From c14b6ab29e64fa679c24c74a5965de78a6183823 Mon Sep 17 00:00:00 2001 From: aibrahem550 Date: Mon, 4 Mar 2024 19:36:52 +0400 Subject: [PATCH] commit --- jobs/sql/extractions/all_encounters.sql | 87 ++++++++----------------- 1 file changed, 26 insertions(+), 61 deletions(-) diff --git a/jobs/sql/extractions/all_encounters.sql b/jobs/sql/extractions/all_encounters.sql index cc06217..3c4a98e 100644 --- a/jobs/sql/extractions/all_encounters.sql +++ b/jobs/sql/extractions/all_encounters.sql @@ -4,8 +4,8 @@ SET @partition = '${partitionNum}'; set sql_safe_updates = 0; set @next_appt_date_concept_id = CONCEPT_FROM_MAPPING('PIH', 5096); -drop temporary table if exists temp_all_encounters; -create temporary table temp_all_encounters +drop temporary table if exists temp_encounter; +create temporary table temp_encounter ( encounter_id int, encounter_datetime datetime, @@ -13,7 +13,9 @@ create temporary table temp_all_encounters visit_id int, creator int(11), user_entered varchar(255), + location_id int, encounter_location varchar(255), + encounter_type int, encounter_type_name varchar(50), entered_datetime datetime, emr_id varchar(15), @@ -22,77 +24,40 @@ create temporary table temp_all_encounters ); -- If there is not a previous watermark, initialize with all encounters -insert into temp_all_encounters (encounter_id) -select encounter_id from encounter +insert into temp_encounter (encounter_id, encounter_datetime, encounter_type, location_id, patient_id, visit_id, creator, entered_datetime, voided) +select encounter_id, encounter_datetime, encounter_type, location_id, patient_id, visit_id, creator, date_created, voided +from encounter where voided = 0 and @previousWatermark is null; -- If there is a previous watermark, initialize with only those encounters since that watermark -insert into temp_all_encounters (encounter_id) -select encounter_id from encounter +insert into temp_encounter (encounter_id, encounter_datetime, encounter_type, location_id, patient_id, visit_id, creator, entered_datetime, voided ) +select encounter_id, encounter_datetime, +encounter_type, location_id, encounter.patient_id, visit_id, creator, date_created, voided +from encounter inner join dbevent_patient dp on encounter.patient_id = dp.patient_id where voided = 0 and @previousWatermark is not null and dp.last_updated >= @previousWatermark and dp.last_updated <= @newWatermark; -create index temp_all_encounters_encounterId ON temp_all_encounters (encounter_id); --- Load the encounters -update temp_all_encounters t -inner join encounter e on t.encounter_id = e.encounter_id -set t.encounter_datetime = e.encounter_datetime, - t.encounter_type_name = encounter_type_name_from_id(e.encounter_type), - t.encounter_location = location_name(e.location_id), - t.patient_id = e.patient_id, - t.visit_id = e.visit_id, - t.user_entered = person_name_of_user(e.creator), - t.entered_datetime = e.date_created, - t.voided = e.voided -; +CREATE INDEX temp_all_encounters_encounterId ON temp_encounter (encounter_id); +CREATE INDEX temp_all_encounters_patientId ON temp_encounter (patient_id); -CREATE INDEX temp_all_encounters_patientId ON temp_all_encounters (patient_id); +UPDATE temp_encounter t SET t.encounter_type_name = encounter_type_name_from_id(t.encounter_type); +UPDATE temp_encounter t SET t.encounter_location = location_name(t.location_id); +UPDATE temp_encounter t SET t.user_entered = person_name_of_user(t.creator); +UPDATE temp_encounter t SET t.emr_id = patient_identifier(t.patient_id, 'ZL EMR ID'); --- next visit date --- all next appt date obs loaded to temp table before looking up for each encounter --- this avoids having to access the full obs table for each encounter -DROP TABLE IF EXISTS temp_next_appt_obs; -CREATE TEMPORARY TABLE temp_next_appt_obs -select encounter_id, max(value_datetime) "next_appt_date" -from obs -where concept_id = @next_appt_date_concept_id - and voided = 0 -group by encounter_id; +DROP TABLE IF EXISTS temp_obs; +CREATE TEMPORARY TABLE temp_obs AS +SELECT o.person_id, o.encounter_id, o.obs_id , o.concept_id, o.value_datetime, o.voided , o.date_created +FROM temp_encounter te INNER JOIN obs o ON te.encounter_id=o.encounter_id +WHERE o.voided =0 +AND concept_id = @next_appt_date_concept_id; -create index temp_next_appt_obs_ei on temp_next_appt_obs (encounter_id); - -update temp_all_encounters te - inner join temp_next_appt_obs tvo on tvo.encounter_id = te.encounter_id -set te.next_appt_date = tvo.next_appt_date -where te.voided = 0; - --- emr_id --- unique patients loaded to temp table before looking up emr_id and joining back in to the temp_all_encounters table -drop temporary table if exists temp_emrids; -create temporary table temp_emrids -( - patient_id int(11), - emr_id varchar(50) -); - -insert into temp_emrids(patient_id) -select DISTINCT patient_id -from temp_all_encounters -; -create index temp_emrids_patient_id on temp_emrids (patient_id); - -update temp_emrids t -set emr_id = patient_identifier(patient_id, 'ZL EMR ID'); - -update temp_all_encounters t - inner join temp_emrids te on te.patient_id = t.patient_id -set t.emr_id = te.emr_id -; +UPDATE temp_encounter t SET t.next_appt_date = obs_value_datetime_from_temp(t.encounter_id, 'PIH', '5096'); -- final query select emr_id, @@ -106,5 +71,5 @@ select emr_id, user_entered, next_appt_date, voided -from temp_all_encounters t -ORDER BY t.patient_id, t.encounter_id; +from temp_encounter t +ORDER BY t.patient_id, t.encounter_id; \ No newline at end of file