancer type - WHEN obs REGEXP "!!6540=" THEN @cancer_subtype := GetValues(obs, 6540) -- Skin cancer type - WHEN obs REGEXP "!!6528=" THEN @cancer_subtype := GetValues(obs, 6528) -- Head and neck cancer type - WHEN obs REGEXP "!!6514=" THEN @cancer_subtype := GetValues(obs, 6514) -- Genitourinary cancer type - WHEN obs REGEXP "!!6520=" THEN @cancer_subtype := GetValues(obs, 6520) -- Gastrointestinal cancer - WHEN obs REGEXP "!!10132=" THEN @cancer_subtype := GetValues(obs, 10132) -- Non-small cell lung cancer type - ELSE @cancer_subtype := null - END AS cancer_subtype, - CASE - WHEN obs regexp "!!9841=" THEN @breast_cancer_type := GetValues(obs, 9841) - ELSE @breast_cancer_type := NULL - END AS breast_cancer_type, - CASE - WHEN obs regexp "!!9847=" THEN @non_cancer_diagnosis := GetValues(obs, 9847) - ELSE @non_cancer_diagnosis := NULL - END AS non_cancer_diagnosis, - CASE - WHEN obs regexp "!!6582=" THEN @cancer_stage := GetValues(obs, 6582) - ELSE @cancer_stage := NULL - END AS cancer_stage, - CASE - WHEN obs regexp "!!9868=" THEN @overall_cancer_stage_group := GetValues(obs,9868) - ELSE @overall_cancer_stage_group:= NULL - END AS overall_cancer_stage_group, - CASE - WHEN obs regexp "!!9869=(1260)!!" THEN @cur_onc_meds := NULL - WHEN obs regexp "!!9918=" THEN @cur_onc_meds := GetValues(obs, 9918) - -- WHEN obs regexp "!!7196=" THEN @cur_onc_meds := GetValues(obs, 7196) - -- WHEN obs regexp "!!6643=" THEN @cur_onc_meds := GetValues(obs, 6643) - WHEN @prev_id=@cur_id THEN @cur_onc_meds - ELSE @cur_onc_meds:= NULL - END AS cur_onc_meds, - CASE - WHEN obs regexp "!!1899=" THEN @cur_onc_meds_dose := GetValues(obs, 1899) - ELSE @cur_onc_meds_dose := NULL - END AS cur_onc_meds_dose, - CASE - WHEN obs regexp "!!1896=" THEN @cur_onc_meds_frequency := GetValues(obs, 1896) - ELSE @cur_onc_meds_frequency := NULL - END AS cur_onc_meds_frequency, - CASE - WHEN obs regexp "!!9869=(1256|1259)" or (obs regexp "!!9869=(1257|1259)!!" and @cur_onc_meds_start_date is NULL ) THEN @cur_onc_meds_start_date := DATE(t1.encounter_datetime) - WHEN obs regexp "!!9869=(1260)!!" THEN @cur_onc_meds_start_date := NULL - WHEN @prev_id != @cur_id THEN @cur_onc_meds_start_date := NULL - ELSE @cur_onc_meds_start_date - END AS cur_onc_meds_start_date, - NULL AS cur_onc_meds_end_date, - CASE - WHEN obs regexp "!!8723=" THEN @oncology_treatment_plan := GetValues(obs, 8723) - ELSE @oncology_treatment_plan := NULL - END AS oncology_treatment_plan, - CASE - WHEN obs regexp "!!6575=" THEN @chemotherapy := GetValues(obs, 6575) - ELSE @chemotherapy := NULL - END AS chemotherapy, - CASE - WHEN obs regexp "!!6643=" THEN @current_chemo_cycle := GetValues(obs, 6643) - ELSE @current_chemo_cycle := NULL - END AS current_chemo_cycle, - CASE - WHEN obs regexp "!!6644=" THEN @total_chemo_cycles_planned := GetValues(obs, 6644) - ELSE @total_chemo_cycles_planned := NULL - END AS total_chemo_cycles_planned, - CASE - WHEN obs regexp "!!7222=" THEN @therapeutic_notes := GetValues(obs, 7222) - ELSE @therapeutic_notes := NULL - END AS therapeutic_notes, - CASE - WHEN obs regexp "!!9848=" THEN @cancer_diagnosis_status := GetValues(obs, 9848) - ELSE @cancer_diagnosis_status := NULL - END AS cancer_diagnosis_status, - CASE - WHEN obs regexp "!!8725=" THEN @reasons_for_surgery := GetValues(obs, 8725) - ELSE NULL - END AS reasons_for_surgery, - CASE - WHEN obs regexp "!!2206=" THEN @chemotherapy_intent := GetValues(obs, 2206) - ELSE @chemotherapy_intent := NULL - END AS chemotherapy_intent, - CASE - WHEN obs regexp "!!9869=" THEN @chemotherapy_plan := GetValues(obs, 9869) - ELSE @chemotherapy_plan := NULL - END AS chemotherapy_plan, - CASE - WHEN obs regexp "!!9946=" THEN @chemotherapy_regimen := GetValues(obs, 9946) - ELSE @chemotherapy_regimen := NULL - END AS chemotherapy_regimen, - CASE - WHEN obs regexp "!!7463=" THEN @drug_route := GetValues(obs, 7463) - ELSE @drug_route := NULL - END AS drug_route, - CASE - WHEN obs regexp "!!9918=" THEN @medication_history := GetValues(obs, 9918) - ELSE @medication_history := NULL - END AS medication_history, - CASE - WHEN obs regexp "!!10198=" THEN @other_meds_added := GetValues(obs, 10198) - ELSE @other_meds_added := NULL - END AS other_meds_added, - CASE - WHEN obs regexp "!!9710=" THEN @sickle_cell_drugs := GetValues(obs, 9710) - ELSE @sickle_cell_drugs := NULL - END AS sickle_cell_drugs - FROM flat_onc_patient_history_0 t1 - JOIN - amrs.person p using (person_id) - ORDER BY person_id, date(encounter_datetime) desc, encounter_type_sort_index desc - ); - - SET @prev_id := NULL; - SET @cur_id := NULL; + SET @prev_rtc_date := NULL; + SET @rtc_date := NULL; + SET @diagnosis := NULL; + SET @diagnosis_method := NULL; + SET @result_of_diagnosis := NULL; + SET @diagnosis_date := NULL; + SET @breast_exam_findings_this_visit := NULL; + SET @via_or_via_vili_test_result := NULL; + SET @prior_via_result := NULL; + SET @prior_via_date := NULL; + SET @hiv_status := NULL; + SET @cancer_type := NULL; + SET @cancer_subtype := NULL; + SET @breast_cancer_type := NULL; + SET @non_cancer_diagnosis := NULL; + SET @cancer_stage := NULL; + SET @overall_cancer_stage_group := NULL; + SET @cur_onc_meds_start_date := NULL; + SET @cur_onc_meds_end_date := NULL; + SET @cur_onc_meds := NULL; + SET @cur_onc_meds_dose := NULL; + SET @cur_onc_meds_frequency := NULL; + SET @oncology_treatment_plan := NULL; + SET @chemotherapy := NULL; + SET @current_chemo_cycle := NULL; + SET @total_chemo_cycles_planned := NULL; + SET @therapeutic_notes := NULL; + SET @cancer_diagnosis_status := NULL; + SET @reasons_for_surgery := NULL; + SET @chemotherapy_intent := NULL; + SET @chemotherapy_plan := NULL; + SET @chemotherapy_regimen := NULL; + SET @drug_route := NULL; + SET @medication_history := NULL; + SET @other_meds_added := NULL; + SET @sickle_cell_drugs := NULL; + SET @lab_encounter_type := 99999; + SET @prev_id := NULL; + SET @cur_id := NULL; + SET @enrollment_date := NULL; + SET @cur_rtc_date := NULL; + SET @prev_rtc_date := NULL; + + DROP TEMPORARY TABLE IF EXISTS flat_onc_patient_history_1; + CREATE TEMPORARY TABLE flat_onc_patient_history_1 #(index encounter_id (encounter_id)) + (SELECT + @prev_id := @cur_id AS prev_id, + @cur_id := t1.person_id AS cur_id, + t1.person_id, + t1.uuid, + t1.encounter_id, + t1.encounter_datetime, + t1.encounter_type, + t1.name as `encounter_type_name`, + t1.visit_id, + t1.visit_type_id, + t1.visit_start_datetime, + t1.location_id, + t1.program_id, + t1.is_clinical_encounter, + CASE + WHEN @prev_id != @cur_id AND t1.encounter_type IN (21, @lab_encounter_type) THEN @enrollment_date := NULL + WHEN @prev_id != @cur_id THEN @enrollment_date := encounter_datetime + WHEN t1.encounter_type NOT IN (21, @lab_encounter_type) AND @enrollment_date IS NULL THEN @enrollment_date := encounter_datetime + ELSE @enrollment_date + END AS enrollment_date, + CASE + WHEN @prev_id = @cur_id THEN @prev_rtc_date := @cur_rtc_date + ELSE @prev_rtc_date := NULL + END AS prev_rtc_date, + CASE + WHEN obs regexp "!!5096=" THEN @cur_rtc_date := REPLACE(REPLACE((substring_index(substring(obs,locate("!!5096=", obs)), @sep, 1)),"!!5096=",""),"!!","") + WHEN @prev_id = @cur_id THEN IF (@cur_rtc_date > encounter_datetime, @cur_rtc_date, NULL) + ELSE @cur_rtc_date := NULL + END AS rtc_date, + CASE + WHEN obs regexp "!!7179=" THEN @diagnosis := REPLACE(REPLACE((substring_index(substring(obs,locate("!!7179=",obs)),@sep,1)),"!!7179=",""),"!!","") + ELSE @diagnosis := NULL + END AS diagnosis, + @diagnosis_method := GetValues(obs, 6504) AS diagnosis_method, + @result_of_diagnosis := CAST(REPLACE(REPLACE((substring_index(substring(obs,locate("!!7191=",obs)),@sep,1)),"!!7191=",""),"!!","") AS unsigned) AS result_of_diagnosis, + CASE + WHEN obs regexp "!!9728=" THEN @diagnosis_date := REPLACE(REPLACE((substring_index(substring(obs,locate("!!9728=",obs)),@sep,1)),"!!9728=",""),"!!","") + ELSE @diagnosis_date := NULL + END AS diagnosis_date, + CASE + WHEN t1.encounter_type = 86 AND obs REGEXP "!!6251=" THEN @breast_exam_findings_this_visit := REPLACE(SUBSTRING(GetValues(obs, 6251), -5), '#', '') + ELSE @breast_exam_findings_this_visit := NULL + END AS breast_exam_findings_this_visit, + CASE + WHEN t1.encounter_type = 69 AND obs REGEXP "!!9434=664!!" OR GetValues(obs, 9590) LIKE '%1115%' THEN @via_or_via_vili_test_result := 1 -- Negative + WHEN t1.encounter_type = 69 AND obs REGEXP "!!9434=703!!" OR GetValues(obs, 9590) IS NOT NULL AND GetValues(obs, 9590) NOT LIKE '%1115%' THEN @via_or_via_vili_test_result := 2 -- Positive + WHEN t1.encounter_type = 69 AND obs REGEXP "!!9434=6971!!" THEN @via_or_via_vili_test_result := 3 -- Suspicious of cancer + ELSE @via_or_via_vili_test_result := null + END AS via_or_via_vili_test_result, + CASE + WHEN t1.encounter_type = 69 AND obs REGEXP "!!7381=664!!" THEN @prior_via_result := 1 -- Positive + WHEN t1.encounter_type = 69 AND obs REGEXP "!!7381=703!!" THEN @prior_via_result := 2 -- Negative + ELSE @prior_via_result := null + END AS prior_via_result, + CASE + WHEN t1.encounter_type = 69 AND obs REGEXP "!!7381=" THEN @prior_via_date := GetValues(obs_datetimes, 7381) -- Could be buggy! + ELSE @prior_via_date := null + END AS prior_via_date, + CASE + WHEN obs regexp "!!6709=" THEN @hiv_status := GetValues(obs, 6709) + ELSE @hiv_status := NULL + END AS hiv_status, + CASE + WHEN obs regexp "!!6042=6555!!" THEN @cancer_type := 6555 + WHEN obs regexp "!!7176=" THEN @cancer_type := GetValues(obs, 7176) + ELSE @cancer_type := NULL + END AS cancer_type, + CASE + WHEN obs REGEXP "!!9841=" THEN @cancer_subtype := GetValues(obs, 9841) -- Breast cancer type + WHEN obs REGEXP "!!6536=" THEN @cancer_subtype := GetValues(obs, 6536) -- Gynecologic cancer type + WHEN obs REGEXP "!!9843=" THEN @cancer_subtype := GetValues(obs, 9843) -- Sarcoma cancer type + WHEN obs REGEXP "!!9844=" THEN @cancer_subtype := GetValues(obs, 9844) -- Leukemia cancer type + WHEN obs REGEXP "!!6551=" THEN @cancer_subtype := GetValues(obs, 6551) -- Lymphoma cancer type + WHEN obs REGEXP "!!9846=" THEN @cancer_subtype := GetValues(obs, 9846) -- Other solid cancer type + WHEN obs REGEXP "!!6540=" THEN @cancer_subtype := GetValues(obs, 6540) -- Skin cancer type + WHEN obs REGEXP "!!6528=" THEN @cancer_subtype := GetValues(obs, 6528) -- Head and neck cancer type + WHEN obs REGEXP "!!6514=" THEN @cancer_subtype := GetValues(obs, 6514) -- Genitourinary cancer type + WHEN obs REGEXP "!!6520=" THEN @cancer_subtype := GetValues(obs, 6520) -- Gastrointestinal cancer + WHEN obs REGEXP "!!10132=" THEN @cancer_subtype := GetValues(obs, 10132) -- Non-small cell lung cancer type + ELSE @cancer_subtype := null + END AS cancer_subtype, + CASE + WHEN obs regexp "!!9841=" THEN @breast_cancer_type := GetValues(obs, 9841) + ELSE @breast_cancer_type := NULL + END AS breast_cancer_type, + CASE + WHEN obs regexp "!!9847=" THEN @non_cancer_diagnosis := GetValues(obs, 9847) + ELSE @non_cancer_diagnosis := NULL + END AS non_cancer_diagnosis, + CASE + WHEN obs regexp "!!6582=" THEN @cancer_stage := GetValues(obs, 6582) + ELSE @cancer_stage := NULL + END AS cancer_stage, + CASE + WHEN obs regexp "!!9868=" THEN @overall_cancer_stage_group := GetValues(obs,9868) + ELSE @overall_cancer_stage_group:= NULL + END AS overall_cancer_stage_group, + CASE + WHEN obs regexp "!!9869=(1260)!!" THEN @cur_onc_meds := NULL + WHEN obs regexp "!!9918=" THEN @cur_onc_meds := GetValues(obs, 9918) + -- WHEN obs regexp "!!7196=" THEN @cur_onc_meds := GetValues(obs, 7196) + -- WHEN obs regexp "!!6643=" THEN @cur_onc_meds := GetValues(obs, 6643) + WHEN @prev_id=@cur_id THEN @cur_onc_meds + ELSE @cur_onc_meds:= NULL + END AS cur_onc_meds, + CASE + WHEN obs regexp "!!1899=" THEN @cur_onc_meds_dose := GetValues(obs, 1899) + ELSE @cur_onc_meds_dose := NULL + END AS cur_onc_meds_dose, + CASE + WHEN obs regexp "!!1896=" THEN @cur_onc_meds_frequency := GetValues(obs, 1896) + ELSE @cur_onc_meds_frequency := NULL + END AS cur_onc_meds_frequency, + CASE + WHEN obs regexp "!!9869=(1256|1259)" or (obs regexp "!!9869=(1257|1259)!!" and @cur_onc_meds_start_date is NULL ) THEN @cur_onc_meds_start_date := DATE(t1.encounter_datetime) + WHEN obs regexp "!!9869=(1260)!!" THEN @cur_onc_meds_start_date := NULL + WHEN @prev_id != @cur_id THEN @cur_onc_meds_start_date := NULL + ELSE @cur_onc_meds_start_date + END AS cur_onc_meds_start_date, + NULL AS cur_onc_meds_end_date, + CASE + WHEN obs regexp "!!8723=" THEN @oncology_treatment_plan := GetValues(obs, 8723) + ELSE @oncology_treatment_plan := NULL + END AS oncology_treatment_plan, + CASE + WHEN obs regexp "!!6575=" THEN @chemotherapy := GetValues(obs, 6575) + ELSE @chemotherapy := NULL + END AS chemotherapy, + CASE + WHEN obs regexp "!!6643=" THEN @current_chemo_cycle := GetValues(obs, 6643) + ELSE @current_chemo_cycle := NULL + END AS current_chemo_cycle, + CASE + WHEN obs regexp "!!6644=" THEN @total_chemo_cycles_planned := GetValues(obs, 6644) + ELSE @total_chemo_cycles_planned := NULL + END AS total_chemo_cycles_planned, + CASE + WHEN obs regexp "!!7222=" THEN @therapeutic_notes := GetValues(obs, 7222) + ELSE @therapeutic_notes := NULL + END AS therapeutic_notes, + CASE + WHEN obs regexp "!!9848=" THEN @cancer_diagnosis_status := GetValues(obs, 9848) + ELSE @cancer_diagnosis_status := NULL + END AS cancer_diagnosis_status, + CASE + WHEN obs regexp "!!8725=" THEN @reasons_for_surgery := GetValues(obs, 8725) + ELSE NULL + END AS reasons_for_surgery, + CASE + WHEN obs regexp "!!2206=" THEN @chemotherapy_intent := GetValues(obs, 2206) + ELSE @chemotherapy_intent := NULL + END AS chemotherapy_intent, + CASE + WHEN obs regexp "!!9869=" THEN @chemotherapy_plan := GetValues(obs, 9869) + ELSE @chemotherapy_plan := NULL + END AS chemotherapy_plan, + CASE + WHEN obs regexp "!!9946=" THEN @chemotherapy_regimen := GetValues(obs, 9946) + ELSE @chemotherapy_regimen := NULL + END AS chemotherapy_regimen, + CASE + WHEN obs regexp "!!7463=" THEN @drug_route := GetValues(obs, 7463) + ELSE @drug_route := NULL + END AS drug_route, + CASE + WHEN obs regexp "!!9918=" THEN @medication_history := GetValues(obs, 9918) + ELSE @medication_history := NULL + END AS medication_history, + CASE + WHEN obs regexp "!!10198=" THEN @other_meds_added := GetValues(obs, 10198) + ELSE @other_meds_added := NULL + END AS other_meds_added, + CASE + WHEN obs regexp "!!9710=" THEN @sickle_cell_drugs := GetValues(obs, 9710) + ELSE @sickle_cell_drugs := NULL + END AS sickle_cell_drugs + FROM flat_onc_patient_history_0 t1 + JOIN + amrs.person p using (person_id) + ORDER BY person_id, date(encounter_datetime) desc, encounter_type_sort_index desc + ); + + SET @prev_id := NULL; + SET @cur_id := NULL; - ALTER TABLE flat_onc_patient_history_1 drop prev_id, drop cur_id; + ALTER TABLE flat_onc_patient_history_1 drop prev_id, drop cur_id; - SELECT COUNT(*) INTO @new_encounter_rows FROM flat_onc_patient_history_1; - - SELECT @new_encounter_rows; - SET @total_rows_written := @total_rows_written + @new_encounter_rows; - SELECT @total_rows_written; + SELECT COUNT(*) INTO @new_encounter_rows FROM flat_onc_patient_history_1; + + SELECT @new_encounter_rows; + SET @total_rows_written := @total_rows_written + @new_encounter_rows; + SELECT @total_rows_written; - SET @dyn_sql=CONCAT('REPLACE INTO ', @write_table, - '(SELECT - NULL, - person_id, - uuid, - encounter_id, - encounter_datetime, - encounter_type, - encounter_type_name, - visit_id, - visit_type_id, - visit_start_datetime, - location_id, - program_id, - is_clinical_encounter, - enrollment_date, - prev_rtc_date, - rtc_date, - diagnosis, - diagnosis_method, - result_of_diagnosis, - diagnosis_date, - breast_exam_findings, - prior_via_test_result, - prior_via_test_result_date, - via_test_result, - hiv_status, - cancer_type, - cancer_subtype, - breast_cancer_type, - non_cancer_diagnosis, - cancer_stage, - overall_cancer_stage_group, - cur_onc_meds, - cur_onc_meds_dose, - cur_onc_meds_frequency, - cur_onc_meds_start_date, - cur_onc_meds_end_date, - oncology_treatment_plan, - chemotherapy, - current_chemo_cycle, - total_chemo_cycles_planned, - therapeutic_notes, - cancer_diagnosis_status, - reasons_for_surgery, - chemotherapy_intent, - chemotherapy_plan, - chemotherapy_regimen, - drug_route, - medication_history, - other_meds_added, - sickle_cell_drugs - FROM - flat_onc_patient_history_1)'); + SET @dyn_sql=CONCAT('REPLACE INTO ', @write_table, + '(SELECT + NULL, + person_id, + uuid, + encounter_id, + encounter_datetime, + encounter_type, + encounter_type_name, + visit_id, + visit_type_id, + visit_start_datetime, + location_id, + program_id, + is_clinical_encounter, + enrollment_date, + prev_rtc_date, + rtc_date, + diagnosis, + diagnosis_method, + result_of_diagnosis, + diagnosis_date, + breast_exam_findings_this_visit, + via_or_via_vili_test_result, + prior_via_result, + prior_via_date, + hiv_status, + cancer_type, + cancer_subtype, + breast_cancer_type, + non_cancer_diagnosis, + cancer_stage, + overall_cancer_stage_group, + cur_onc_meds, + cur_onc_meds_dose, + cur_onc_meds_frequency, + cur_onc_meds_start_date, + cur_onc_meds_end_date, + oncology_treatment_plan, + chemotherapy, + current_chemo_cycle, + total_chemo_cycles_planned, + therapeutic_notes, + cancer_diagnosis_status, + reasons_for_surgery, + chemotherapy_intent, + chemotherapy_plan, + chemotherapy_regimen, + drug_route, + medication_history, + other_meds_added, + sickle_cell_drugs + FROM + flat_onc_patient_history_1)'); - PREPARE s1 FROM @dyn_sql; - EXECUTE s1; - DEALLOCATE PREPARE s1; + PREPARE s1 FROM @dyn_sql; + EXECUTE s1; + DEALLOCATE PREPARE s1; - SET @dyn_sql := CONCAT('DELETE t1 FROM ',@queue_table,' t1 JOIN flat_onc_patient_history_build_queue__0 t2 using (person_id);'); - PREPARE s1 FROM @dyn_sql; - EXECUTE s1; - DEALLOCATE PREPARE s1; - - - #SELECT @person_ids_count := (SELECT count(*) FROM flat_onc_patient_history_build_queue_2); - SET @dyn_sql := CONCAT('SELECT count(*) into @person_ids_count FROM ',@queue_table,';'); - PREPARE s1 FROM @dyn_sql; - EXECUTE s1; - DEALLOCATE PREPARE s1; + SET @dyn_sql := CONCAT('DELETE t1 FROM ',@queue_table,' t1 JOIN flat_onc_patient_history_build_queue__0 t2 using (person_id);'); + PREPARE s1 FROM @dyn_sql; + EXECUTE s1; + DEALLOCATE PREPARE s1; + + SET @dyn_sql := CONCAT('SELECT count(*) into @person_ids_count FROM ',@queue_table,';'); + PREPARE s1 FROM @dyn_sql; + EXECUTE s1; + DEALLOCATE PREPARE s1; - SET @cycle_length := TIMESTAMPDIFF(second,@loop_start_time,now()); - SET @total_time := @total_time + @cycle_length; - SET @cycle_number := @cycle_number + 1; + SET @cycle_length := TIMESTAMPDIFF(second,@loop_start_time,now()); + SET @total_time := @total_time + @cycle_length; + SET @cycle_number := @cycle_number + 1; + + SET @remaining_time := CEIL((@total_time / @cycle_number) * CEIL(@person_ids_count / cycle_size) / 60); + SELECT + @person_ids_count AS 'persons remaining', + @cycle_length AS 'Cycle time (s)', + CEIL(@person_ids_count / cycle_size) AS remaining_cycles, + @remaining_time AS 'Est time remaining (min)'; + END WHILE; - SET @remaining_time := CEIL((@total_time / @cycle_number) * CEIL(@person_ids_count / cycle_size) / 60); - SELECT - @person_ids_count AS 'persons remaining', - @cycle_length AS 'Cycle time (s)', - CEIL(@person_ids_count / cycle_size) AS remaining_cycles, - @remaining_time AS 'Est time remaining (min)'; - END WHILE; + IF (@query_type="build") THEN + SET @dyn_sql := CONCAT('DROP TABLE ',@queue_table,';'); + PREPARE s1 FROM @dyn_sql; + EXECUTE s1; + DEALLOCATE PREPARE s1; - IF (@query_type="build") THEN - SET @dyn_sql := CONCAT('DROP TABLE ',@queue_table,';'); - PREPARE s1 FROM @dyn_sql; - EXECUTE s1; - DEALLOCATE PREPARE s1; - - SET @total_rows_to_write=0; - SET @dyn_sql := CONCAT("Select count(*) into @total_rows_to_write FROM ",@write_table); - PREPARE s1 FROM @dyn_sql; - EXECUTE s1; - DEALLOCATE PREPARE s1; - - SET @start_write := now(); - SELECT CONCAT(@start_write,' : Writing ', @total_rows_to_write,' to ', @primary_table); + SET @total_rows_to_write=0; + SET @dyn_sql := CONCAT("Select count(*) into @total_rows_to_write FROM ",@write_table); + PREPARE s1 FROM @dyn_sql; + EXECUTE s1; + DEALLOCATE PREPARE s1; + + SET @start_write := now(); + SELECT CONCAT(@start_write,' : Writing ', @total_rows_to_write,' to ', @primary_table); - SET @dyn_sql := CONCAT('REPLACE INTO ', @primary_table, - '(SELECT * FROM ', @write_table,');'); - PREPARE s1 FROM @dyn_sql; - EXECUTE s1; - DEALLOCATE PREPARE s1; - - SET @finish_write := now(); - SET @time_to_write := TIMESTAMPDIFF(second, @start_write, @finish_write); - SELECT CONCAT(@finish_write,' : Completed writing rows. Time to write to primary table: ', @time_to_write, ' seconds '); - - SET @dyn_sql := CONCAT('DROP TABLE ', @write_table, ';'); - PREPARE s1 FROM @dyn_sql; - EXECUTE s1; - DEALLOCATE PREPARE s1; - END IF; + SET @dyn_sql := CONCAT('REPLACE INTO ', @primary_table, + '(SELECT * FROM ', @write_table,');'); + PREPARE s1 FROM @dyn_sql; + EXECUTE s1; + DEALLOCATE PREPARE s1; + + SET @finish_write := now(); + SET @time_to_write := TIMESTAMPDIFF(second, @start_write, @finish_write); + SELECT CONCAT(@finish_write,' : Completed writing rows. Time to write to primary table: ', @time_to_write, ' seconds '); + + SET @dyn_sql := CONCAT('DROP TABLE ', @write_table, ';'); + PREPARE s1 FROM @dyn_sql; + EXECUTE s1; + DEALLOCATE PREPARE s1; + END IF; - SET @ave_cycle_length := CEIL(@total_time/@cycle_number); - SELECT CONCAT('Average Cycle Length: ', @ave_cycle_length, ' second(s)'); - SET @end := now(); - INSERT INTO etl.flat_log values (@start, @last_date_created, @table_version, TIMESTAMPDIFF(second, @start, @end)); - SELECT CONCAT(@table_version,' : Time to complete: ', TIMESTAMPDIFF(MINUTE, @start, @end),' minutes'); -END$$ -DELIMITER ; + SET @ave_cycle_length := CEIL(@total_time/@cycle_number); + SELECT CONCAT('Average Cycle Length: ', @ave_cycle_length, ' second(s)'); + SET @end := now(); + INSERT INTO etl.flat_log values (@start, @last_date_created, @table_version, TIMESTAMPDIFF(second, @start, @end)); + SELECT CONCAT(@table_version,' : Time to complete: ', TIMESTAMPDIFF(MINUTE, @start, @end),' minutes'); +END \ No newline at end of file