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87 changes: 26 additions & 61 deletions jobs/sql/extractions/all_encounters.sql
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Original file line number Diff line number Diff line change
Expand Up @@ -4,16 +4,18 @@ 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,
patient_id int,
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),
Expand All @@ -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,
Expand All @@ -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;