From 72aba94dcadb777262d28f8497251e0aa5293ac5 Mon Sep 17 00:00:00 2001 From: dmdesimone Date: Fri, 15 Apr 2022 15:41:15 +0200 Subject: [PATCH] Update covid_visit.sql --- jobs/sql/extractions/covid_visit.sql | 886 ++++++++++++++++++++++----- 1 file changed, 727 insertions(+), 159 deletions(-) diff --git a/jobs/sql/extractions/covid_visit.sql b/jobs/sql/extractions/covid_visit.sql index 5306bf2..65fb77a 100644 --- a/jobs/sql/extractions/covid_visit.sql +++ b/jobs/sql/extractions/covid_visit.sql @@ -130,6 +130,7 @@ CREATE TEMPORARY TABLE temp_covid_visit clinical_management_plan TEXT, nursing_note TEXT, mh_referral VARCHAR(11), + mh_note_obs_group_id INT(11), mh_note TEXT ); @@ -151,12 +152,23 @@ SELECT DATE(encounter_datetime), ENCOUNTER_LOCATION_NAME(encounter_id), date_created, - username(creator) + creator FROM encounter WHERE voided = 0 - AND encounter_type IN (ENCOUNTER_TYPE('COVID-19 Admission'), ENCOUNTER_TYPE('COVID-19 Progress')); + AND encounter_type IN (ENCOUNTER_TYPE('COVID-19 Admission'), ENCOUNTER_TYPE('COVID-19 Progress')) +; + +DROP TEMPORARY TABLE IF EXISTS temp_covid_obs; +create temporary table temp_covid_obs +select o.obs_id, o.obs_group_id , o.encounter_id, o.person_id, o.concept_id, o.value_coded, o.value_numeric, o.value_text,o.value_datetime +from obs o +inner join temp_covid_visit t on t.encounter_id = o.encounter_id +where o.voided = 0; + +create index temp_covid_obs_concept_id on temp_covid_obs(concept_id); +create index temp_covid_obs_ei on temp_covid_obs(encounter_id); UPDATE temp_covid_visit tc LEFT JOIN encounter_type et ON tc.encounter_type_id = et.encounter_type_id SET encounter_type = et.name; @@ -170,293 +182,847 @@ FROM person_attribute a INNER JOIN person_attribute_type t ON a.person_attribute_type_id = t.person_attribute_type_id - WHERE a.value = 'true' AND t.name = 'Test Patient'); ### COVID 19 admission -- case condition -UPDATE temp_covid_visit SET case_condition = OBS_VALUE_CODED_LIST(encounter_id, 'CIEL', '159640', 'en'); +-- UPDATE temp_covid_visit SET case_condition = OBS_VALUE_CODED_LIST(encounter_id, 'CIEL', '159640', 'en'); +update temp_covid_visit t +inner join + (select o.encounter_id, GROUP_CONCAT(distinct concept_name(o.value_coded,'en') separator ' | ') as ret + from temp_covid_obs o + where o.concept_id = concept_from_mapping('CIEL', '159640') + group by o.encounter_id) i on i.encounter_id = t.encounter_id +set t.case_condition = i.ret; + + ### COVID 19 Progress FORM -- overall_condition -UPDATE temp_covid_visit SET overall_condition = OBS_VALUE_CODED_LIST(encounter_id, 'CIEL', '159640', 'en'); +-- UPDATE temp_covid_visit SET overall_condition = OBS_VALUE_CODED_LIST(encounter_id, 'CIEL', '159640', 'en'); +update temp_covid_visit t +inner join + (select o.encounter_id, GROUP_CONCAT(distinct concept_name(o.value_coded,'en') separator ' | ') as ret + from temp_covid_obs o + where o.concept_id = concept_from_mapping('CIEL', '159640') + group by o.encounter_id) i on i.encounter_id = t.encounter_id +set t.overall_condition = i.ret; -- Fever -UPDATE temp_covid_visit SET fever = OBS_SINGLE_VALUE_CODED(encounter_id, 'CIEL', '1728', 'PIH', 'FEVER'); +-- UPDATE temp_covid_visit SET fever = OBS_SINGLE_VALUE_CODED(encounter_id, 'CIEL', '1728', 'PIH', 'FEVER'); +update temp_covid_visit t +inner join temp_covid_obs o on o.encounter_id = t.encounter_id + and o.concept_id = concept_from_mapping('CIEL', '1728') + and o.value_coded = concept_from_mapping('PIH', 'FEVER') +set fever = if(o.concept_id is null, null,'1' ); -- cough -UPDATE temp_covid_visit SET cough = OBS_SINGLE_VALUE_CODED(encounter_id, 'CIEL', '1728', 'PIH', 'COUGH'); +-- UPDATE temp_covid_visit SET cough = OBS_SINGLE_VALUE_CODED(encounter_id, 'CIEL', '1728', 'PIH', 'COUGH'); +update temp_covid_visit t +inner join temp_covid_obs o on o.encounter_id = t.encounter_id + and o.concept_id = concept_from_mapping('CIEL', '1728') + and o.value_coded = concept_from_mapping('PIH', 'COUGH') +set cough = if(o.concept_id is null, null,'1' ); -- cough -UPDATE temp_covid_visit SET productive_cough = OBS_SINGLE_VALUE_CODED(encounter_id, 'CIEL', '1728', 'PIH', 'PRODUCTIVE COUGH'); +-- UPDATE temp_covid_visit SET productive_cough = OBS_SINGLE_VALUE_CODED(encounter_id, 'CIEL', '1728', 'PIH', 'PRODUCTIVE COUGH'); +update temp_covid_visit t +inner join temp_covid_obs o on o.encounter_id = t.encounter_id + and o.concept_id = concept_from_mapping('CIEL', '1728') + and o.value_coded = concept_from_mapping('PIH', 'PRODUCTIVE COUGH') +set productive_cough = if(o.concept_id is null, null,'1' ); -- shortness of breath -UPDATE temp_covid_visit SET shortness_of_breath = OBS_SINGLE_VALUE_CODED(encounter_id, 'CIEL', '1728', 'CIEL', '141600'); +-- UPDATE temp_covid_visit SET shortness_of_breath = OBS_SINGLE_VALUE_CODED(encounter_id, 'CIEL', '1728', 'CIEL', '141600'); +update temp_covid_visit t +inner join temp_covid_obs o on o.encounter_id = t.encounter_id + and o.concept_id = concept_from_mapping('CIEL', '1728') + and o.value_coded = concept_from_mapping( 'CIEL', '141600') +set shortness_of_breath = if(o.concept_id is null, null,'1' ); -- sore_throat -UPDATE temp_covid_visit SET sore_throat = OBS_SINGLE_VALUE_CODED(encounter_id, 'CIEL', '1728', 'CIEL', '158843'); +-- UPDATE temp_covid_visit SET sore_throat = OBS_SINGLE_VALUE_CODED(encounter_id, 'CIEL', '1728', 'CIEL', '158843'); +update temp_covid_visit t +inner join temp_covid_obs o on o.encounter_id = t.encounter_id + and o.concept_id = concept_from_mapping('CIEL', '1728') + and o.value_coded = concept_from_mapping('CIEL', '158843') +set sore_throat = if(o.concept_id is null, null,'1' ); -- rhinorrhea -UPDATE temp_covid_visit SET rhinorrhea = OBS_SINGLE_VALUE_CODED(encounter_id, 'CIEL', '1728', 'CIEL', '165501'); +-- UPDATE temp_covid_visit SET rhinorrhea = OBS_SINGLE_VALUE_CODED(encounter_id, 'CIEL', '1728', 'CIEL', '165501'); +update temp_covid_visit t +inner join temp_covid_obs o on o.encounter_id = t.encounter_id + and o.concept_id = concept_from_mapping('CIEL', '1728') + and o.value_coded = concept_from_mapping('CIEL', '165501') +set rhinorrhea = if(o.concept_id is null, null,'1' ); -- headache -UPDATE temp_covid_visit SET headache = OBS_SINGLE_VALUE_CODED(encounter_id, 'CIEL', '1728', 'PIH', 'HEADACHE'); +-- UPDATE temp_covid_visit SET headache = OBS_SINGLE_VALUE_CODED(encounter_id, 'CIEL', '1728', 'PIH', 'HEADACHE'); +update temp_covid_visit t +inner join temp_covid_obs o on o.encounter_id = t.encounter_id + and o.concept_id = concept_from_mapping('CIEL', '1728') + and o.value_coded = concept_from_mapping('PIH', 'HEADACHE') +set headache = if(o.concept_id is null, null,'1' ); -- chest pain -UPDATE temp_covid_visit SET chest_pain = OBS_SINGLE_VALUE_CODED(encounter_id, 'CIEL', '1728', 'PIH', 'CHEST PAIN'); +-- UPDATE temp_covid_visit SET chest_pain = OBS_SINGLE_VALUE_CODED(encounter_id, 'CIEL', '1728', 'PIH', 'CHEST PAIN'); +update temp_covid_visit t +inner join temp_covid_obs o on o.encounter_id = t.encounter_id + and o.concept_id = concept_from_mapping('CIEL', '1728') + and o.value_coded = concept_from_mapping('PIH', 'FEVER') +set fever = if(o.concept_id is null, null,'1' ); -- muscle pain -UPDATE temp_covid_visit SET muscle_pain = OBS_SINGLE_VALUE_CODED(encounter_id, 'CIEL', '1728', 'PIH', 'MUSCLE PAIN'); +-- UPDATE temp_covid_visit SET muscle_pain = OBS_SINGLE_VALUE_CODED(encounter_id, 'CIEL', '1728', 'PIH', 'MUSCLE PAIN'); +update temp_covid_visit t +inner join temp_covid_obs o on o.encounter_id = t.encounter_id + and o.concept_id = concept_from_mapping('CIEL', '1728') + and o.value_coded = concept_from_mapping('PIH', 'MUSCLE PAIN') +set muscle_pain = if(o.concept_id is null, null,'1' ); -- fatigue -UPDATE temp_covid_visit SET fatigue = OBS_SINGLE_VALUE_CODED(encounter_id, 'CIEL', '1728', 'PIH', 'FATIGUE'); +-- UPDATE temp_covid_visit SET fatigue = OBS_SINGLE_VALUE_CODED(encounter_id, 'CIEL', '1728', 'PIH', 'FATIGUE'); +update temp_covid_visit t +inner join temp_covid_obs o on o.encounter_id = t.encounter_id + and o.concept_id = concept_from_mapping('CIEL', '1728') + and o.value_coded = concept_from_mapping('PIH', 'FATIGUE') +set fatigue = if(o.concept_id is null, null,'1' ); -- nausea and vomiting concept_id 3318 instead of 2530 -UPDATE temp_covid_visit SET vomiting = OBS_SINGLE_VALUE_CODED(encounter_id, 'CIEL', '1728', 'CIEL', '133473'); +-- UPDATE temp_covid_visit SET vomiting = OBS_SINGLE_VALUE_CODED(encounter_id, 'CIEL', '1728', 'CIEL', '133473'); +update temp_covid_visit t +inner join temp_covid_obs o on o.encounter_id = t.encounter_id + and o.concept_id = concept_from_mapping('CIEL', '1728') + and o.value_coded = concept_from_mapping('CIEL', '133473') +set vomiting = if(o.concept_id is null, null,'1' ); -- diarrhea -UPDATE temp_covid_visit SET vomiting = OBS_SINGLE_VALUE_CODED(encounter_id, 'CIEL', '1728', 'PIH', 'DIARRHEA'); +-- UPDATE temp_covid_visit SET diarrhea = OBS_SINGLE_VALUE_CODED(encounter_id, 'CIEL', '1728', 'PIH', 'DIARRHEA'); +update temp_covid_visit t +inner join temp_covid_obs o on o.encounter_id = t.encounter_id + and o.concept_id = concept_from_mapping('CIEL', '1728') + and o.value_coded = concept_from_mapping('PIH', 'DIARRHEA') +set diarrhea = if(o.concept_id is null, null,'1' ); -- loss of taste -UPDATE temp_covid_visit SET loss_of_taste = OBS_SINGLE_VALUE_CODED(encounter_id, 'CIEL', '1728', 'CIEL', '135588'); +-- UPDATE temp_covid_visit SET loss_of_taste = OBS_SINGLE_VALUE_CODED(encounter_id, 'CIEL', '1728', 'CIEL', '135588'); +update temp_covid_visit t +inner join temp_covid_obs o on o.encounter_id = t.encounter_id + and o.concept_id = concept_from_mapping('CIEL', '1728') + and o.value_coded = concept_from_mapping('CIEL', '135588') +set loss_of_taste = if(o.concept_id is null, null,'1' ); -- loss of sense of smell -UPDATE temp_covid_visit SET sense_of_smell_loss = OBS_SINGLE_VALUE_CODED(encounter_id, 'CIEL', '1728', 'CIEL', '135589'); +-- UPDATE temp_covid_visit SET sense_of_smell_loss = OBS_SINGLE_VALUE_CODED(encounter_id, 'CIEL', '1728', 'CIEL', '135589'); +update temp_covid_visit t +inner join temp_covid_obs o on o.encounter_id = t.encounter_id + and o.concept_id = concept_from_mapping('CIEL', '1728') + and o.value_coded = concept_from_mapping('CIEL', '135589') +set sense_of_smell_loss = if(o.concept_id is null, null,'1' ); -- loss of sense of smell -UPDATE temp_covid_visit SET sense_of_smell_loss = OBS_SINGLE_VALUE_CODED(encounter_id, 'CIEL', '1728', 'CIEL', '135589'); +-- UPDATE temp_covid_visit SET sense_of_smell_loss = OBS_SINGLE_VALUE_CODED(encounter_id, 'CIEL', '1728', 'CIEL', '135589'); +update temp_covid_visit t +inner join temp_covid_obs o on o.encounter_id = t.encounter_id + and o.concept_id = concept_from_mapping('CIEL', '1728') + and o.value_coded = concept_from_mapping('CIEL', '135589') +set sense_of_smell_loss = if(o.concept_id is null, null,'1' ); -- confusion -UPDATE temp_covid_visit SET confusion = OBS_SINGLE_VALUE_CODED(encounter_id, 'CIEL', '1728', 'PIH', 'CONFUSION'); +-- UPDATE temp_covid_visit SET confusion = OBS_SINGLE_VALUE_CODED(encounter_id, 'CIEL', '1728', 'PIH', 'CONFUSION'); +update temp_covid_visit t +inner join temp_covid_obs o on o.encounter_id = t.encounter_id + and o.concept_id = concept_from_mapping('CIEL', '1728') + and o.value_coded = concept_from_mapping('PIH', 'CONFUSION') +set confusion = if(o.concept_id is null, null,'1' ); -- panic attack -UPDATE temp_covid_visit SET panic_attack = OBS_SINGLE_VALUE_CODED(encounter_id, 'CIEL', '1728', 'CIEL', '130967'); +-- UPDATE temp_covid_visit SET panic_attack = OBS_SINGLE_VALUE_CODED(encounter_id, 'CIEL', '1728', 'CIEL', '130967'); +update temp_covid_visit t +inner join temp_covid_obs o on o.encounter_id = t.encounter_id + and o.concept_id = concept_from_mapping('CIEL', '1728') + and o.value_coded = concept_from_mapping( 'CIEL', '130967') +set panic_attack = if(o.concept_id is null, null,'1' ); -- suicidal thoughts -UPDATE temp_covid_visit SET suicidal_thoughts = OBS_SINGLE_VALUE_CODED(encounter_id, 'CIEL', '1728', 'CIEL', '125562'); +-- UPDATE temp_covid_visit SET suicidal_thoughts = OBS_SINGLE_VALUE_CODED(encounter_id, 'CIEL', '1728', 'CIEL', '125562'); +update temp_covid_visit t +inner join temp_covid_obs o on o.encounter_id = t.encounter_id + and o.concept_id = concept_from_mapping('CIEL', '1728') + and o.value_coded = concept_from_mapping('CIEL', '125562') +set suicidal_thoughts = if(o.concept_id is null, null,'1' ); -- attempted suicide -UPDATE temp_covid_visit SET attempted_suicide = OBS_SINGLE_VALUE_CODED(encounter_id, 'CIEL', '1728', 'CIEL', '148143'); - --- Symptom name, uncoded (text) -UPDATE temp_covid_visit SET other_symptom = OBS_VALUE_TEXT(encounter_id, 'CIEL', '165996'); +-- UPDATE temp_covid_visit SET attempted_suicide = OBS_SINGLE_VALUE_CODED(encounter_id, 'CIEL', '1728', 'CIEL', '148143'); +update temp_covid_visit t +inner join temp_covid_obs o on o.encounter_id = t.encounter_id + and o.concept_id = concept_from_mapping('CIEL', '1728') + and o.value_coded = concept_from_mapping( 'CIEL', '148143') +set attempted_suicide = if(o.concept_id is null, null,'1' ); --- vitals -UPDATE temp_covid_visit SET temp = OBS_VALUE_NUMERIC(encounter_id, 'CIEL', '5088'); -UPDATE temp_covid_visit SET heart_rate = OBS_VALUE_NUMERIC(encounter_id, 'CIEL', '5087'); -UPDATE temp_covid_visit SET respiratory_rate = OBS_VALUE_NUMERIC(encounter_id, 'CIEL', '5242'); - -UPDATE temp_covid_visit SET bp_systolic = OBS_VALUE_NUMERIC(encounter_id, 'CIEL', '5085'); +-- Symptom name, uncoded (text) +-- UPDATE temp_covid_visit SET other_symptom = OBS_VALUE_TEXT(encounter_id, 'CIEL', '165996'); +update temp_covid_visit t +inner join temp_covid_obs o on o.encounter_id = t.encounter_id and o.concept_id = concept_from_mapping('CIEL', '165996') +set t.other_symptom = o.value_text +; -UPDATE temp_covid_visit SET bp_diastolic = OBS_VALUE_NUMERIC(encounter_id, 'CIEL', '5086'); -UPDATE temp_covid_visit SET SpO2 = OBS_VALUE_NUMERIC(encounter_id, 'CIEL', '5092'); +-- vitals +-- UPDATE temp_covid_visit SET temp = OBS_VALUE_NUMERIC(encounter_id, 'CIEL', '5088'); +update temp_covid_visit t +inner join temp_covid_obs o on o.encounter_id = t.encounter_id and o.concept_id = concept_from_mapping('CIEL', '5088') +set t.temp = o.value_numeric +; + +-- UPDATE temp_covid_visit SET heart_rate = OBS_VALUE_NUMERIC(encounter_id, 'CIEL', '5087'); +update temp_covid_visit t +inner join temp_covid_obs o on o.encounter_id = t.encounter_id and o.concept_id = concept_from_mapping('CIEL', '5087') +set t.heart_rate = o.value_numeric +; + +-- UPDATE temp_covid_visit SET respiratory_rate = OBS_VALUE_NUMERIC(encounter_id, 'CIEL', '5242'); +update temp_covid_visit t +inner join temp_covid_obs o on o.encounter_id = t.encounter_id and o.concept_id = concept_from_mapping('CIEL', '5242') +set t.respiratory_rate = o.value_numeric +; + +-- UPDATE temp_covid_visit SET bp_systolic = OBS_VALUE_NUMERIC(encounter_id, 'CIEL', '5085'); +update temp_covid_visit t +inner join temp_covid_obs o on o.encounter_id = t.encounter_id and o.concept_id = concept_from_mapping('CIEL', '5085') +set t.bp_systolic = o.value_numeric +; + +-- UPDATE temp_covid_visit SET bp_diastolic = OBS_VALUE_NUMERIC(encounter_id, 'CIEL', '5086'); +update temp_covid_visit t +inner join temp_covid_obs o on o.encounter_id = t.encounter_id and o.concept_id = concept_from_mapping('CIEL', '5086') +set t.bp_diastolic = o.value_numeric +; + +-- UPDATE temp_covid_visit SET SpO2 = OBS_VALUE_NUMERIC(encounter_id, 'CIEL', '5092'); +update temp_covid_visit t +inner join temp_covid_obs o on o.encounter_id = t.encounter_id and o.concept_id = concept_from_mapping('CIEL', '5092') +set t.SpO2 = o.value_numeric +; -- room air -UPDATE temp_covid_visit SET room_air = OBS_SINGLE_VALUE_CODED(encounter_id, 'CIEL', '162739', 'CIEL', '162735'); +-- UPDATE temp_covid_visit SET room_air = OBS_SINGLE_VALUE_CODED(encounter_id, 'CIEL', '162739', 'CIEL', '162735'); +update temp_covid_visit t +inner join temp_covid_obs o on o.encounter_id = t.encounter_id + and o.concept_id = concept_from_mapping('CIEL', '162739') + and o.value_coded = concept_from_mapping('CIEL', '162735') +set room_air = if(o.concept_id is null, null,'1' ); --- Cap refill and Cap refill time -UPDATE temp_covid_visit SET cap_refill = OBS_VALUE_CODED_LIST(encounter_id, 'CIEL', '165890', 'en'); -UPDATE temp_covid_visit SET cap_refill_time = OBS_VALUE_NUMERIC(encounter_id, 'CIEL', '162513'); +-- Cap refill and Cap refill time +-- UPDATE temp_covid_visit SET cap_refill = OBS_VALUE_CODED_LIST(encounter_id, 'CIEL', '165890', 'en'); +update temp_covid_visit t +inner join + (select o.encounter_id, GROUP_CONCAT(distinct concept_name(o.value_coded,'en') separator ' | ') as ret + from temp_covid_obs o + where o.concept_id = concept_from_mapping('CIEL', '165890') + group by o.encounter_id) i on i.encounter_id = t.encounter_id +set t.cap_refill = i.ret; + +-- UPDATE temp_covid_visit SET cap_refill_time = OBS_VALUE_NUMERIC(encounter_id, 'CIEL', '162513'); +update temp_covid_visit t +inner join temp_covid_obs o on o.encounter_id = t.encounter_id and o.concept_id = concept_from_mapping('CIEL', '162513') +set t.cap_refill_time = o.value_numeric +; -- Pain -UPDATE temp_covid_visit SET pain = OBS_VALUE_CODED_LIST(encounter_id, 'CIEL', '166000', 'en'); +-- UPDATE temp_covid_visit SET pain = OBS_VALUE_CODED_LIST(encounter_id, 'CIEL', '166000', 'en'); +update temp_covid_visit t +inner join + (select o.encounter_id, GROUP_CONCAT(distinct concept_name(o.value_coded,'en') separator ' | ') as ret + from temp_covid_obs o + where o.concept_id = concept_from_mapping('CIEL', '166000') + group by o.encounter_id) i on i.encounter_id = t.encounter_id +set t.pain = i.ret; + ########## Phyical Exams -UPDATE temp_covid_visit SET general_exam = OBS_VALUE_CODED_LIST(encounter_id, 'CIEL', '1119', 'en'); -UPDATE temp_covid_visit SET general_findings = OBS_VALUE_TEXT(encounter_id, 'CIEL', '163042'); +-- UPDATE temp_covid_visit SET general_exam = OBS_VALUE_CODED_LIST(encounter_id, 'CIEL', '1119', 'en'); +update temp_covid_visit t +inner join + (select o.encounter_id, GROUP_CONCAT(distinct concept_name(o.value_coded,'en') separator ' | ') as ret + from temp_covid_obs o + where o.concept_id = concept_from_mapping('CIEL', '1119') + group by o.encounter_id) i on i.encounter_id = t.encounter_id +set t.general_exam = i.ret; + +-- UPDATE temp_covid_visit SET general_findings = OBS_VALUE_TEXT(encounter_id, 'CIEL', '163042'); +update temp_covid_visit t +inner join temp_covid_obs o on o.encounter_id = t.encounter_id and o.concept_id = concept_from_mapping('CIEL', '163042') +set t.general_findings = o.value_text; -- HEENT -UPDATE temp_covid_visit SET heent = OBS_VALUE_CODED_LIST(encounter_id, 'CIEL', '1122', 'en'); -UPDATE temp_covid_visit SET heent_findings = OBS_VALUE_TEXT(encounter_id, 'CIEL', '163045'); +-- UPDATE temp_covid_visit SET heent = OBS_VALUE_CODED_LIST(encounter_id, 'CIEL', '1122', 'en'); +update temp_covid_visit t +inner join + (select o.encounter_id, GROUP_CONCAT(distinct concept_name(o.value_coded,'en') separator ' | ') as ret + from temp_covid_obs o + where o.concept_id = concept_from_mapping('CIEL', '1122') + group by o.encounter_id) i on i.encounter_id = t.encounter_id +set t.heent = i.ret; + +-- UPDATE temp_covid_visit SET heent_findings = OBS_VALUE_TEXT(encounter_id, 'CIEL', '163045'); +update temp_covid_visit t +inner join temp_covid_obs o on o.encounter_id = t.encounter_id and o.concept_id = concept_from_mapping('CIEL', '163045') +set t.heent_findings = o.value_text; -- Neck -UPDATE temp_covid_visit SET neck = OBS_VALUE_CODED_LIST(encounter_id, 'CIEL', '163388', 'en'); -UPDATE temp_covid_visit SET neck_findings = OBS_VALUE_TEXT(encounter_id, 'CIEL', '165983'); +-- UPDATE temp_covid_visit SET neck = OBS_VALUE_CODED_LIST(encounter_id, 'CIEL', '163388', 'en'); +update temp_covid_visit t +inner join + (select o.encounter_id, GROUP_CONCAT(distinct concept_name(o.value_coded,'en') separator ' | ') as ret + from temp_covid_obs o + where o.concept_id = concept_from_mapping('CIEL', '163388') + group by o.encounter_id) i on i.encounter_id = t.encounter_id +set t.neck = i.ret; + +-- UPDATE temp_covid_visit SET neck_findings = OBS_VALUE_TEXT(encounter_id, 'CIEL', '165983'); +update temp_covid_visit t +inner join temp_covid_obs o on o.encounter_id = t.encounter_id and o.concept_id = concept_from_mapping('CIEL', '165983') +set t.neck_findings = o.value_text +; -- chest -UPDATE temp_covid_visit SET chest = OBS_VALUE_CODED_LIST(encounter_id, 'CIEL', '1123', 'en'); -UPDATE temp_covid_visit SET chest_findings = OBS_VALUE_TEXT(encounter_id, 'CIEL', '160689'); +-- UPDATE temp_covid_visit SET chest = OBS_VALUE_CODED_LIST(encounter_id, 'CIEL', '1123', 'en'); +update temp_covid_visit t +inner join + (select o.encounter_id, GROUP_CONCAT(distinct concept_name(o.value_coded,'en') separator ' | ') as ret + from temp_covid_obs o + where o.concept_id = concept_from_mapping('CIEL', '1123') + group by o.encounter_id) i on i.encounter_id = t.encounter_id +set t.chest = i.ret; + +-- UPDATE temp_covid_visit SET chest_findings = OBS_VALUE_TEXT(encounter_id, 'CIEL', '160689'); +update temp_covid_visit t +inner join temp_covid_obs o on o.encounter_id = t.encounter_id and o.concept_id = concept_from_mapping('CIEL', '160689') +set t.chest_findings = o.value_text +; -- cardiac -UPDATE temp_covid_visit SET cardiac = OBS_VALUE_CODED_LIST(encounter_id, 'CIEL', '1124', 'en'); -UPDATE temp_covid_visit SET cardiac_findings = OBS_VALUE_TEXT(encounter_id, 'CIEL', '163046'); +-- UPDATE temp_covid_visit SET cardiac = OBS_VALUE_CODED_LIST(encounter_id, 'CIEL', '1124', 'en'); +update temp_covid_visit t +inner join + (select o.encounter_id, GROUP_CONCAT(distinct concept_name(o.value_coded,'en') separator ' | ') as ret + from temp_covid_obs o + where o.concept_id = concept_from_mapping('CIEL', '1124') + group by o.encounter_id) i on i.encounter_id = t.encounter_id +set t.cardiac = i.ret; + +-- UPDATE temp_covid_visit SET cardiac_findings = OBS_VALUE_TEXT(encounter_id, 'CIEL', '163046'); +update temp_covid_visit t +inner join temp_covid_obs o on o.encounter_id = t.encounter_id and o.concept_id = concept_from_mapping('CIEL', '163046') +set t.cardiac_findings = o.value_text +; -- abdominal -UPDATE temp_covid_visit SET abdominal = OBS_VALUE_CODED_LIST(encounter_id, 'CIEL', '1125', 'en'); -UPDATE temp_covid_visit SET abdominal_findings = OBS_VALUE_TEXT(encounter_id, 'CIEL', '160947'); +-- UPDATE temp_covid_visit SET abdominal = OBS_VALUE_CODED_LIST(encounter_id, 'CIEL', '1125', 'en'); +update temp_covid_visit t +inner join + (select o.encounter_id, GROUP_CONCAT(distinct concept_name(o.value_coded,'en') separator ' | ') as ret + from temp_covid_obs o + where o.concept_id = concept_from_mapping('CIEL', '1125') + group by o.encounter_id) i on i.encounter_id = t.encounter_id +set t.abdominal = i.ret; + +-- UPDATE temp_covid_visit SET abdominal_findings = OBS_VALUE_TEXT(encounter_id, 'CIEL', '160947'); +update temp_covid_visit t +inner join temp_covid_obs o on o.encounter_id = t.encounter_id and o.concept_id = concept_from_mapping('CIEL', '160947') +set t.abdominal_findings = o.value_text +; -- urogenital -UPDATE temp_covid_visit SET urogenital = OBS_VALUE_CODED_LIST(encounter_id, 'CIEL', '1126', 'en'); -UPDATE temp_covid_visit SET urogenital_findings = OBS_VALUE_TEXT(encounter_id, 'CIEL', '163047'); +-- UPDATE temp_covid_visit SET urogenital = OBS_VALUE_CODED_LIST(encounter_id, 'CIEL', '1126', 'en'); +update temp_covid_visit t +inner join + (select o.encounter_id, GROUP_CONCAT(distinct concept_name(o.value_coded,'en') separator ' | ') as ret + from temp_covid_obs o + where o.concept_id = concept_from_mapping('CIEL', '1126') + group by o.encounter_id) i on i.encounter_id = t.encounter_id +set t.urogenital = i.ret; + +-- UPDATE temp_covid_visit SET urogenital_findings = OBS_VALUE_TEXT(encounter_id, 'CIEL', '163047'); +update temp_covid_visit t +inner join temp_covid_obs o on o.encounter_id = t.encounter_id and o.concept_id = concept_from_mapping('CIEL', '163047') +set t.urogenital_findings = o.value_text +; -- rectal -UPDATE temp_covid_visit SET rectal = OBS_VALUE_CODED_LIST(encounter_id, 'CIEL', '163746', 'en'); -UPDATE temp_covid_visit SET rectal_findings = OBS_VALUE_TEXT(encounter_id, 'CIEL', '160961'); +-- UPDATE temp_covid_visit SET rectal = OBS_VALUE_CODED_LIST(encounter_id, 'CIEL', '163746', 'en'); +update temp_covid_visit t +inner join + (select o.encounter_id, GROUP_CONCAT(distinct concept_name(o.value_coded,'en') separator ' | ') as ret + from temp_covid_obs o + where o.concept_id = concept_from_mapping('CIEL', '163746') + group by o.encounter_id) i on i.encounter_id = t.encounter_id +set t.rectal = i.ret; + +-- UPDATE temp_covid_visit SET rectal_findings = OBS_VALUE_TEXT(encounter_id, 'CIEL', '160961'); +update temp_covid_visit t +inner join temp_covid_obs o on o.encounter_id = t.encounter_id and o.concept_id = concept_from_mapping('CIEL', '160961') +set t.rectal_findings = o.value_text +; -- musculoskeletal -UPDATE temp_covid_visit SET musculoskeletal = OBS_VALUE_CODED_LIST(encounter_id, 'CIEL', '1128', 'en'); -UPDATE temp_covid_visit SET musculoskeletal_findings = OBS_VALUE_TEXT(encounter_id, 'CIEL', '163048'); +-- UPDATE temp_covid_visit SET musculoskeletal = OBS_VALUE_CODED_LIST(encounter_id, 'CIEL', '1128', 'en'); +update temp_covid_visit t +inner join + (select o.encounter_id, GROUP_CONCAT(distinct concept_name(o.value_coded,'en') separator ' | ') as ret + from temp_covid_obs o + where o.concept_id = concept_from_mapping('CIEL', '1128') + group by o.encounter_id) i on i.encounter_id = t.encounter_id +set t.musculoskeletal = i.ret; + +-- UPDATE temp_covid_visit SET musculoskeletal_findings = OBS_VALUE_TEXT(encounter_id, 'CIEL', '163048'); +update temp_covid_visit t +inner join temp_covid_obs o on o.encounter_id = t.encounter_id and o.concept_id = concept_from_mapping('CIEL', '163048') +set t.musculoskeletal_findings = o.value_text +; -- lymph -UPDATE temp_covid_visit SET lymph = OBS_VALUE_CODED_LIST(encounter_id, 'CIEL', '1121', 'en'); -UPDATE temp_covid_visit SET lymph_findings = OBS_VALUE_TEXT(encounter_id, 'CIEL', '166005'); +-- UPDATE temp_covid_visit SET lymph = OBS_VALUE_CODED_LIST(encounter_id, 'CIEL', '1121', 'en'); +update temp_covid_visit t +inner join + (select o.encounter_id, GROUP_CONCAT(distinct concept_name(o.value_coded,'en') separator ' | ') as ret + from temp_covid_obs o + where o.concept_id = concept_from_mapping('CIEL', '1121') + group by o.encounter_id) i on i.encounter_id = t.encounter_id +set t.lymph = i.ret; + +-- UPDATE temp_covid_visit SET lymph_findings = OBS_VALUE_TEXT(encounter_id, 'CIEL', '166005'); +update temp_covid_visit t +inner join temp_covid_obs o on o.encounter_id = t.encounter_id and o.concept_id = concept_from_mapping('CIEL', '166005') +set t.lymph_findings = o.value_text +; -- skin -UPDATE temp_covid_visit SET skin = OBS_VALUE_CODED_LIST(encounter_id, 'CIEL', '1120', 'en'); -UPDATE temp_covid_visit SET skin_findings = OBS_VALUE_TEXT(encounter_id, 'CIEL', '160981'); +-- UPDATE temp_covid_visit SET skin = OBS_VALUE_CODED_LIST(encounter_id, 'CIEL', '1120', 'en'); +update temp_covid_visit t +inner join + (select o.encounter_id, GROUP_CONCAT(distinct concept_name(o.value_coded,'en') separator ' | ') as ret + from temp_covid_obs o + where o.concept_id = concept_from_mapping('CIEL', '1120') + group by o.encounter_id) i on i.encounter_id = t.encounter_id +set t.skin = i.ret; + +-- UPDATE temp_covid_visit SET skin_findings = OBS_VALUE_TEXT(encounter_id, 'CIEL', '160981'); +update temp_covid_visit t +inner join temp_covid_obs o on o.encounter_id = t.encounter_id and o.concept_id = concept_from_mapping('CIEL', '160981') +set t.skin_findings = o.value_text +; -- neuro -UPDATE temp_covid_visit SET neuro = OBS_VALUE_CODED_LIST(encounter_id, 'CIEL', '1129', 'en'); -UPDATE temp_covid_visit SET neuro_findings = OBS_VALUE_TEXT(encounter_id, 'CIEL', '163109'); +-- UPDATE temp_covid_visit SET neuro = OBS_VALUE_CODED_LIST(encounter_id, 'CIEL', '1129', 'en'); +update temp_covid_visit t +inner join + (select o.encounter_id, GROUP_CONCAT(distinct concept_name(o.value_coded,'en') separator ' | ') as ret + from temp_covid_obs o + where o.concept_id = concept_from_mapping('CIEL', '1129') + group by o.encounter_id) i on i.encounter_id = t.encounter_id +set t.neuro = i.ret; + +-- UPDATE temp_covid_visit SET neuro_findings = OBS_VALUE_TEXT(encounter_id, 'CIEL', '163109'); +update temp_covid_visit t +inner join temp_covid_obs o on o.encounter_id = t.encounter_id and o.concept_id = concept_from_mapping('CIEL', '163109') +set t.neuro_findings = o.value_text +; -- avpu -UPDATE temp_covid_visit SET avpu = OBS_VALUE_CODED_LIST(encounter_id, 'CIEL', '162643', 'en'); +-- UPDATE temp_covid_visit SET avpu = OBS_VALUE_CODED_LIST(encounter_id, 'CIEL', '162643', 'en'); +update temp_covid_visit t +inner join + (select o.encounter_id, GROUP_CONCAT(distinct concept_name(o.value_coded,'en') separator ' | ') as ret + from temp_covid_obs o + where o.concept_id = concept_from_mapping('CIEL', '162643') + group by o.encounter_id) i on i.encounter_id = t.encounter_id +set t.avpu = i.ret; -- other -UPDATE temp_covid_visit SET other_findings = OBS_VALUE_TEXT(encounter_id, 'CIEL', '163042'); +-- UPDATE temp_covid_visit SET other_findings = OBS_VALUE_TEXT(encounter_id, 'CIEL', '163042'); +update temp_covid_visit t +inner join temp_covid_obs o on o.encounter_id = t.encounter_id and o.concept_id = concept_from_mapping('CIEL', '163045') +set t.heent_findings = o.value_text +; -- Awake -UPDATE temp_covid_visit SET awake = OBS_SINGLE_VALUE_CODED(encounter_id, 'CIEL', '162643', 'CIEL', '160282'); +-- UPDATE temp_covid_visit SET awake = OBS_SINGLE_VALUE_CODED(encounter_id, 'CIEL', '162643', 'CIEL', '160282'); + +update temp_covid_visit t +inner join temp_covid_obs o on o.encounter_id = t.encounter_id + and o.concept_id = concept_from_mapping('CIEL', '162643') + and o.value_coded = concept_from_mapping('CIEL', '160282') +set awake = if(o.concept_id is null, null,'1' ); + -- Responds to pain -UPDATE temp_covid_visit SET pain_response = OBS_SINGLE_VALUE_CODED(encounter_id, 'CIEL', '162643', 'CIEL', '162644'); +-- UPDATE temp_covid_visit SET pain_response = OBS_SINGLE_VALUE_CODED(encounter_id, 'CIEL', '162643', 'CIEL', '162644'); +update temp_covid_visit t +inner join temp_covid_obs o on o.encounter_id = t.encounter_id + and o.concept_id = concept_from_mapping('CIEL', '162643') + and o.value_coded = concept_from_mapping('CIEL', '162644') +set pain_response = if(o.concept_id is null, null,'1' ) +; + -- Responds to voice -UPDATE temp_covid_visit SET voice_response = OBS_SINGLE_VALUE_CODED(encounter_id, 'CIEL', '162643', 'CIEL', '162645'); +-- UPDATE temp_covid_visit SET voice_response = OBS_SINGLE_VALUE_CODED(encounter_id, 'CIEL', '162643', 'CIEL', '162645'); +update temp_covid_visit t +inner join temp_covid_obs o on o.encounter_id = t.encounter_id + and o.concept_id = concept_from_mapping('CIEL', '162643') + and o.value_coded = concept_from_mapping('CIEL', '162645') +set voice_response = if(o.concept_id is null, null,'1' ) +; -- Unresponsive -UPDATE temp_covid_visit SET unresponsive = OBS_SINGLE_VALUE_CODED(encounter_id, 'CIEL', '162643', 'CIEL', '159508'); +-- UPDATE temp_covid_visit SET unresponsive = OBS_SINGLE_VALUE_CODED(encounter_id, 'CIEL', '162643', 'CIEL', '159508'); +update temp_covid_visit t +inner join temp_covid_obs o on o.encounter_id = t.encounter_id + and o.concept_id = concept_from_mapping('CIEL', '162643') + and o.value_coded = concept_from_mapping('CIEL', '159508') +set unresponsive = if(o.concept_id is null, null,'1' ) +; -- dexamethasone -UPDATE temp_covid_visit SET dexamethasone = OBS_SINGLE_VALUE_CODED(encounter_id, 'PIH', 'Medication Orders', 'PIH', 'Dexamethasone'); +-- UPDATE temp_covid_visit SET dexamethasone = OBS_SINGLE_VALUE_CODED(encounter_id, 'PIH', 'Medication Orders', 'PIH', 'Dexamethasone'); +update temp_covid_visit t +inner join temp_covid_obs o on o.encounter_id = t.encounter_id + and o.concept_id = concept_from_mapping('PIH', 'Medication Orders') + and o.value_coded = concept_from_mapping('PIH', 'Dexamethasone') +set dexamethasone = if(o.concept_id is null, null,'1' ) +; -- lpv/r -UPDATE temp_covid_visit SET lpv_r = OBS_SINGLE_VALUE_CODED(encounter_id, 'PIH', 'Medication Orders', 'CIEL', '794'); +-- UPDATE temp_covid_visit SET lpv_r = OBS_SINGLE_VALUE_CODED(encounter_id, 'PIH', 'Medication Orders', 'CIEL', '794'); +update temp_covid_visit t +inner join temp_covid_obs o on o.encounter_id = t.encounter_id + and o.concept_id = concept_from_mapping('PIH', 'Medication Orders') + and o.value_coded = concept_from_mapping('CIEL', '794') +set lpv_r = if(o.concept_id is null, null,'1' ) +; -- remdesivir -UPDATE temp_covid_visit SET remdesivir = OBS_SINGLE_VALUE_CODED(encounter_id, 'PIH', 'Medication Orders', 'CIEL', '165878'); +-- UPDATE temp_covid_visit SET remdesivir = OBS_SINGLE_VALUE_CODED(encounter_id, 'PIH', 'Medication Orders', 'CIEL', '165878'); +update temp_covid_visit t +inner join temp_covid_obs o on o.encounter_id = t.encounter_id + and o.concept_id = concept_from_mapping('PIH', 'Medication Orders') + and o.value_coded = concept_from_mapping('CIEL', '165878') +set remdesivir = if(o.concept_id is null, null,'1' ) +; -- ceftriaxone -UPDATE temp_covid_visit SET ceftriaxone = OBS_SINGLE_VALUE_CODED(encounter_id, 'PIH', 'Medication Orders', 'PIH', 'CEFTRIAXONE'); +-- UPDATE temp_covid_visit SET ceftriaxone = OBS_SINGLE_VALUE_CODED(encounter_id, 'PIH', 'Medication Orders', 'PIH', 'CEFTRIAXONE'); +update temp_covid_visit t +inner join temp_covid_obs o on o.encounter_id = t.encounter_id + and o.concept_id = concept_from_mapping('PIH', 'Medication Orders') + and o.value_coded = concept_from_mapping('PIH', 'CEFTRIAXONE') +set ceftriaxone = if(o.concept_id is null, null,'1' ) +; -- amoxicillin -UPDATE temp_covid_visit SET amoxicillin = OBS_SINGLE_VALUE_CODED(encounter_id, 'PIH', 'Medication Orders', 'PIH', 'AMOXICILLIN'); - +-- UPDATE temp_covid_visit SET amoxicillin = OBS_SINGLE_VALUE_CODED(encounter_id, 'PIH', 'Medication Orders', 'PIH', 'AMOXICILLIN'); +update temp_covid_visit t +inner join temp_covid_obs o on o.encounter_id = t.encounter_id + and o.concept_id = concept_from_mapping('PIH', 'Medication Orders') + and o.value_coded = concept_from_mapping('PIH', 'AMOXICILLIN') +set amoxicillin = if(o.concept_id is null, null,'1' ) +; -- doxycycline -UPDATE temp_covid_visit SET doxycycline = OBS_SINGLE_VALUE_CODED(encounter_id, 'PIH', 'Medication Orders', 'PIH', 'DOXYCYCLINE'); - +-- UPDATE temp_covid_visit SET doxycycline = OBS_SINGLE_VALUE_CODED(encounter_id, 'PIH', 'Medication Orders', 'PIH', 'DOXYCYCLINE'); +update temp_covid_visit t +inner join temp_covid_obs o on o.encounter_id = t.encounter_id + and o.concept_id = concept_from_mapping('PIH', 'Medication Orders') + and o.value_coded = concept_from_mapping('PIH', 'DOXYCYCLINE') +set doxycycline = if(o.concept_id is null, null,'1' ) +; -- other_medication -UPDATE temp_covid_visit SET other_medication = OBS_VALUE_TEXT(encounter_id, 'PIH', 'Medication comments (text)'); +-- UPDATE temp_covid_visit SET other_medication = OBS_VALUE_TEXT(encounter_id, 'PIH', 'Medication comments (text)'); +update temp_covid_visit t +inner join temp_covid_obs o on o.encounter_id = t.encounter_id and o.concept_id = concept_from_mapping('PIH', 'Medication comments (text)') +set t.other_medication = o.value_text +; -- supportive care -UPDATE temp_covid_visit SET supportive_care = OBS_VALUE_CODED_LIST(encounter_id, 'CIEL', '165995', 'en'); +-- UPDATE temp_covid_visit SET supportive_care = OBS_VALUE_CODED_LIST(encounter_id, 'CIEL', '165995', 'en'); +update temp_covid_visit t +inner join + (select o.encounter_id, GROUP_CONCAT(distinct concept_name(o.value_coded,'en') separator ' | ') as ret + from temp_covid_obs o + where o.concept_id = concept_from_mapping('CIEL', '165995') + group by o.encounter_id) i on i.encounter_id = t.encounter_id +set t.supportive_care = i.ret; -- o2therapy value -UPDATE temp_covid_visit SET o2therapy = OBS_VALUE_NUMERIC(encounter_id, 'CIEL', '165986'); +-- UPDATE temp_covid_visit SET o2therapy = OBS_VALUE_NUMERIC(encounter_id, 'CIEL', '165986'); +update temp_covid_visit t +inner join temp_covid_obs o on o.encounter_id = t.encounter_id and o.concept_id = concept_from_mapping( 'CIEL', '165986') +set t.o2therapy = o.value_numeric +; + -- analgesic comments/description -UPDATE temp_covid_visit SET analgesic_specified = OBS_VALUE_TEXT(encounter_id, 'CIEL', '163206'); +-- UPDATE temp_covid_visit SET analgesic_specified = OBS_VALUE_TEXT(encounter_id, 'CIEL', '163206'); +update temp_covid_visit t +inner join temp_covid_obs o on o.encounter_id = t.encounter_id and o.concept_id = concept_from_mapping( 'CIEL', '163206') +set t.analgesic_specified = o.value_numeric +; -- oxygen -UPDATE temp_covid_visit SET oxygen = OBS_SINGLE_VALUE_CODED(encounter_id, 'CIEL', '165995', 'CIEL', '81341'); +-- UPDATE temp_covid_visit SET oxygen = OBS_SINGLE_VALUE_CODED(encounter_id, 'CIEL', '165995', 'CIEL', '81341'); +update temp_covid_visit t +inner join temp_covid_obs o on o.encounter_id = t.encounter_id + and o.concept_id = concept_from_mapping( 'CIEL', '165995') + and o.value_coded = concept_from_mapping('CIEL', '81341') +set oxygen = if(o.concept_id is null, null,'1' ) +; + -- ventilator -UPDATE temp_covid_visit SET ventilator = OBS_SINGLE_VALUE_CODED(encounter_id, 'CIEL', '165995', 'CIEL', '165998'); +-- UPDATE temp_covid_visit SET ventilator = OBS_SINGLE_VALUE_CODED(encounter_id, 'CIEL', '165995', 'CIEL', '165998'); +update temp_covid_visit t +inner join temp_covid_obs o on o.encounter_id = t.encounter_id + and o.concept_id = concept_from_mapping( 'CIEL', '165995') + and o.value_coded = concept_from_mapping('CIEL', '165998') +set ventilator = if(o.concept_id is null, null,'1' ) +; -- mask -UPDATE temp_covid_visit SET mask = OBS_SINGLE_VALUE_CODED(encounter_id, 'CIEL', '165995', 'CIEL', '165989'); - +-- UPDATE temp_covid_visit SET mask = OBS_SINGLE_VALUE_CODED(encounter_id, 'CIEL', '165995', 'CIEL', '165989'); +update temp_covid_visit t +inner join temp_covid_obs o on o.encounter_id = t.encounter_id + and o.concept_id = concept_from_mapping( 'CIEL', '165995') + and o.value_coded = concept_from_mapping('CIEL', '165989') +set mask = if(o.concept_id is null, null,'1' ) +; -- mask with non breather -UPDATE temp_covid_visit SET mask_with_nonbreather = OBS_SINGLE_VALUE_CODED(encounter_id, 'CIEL', '165995', 'CIEL', '165990'); - +-- UPDATE temp_covid_visit SET mask_with_nonbreather = OBS_SINGLE_VALUE_CODED(encounter_id, 'CIEL', '165995', 'CIEL', '165990'); +update temp_covid_visit t +inner join temp_covid_obs o on o.encounter_id = t.encounter_id + and o.concept_id = concept_from_mapping( 'CIEL', '165995') + and o.value_coded = concept_from_mapping('CIEL', '165990') +set mask_with_nonbreather = if(o.concept_id is null, null,'1' ) +; -- nasal cannula -UPDATE temp_covid_visit SET nasal_cannula = OBS_SINGLE_VALUE_CODED(encounter_id, 'CIEL', '165995', 'CIEL', '165893'); - +-- UPDATE temp_covid_visit SET nasal_cannula = OBS_SINGLE_VALUE_CODED(encounter_id, 'CIEL', '165995', 'CIEL', '165893'); +update temp_covid_visit t +inner join temp_covid_obs o on o.encounter_id = t.encounter_id + and o.concept_id = concept_from_mapping( 'CIEL', '165995') + and o.value_coded = concept_from_mapping('CIEL', '165893') +set nasal_cannula = if(o.concept_id is null, null,'1' ) +; -- cpap -UPDATE temp_covid_visit SET cpap = OBS_SINGLE_VALUE_CODED(encounter_id, 'CIEL', '165995', 'CIEL', '165944'); - +-- UPDATE temp_covid_visit SET cpap = OBS_SINGLE_VALUE_CODED(encounter_id, 'CIEL', '165995', 'CIEL', '165944'); +update temp_covid_visit t +inner join temp_covid_obs o on o.encounter_id = t.encounter_id + and o.concept_id = concept_from_mapping( 'CIEL', '165995') + and o.value_coded = concept_from_mapping('CIEL', '165944') +set cpap = if(o.concept_id is null, null,'1' ) +; -- bpap -UPDATE temp_covid_visit SET bpap = OBS_SINGLE_VALUE_CODED(encounter_id, 'CIEL', '165995', 'CIEL', '165988'); - +-- UPDATE temp_covid_visit SET bpap = OBS_SINGLE_VALUE_CODED(encounter_id, 'CIEL', '165995', 'CIEL', '165988'); +update temp_covid_visit t +inner join temp_covid_obs o on o.encounter_id = t.encounter_id + and o.concept_id = concept_from_mapping( 'CIEL', '165995') + and o.value_coded = concept_from_mapping('CIEL', '165988') +set bpap = if(o.concept_id is null, null,'1' ) +; -- fio2 -UPDATE temp_covid_visit SET fio2 = OBS_SINGLE_VALUE_CODED(encounter_id, 'CIEL', '165995', 'CIEL', '165927'); - +-- UPDATE temp_covid_visit SET fio2 = OBS_SINGLE_VALUE_CODED(encounter_id, 'CIEL', '165995', 'CIEL', '165927'); +update temp_covid_visit t +inner join temp_covid_obs o on o.encounter_id = t.encounter_id + and o.concept_id = concept_from_mapping( 'CIEL', '165995') + and o.value_coded = concept_from_mapping('CIEL', '165927') +set fio2 = if(o.concept_id is null, null,'1' ) +; -- ivf fluid -UPDATE temp_covid_visit SET ivf_fluid = OBS_SINGLE_VALUE_CODED(encounter_id, 'CIEL', '165995', 'CIEL', '161911'); - +-- UPDATE temp_covid_visit SET ivf_fluid = OBS_SINGLE_VALUE_CODED(encounter_id, 'CIEL', '165995', 'CIEL', '161911'); +update temp_covid_visit t +inner join temp_covid_obs o on o.encounter_id = t.encounter_id + and o.concept_id = concept_from_mapping( 'CIEL', '165995') + and o.value_coded = concept_from_mapping('CIEL', '161911') +set ivf_fluid = if(o.concept_id is null, null,'1' ) +; ##### Lab Results -UPDATE temp_covid_visit SET hemoglobin = OBS_VALUE_NUMERIC(encounter_id, 'CIEL', '21'); - -UPDATE temp_covid_visit SET hematocrit = OBS_VALUE_NUMERIC(encounter_id, 'CIEL', '1015'); - -UPDATE temp_covid_visit SET wbc = OBS_VALUE_NUMERIC(encounter_id, 'CIEL', '678'); - -UPDATE temp_covid_visit SET platelets = OBS_VALUE_NUMERIC(encounter_id, 'CIEL', '729'); - -UPDATE temp_covid_visit SET lymphocyte = OBS_VALUE_NUMERIC(encounter_id, 'CIEL', '952'); - -UPDATE temp_covid_visit SET neutrophil = OBS_VALUE_NUMERIC(encounter_id, 'CIEL', '1330'); - -UPDATE temp_covid_visit SET crp = OBS_VALUE_NUMERIC(encounter_id, 'CIEL', '161500'); - -UPDATE temp_covid_visit SET sodium = OBS_VALUE_NUMERIC(encounter_id, 'CIEL', '1132'); - -UPDATE temp_covid_visit SET potassium = OBS_VALUE_NUMERIC(encounter_id, 'CIEL', '1133'); - -UPDATE temp_covid_visit SET urea = OBS_VALUE_NUMERIC(encounter_id, 'CIEL', '857'); - -UPDATE temp_covid_visit SET creatinine = OBS_VALUE_NUMERIC(encounter_id, 'CIEL', '790'); - -UPDATE temp_covid_visit SET glucose = OBS_VALUE_NUMERIC(encounter_id, 'CIEL', '887'); - -UPDATE temp_covid_visit SET bilirubin = OBS_VALUE_NUMERIC(encounter_id, 'CIEL', '655'); - -UPDATE temp_covid_visit SET sgpt = OBS_VALUE_NUMERIC(encounter_id, 'CIEL', '654'); - -UPDATE temp_covid_visit SET sgot = OBS_VALUE_NUMERIC(encounter_id, 'CIEL', '653'); - -UPDATE temp_covid_visit SET pH = OBS_VALUE_NUMERIC(encounter_id, 'CIEL', '165984'); - -UPDATE temp_covid_visit SET pcO2 = OBS_VALUE_NUMERIC(encounter_id, 'CIEL', '163595'); - -UPDATE temp_covid_visit SET pO2 = OBS_VALUE_NUMERIC(encounter_id, 'CIEL', '163598'); - -UPDATE temp_covid_visit SET tcO2 = OBS_VALUE_NUMERIC(encounter_id, 'CIEL', '166002'); - -UPDATE temp_covid_visit SET hcO3 = OBS_VALUE_NUMERIC(encounter_id, 'CIEL', '163596'); - -UPDATE temp_covid_visit SET be = OBS_VALUE_NUMERIC(encounter_id, 'CIEL', '163599'); - -UPDATE temp_covid_visit SET sO2 = OBS_VALUE_NUMERIC(encounter_id, 'CIEL', '163597'); - -UPDATE temp_covid_visit SET lactate = OBS_VALUE_NUMERIC(encounter_id, 'CIEL', '165997'); - +-- UPDATE temp_covid_visit SET hemoglobin = OBS_VALUE_NUMERIC(encounter_id, 'CIEL', '21'); +update temp_covid_visit t +inner join temp_covid_obs o on o.encounter_id = t.encounter_id and o.concept_id = concept_from_mapping('CIEL', '21') +set t.hemoglobin = o.value_numeric +; + +-- UPDATE temp_covid_visit SET hematocrit = OBS_VALUE_NUMERIC(encounter_id, 'CIEL', '1015'); +update temp_covid_visit t +inner join temp_covid_obs o on o.encounter_id = t.encounter_id and o.concept_id = concept_from_mapping('CIEL', '1015') +set t.hematocrit = o.value_numeric +; +-- UPDATE temp_covid_visit SET wbc = OBS_VALUE_NUMERIC(encounter_id, 'CIEL', '678'); +update temp_covid_visit t +inner join temp_covid_obs o on o.encounter_id = t.encounter_id and o.concept_id = concept_from_mapping('CIEL', '678') +set t.wbc = o.value_numeric +; +-- UPDATE temp_covid_visit SET platelets = OBS_VALUE_NUMERIC(encounter_id, 'CIEL', '729'); +update temp_covid_visit t +inner join temp_covid_obs o on o.encounter_id = t.encounter_id and o.concept_id = concept_from_mapping('CIEL', '729') +set t.platelets = o.value_numeric +; +-- UPDATE temp_covid_visit SET lymphocyte = OBS_VALUE_NUMERIC(encounter_id, 'CIEL', '952'); +update temp_covid_visit t +inner join temp_covid_obs o on o.encounter_id = t.encounter_id and o.concept_id = concept_from_mapping('CIEL', '952') +set t.lymphocyte = o.value_numeric +; +-- UPDATE temp_covid_visit SET neutrophil = OBS_VALUE_NUMERIC(encounter_id, 'CIEL', '1330'); +update temp_covid_visit t +inner join temp_covid_obs o on o.encounter_id = t.encounter_id and o.concept_id = concept_from_mapping('CIEL', '1330') +set t.neutrophil = o.value_numeric +; +-- UPDATE temp_covid_visit SET crp = OBS_VALUE_NUMERIC(encounter_id, 'CIEL', '161500'); +update temp_covid_visit t +inner join temp_covid_obs o on o.encounter_id = t.encounter_id and o.concept_id = concept_from_mapping('CIEL', '161500') +set t.crp = o.value_numeric +; +-- UPDATE temp_covid_visit SET sodium = OBS_VALUE_NUMERIC(encounter_id, 'CIEL', '1132'); +update temp_covid_visit t +inner join temp_covid_obs o on o.encounter_id = t.encounter_id and o.concept_id = concept_from_mapping('CIEL', '1132') +set t.sodium = o.value_numeric +; +-- UPDATE temp_covid_visit SET potassium = OBS_VALUE_NUMERIC(encounter_id, 'CIEL', '1133'); +update temp_covid_visit t +inner join temp_covid_obs o on o.encounter_id = t.encounter_id and o.concept_id = concept_from_mapping('CIEL', '1133') +set t.potassium = o.value_numeric +; +-- UPDATE temp_covid_visit SET urea = OBS_VALUE_NUMERIC(encounter_id, 'CIEL', '857'); +update temp_covid_visit t +inner join temp_covid_obs o on o.encounter_id = t.encounter_id and o.concept_id = concept_from_mapping('CIEL', '857') +set t.urea = o.value_numeric +; +-- UPDATE temp_covid_visit SET creatinine = OBS_VALUE_NUMERIC(encounter_id, 'CIEL', '790'); +update temp_covid_visit t +inner join temp_covid_obs o on o.encounter_id = t.encounter_id and o.concept_id = concept_from_mapping('CIEL', '790') +set t.creatinine = o.value_numeric +; +-- UPDATE temp_covid_visit SET glucose = OBS_VALUE_NUMERIC(encounter_id, 'CIEL', '887'); +update temp_covid_visit t +inner join temp_covid_obs o on o.encounter_id = t.encounter_id and o.concept_id = concept_from_mapping('CIEL', '887') +set t.temp = o.value_numeric +; +-- UPDATE temp_covid_visit SET bilirubin = OBS_VALUE_NUMERIC(encounter_id, 'CIEL', '655'); +update temp_covid_visit t +inner join temp_covid_obs o on o.encounter_id = t.encounter_id and o.concept_id = concept_from_mapping('CIEL', '655') +set t.glucose = o.value_numeric +; +-- UPDATE temp_covid_visit SET sgpt = OBS_VALUE_NUMERIC(encounter_id, 'CIEL', '654'); +update temp_covid_visit t +inner join temp_covid_obs o on o.encounter_id = t.encounter_id and o.concept_id = concept_from_mapping('CIEL', '654') +set t.sgpt = o.value_numeric +; +-- UPDATE temp_covid_visit SET sgot = OBS_VALUE_NUMERIC(encounter_id, 'CIEL', '653'); +update temp_covid_visit t +inner join temp_covid_obs o on o.encounter_id = t.encounter_id and o.concept_id = concept_from_mapping('CIEL', '653') +set t.sgot = o.value_numeric +; +-- UPDATE temp_covid_visit SET pH = OBS_VALUE_NUMERIC(encounter_id, 'CIEL', '165984'); +update temp_covid_visit t +inner join temp_covid_obs o on o.encounter_id = t.encounter_id and o.concept_id = concept_from_mapping('CIEL', '165984') +set t.pH = o.value_numeric +; +-- UPDATE temp_covid_visit SET pcO2 = OBS_VALUE_NUMERIC(encounter_id, 'CIEL', '163595'); +update temp_covid_visit t +inner join temp_covid_obs o on o.encounter_id = t.encounter_id and o.concept_id = concept_from_mapping('CIEL', '163595') +set t.pcO2 = o.value_numeric +; +-- UPDATE temp_covid_visit SET pO2 = OBS_VALUE_NUMERIC(encounter_id, 'CIEL', '163598'); +update temp_covid_visit t +inner join temp_covid_obs o on o.encounter_id = t.encounter_id and o.concept_id = concept_from_mapping('CIEL', '163598') +set t.pO2 = o.value_numeric +; +-- UPDATE temp_covid_visit SET tcO2 = OBS_VALUE_NUMERIC(encounter_id, 'CIEL', '166002'); +update temp_covid_visit t +inner join temp_covid_obs o on o.encounter_id = t.encounter_id and o.concept_id = concept_from_mapping('CIEL', '166002') +set t.tcO2 = o.value_numeric +; +-- UPDATE temp_covid_visit SET hcO3 = OBS_VALUE_NUMERIC(encounter_id, 'CIEL', '163596'); +update temp_covid_visit t +inner join temp_covid_obs o on o.encounter_id = t.encounter_id and o.concept_id = concept_from_mapping('CIEL', '163596') +set t.hcO3 = o.value_numeric +; +-- UPDATE temp_covid_visit SET be = OBS_VALUE_NUMERIC(encounter_id, 'CIEL', '163599'); +update temp_covid_visit t +inner join temp_covid_obs o on o.encounter_id = t.encounter_id and o.concept_id = concept_from_mapping('CIEL', '163599') +set t.be = o.value_numeric +; +-- UPDATE temp_covid_visit SET sO2 = OBS_VALUE_NUMERIC(encounter_id, 'CIEL', '163597'); +update temp_covid_visit t +inner join temp_covid_obs o on o.encounter_id = t.encounter_id and o.concept_id = concept_from_mapping('CIEL', '163597') +set t.sO2 = o.value_numeric +; +-- UPDATE temp_covid_visit SET lactate = OBS_VALUE_NUMERIC(encounter_id, 'CIEL', '165997'); +update temp_covid_visit t +inner join temp_covid_obs o on o.encounter_id = t.encounter_id and o.concept_id = concept_from_mapping('CIEL', '165997') +set t.lactate = o.value_numeric +; -- clinical management plan -UPDATE temp_covid_visit te SET clinical_management_plan = OBS_VALUE_TEXT(encounter_id, 'CIEL', '162749'); - +-- UPDATE temp_covid_visit te SET clinical_management_plan = OBS_VALUE_TEXT(encounter_id, 'CIEL', '162749'); +update temp_covid_visit t +inner join temp_covid_obs o on o.encounter_id = t.encounter_id and o.concept_id = concept_from_mapping('CIEL', '162749') +set t.clinical_management_plan = o.value_text +; -- nursing note -UPDATE temp_covid_visit SET nursing_note = OBS_VALUE_TEXT(encounter_id, 'CIEL', '166021'); - +-- UPDATE temp_covid_visit SET nursing_note = OBS_VALUE_TEXT(encounter_id, 'CIEL', '166021'); +update temp_covid_visit t +inner join temp_covid_obs o on o.encounter_id = t.encounter_id and o.concept_id = concept_from_mapping('CIEL', '166021') +set t.nursing_note = o.value_text +; -- mh referral -UPDATE temp_covid_visit SET mh_referral = OBS_SINGLE_VALUE_CODED(encounter_id, 'CIEL', '1272', 'PIH', '5489'); - +-- UPDATE temp_covid_visit SET mh_referral = OBS_SINGLE_VALUE_CODED(encounter_id, 'CIEL', '1272', 'PIH', '5489'); +update temp_covid_visit t +inner join temp_covid_obs o on o.encounter_id = t.encounter_id + and o.concept_id = concept_from_mapping( 'CIEL', '1272') + and o.value_coded = concept_from_mapping('PIH', '5489') +set mh_referral = if(o.concept_id is null, null,'1' ) +; -- mh note -UPDATE temp_covid_visit SET mh_note = OBS_FROM_GROUP_ID_VALUE_TEXT(OBS_ID(encounter_id,'PIH','12837',0), 'CIEL', '161011'); - +-- UPDATE temp_covid_visit SET mh_note = OBS_FROM_GROUP_ID_VALUE_TEXT(OBS_ID(encounter_id,'PIH','12837',0), 'CIEL', '161011'); + +update temp_covid_visit t +inner join temp_covid_obs o on o.encounter_id = t.encounter_id + and o.concept_id = concept_from_mapping('PIH','12837') +set t.mh_note_obs_group_id = o.obs_id; + +update temp_covid_visit t +inner join temp_covid_obs o on o.obs_group_id = t.mh_note_obs_group_id + and o.concept_id = concept_from_mapping('PIH','161011') +set t.mh_note = o.value_text +; -- Chest x-ray -UPDATE temp_covid_visit SET x_ray = OBS_SINGLE_VALUE_CODED(encounter_id, 'PIH', '9485', 'PIH', 'Chest 1 view (XRay)'); - +-- UPDATE temp_covid_visit SET x_ray = OBS_SINGLE_VALUE_CODED(encounter_id, 'PIH', '9485', 'PIH', 'Chest 1 view (XRay)'); +update temp_covid_visit t +inner join temp_covid_obs o on o.encounter_id = t.encounter_id + and o.concept_id = concept_from_mapping('PIH', '9485') + and o.value_coded = concept_from_mapping('PIH', 'Chest 1 view (XRay)') +set x_ray = if(o.concept_id is null, null,'1' ) +; -- Cardiac ultrasound -UPDATE temp_covid_visit SET cardiac_ultrasound = OBS_SINGLE_VALUE_CODED(encounter_id, 'PIH', '9485', 'PIH', 'Transthoracic echocardiogram'); +-- UPDATE temp_covid_visit SET cardiac_ultrasound = OBS_SINGLE_VALUE_CODED(encounter_id, 'PIH', '9485', 'PIH', 'Transthoracic echocardiogram'); +update temp_covid_visit t +inner join temp_covid_obs o on o.encounter_id = t.encounter_id + and o.concept_id = concept_from_mapping('PIH', '9485') + and o.value_coded = concept_from_mapping('PIH', 'Transthoracic echocardiogram') +set cardiac_ultrasound = if(o.concept_id is null, null,'1' ) +; -- Abdominal ultrasound -UPDATE temp_covid_visit SET abdominal_ultrasound = OBS_SINGLE_VALUE_CODED(encounter_id, 'PIH', '9485', 'PIH', 'Abdomen (US)'); - +-- UPDATE temp_covid_visit SET abdominal_ultrasound = OBS_SINGLE_VALUE_CODED(encounter_id, 'PIH', '9485', 'PIH', 'Abdomen (US)'); +update temp_covid_visit t +inner join temp_covid_obs o on o.encounter_id = t.encounter_id + and o.concept_id = concept_from_mapping('PIH', '9485') + and o.value_coded = concept_from_mapping('PIH', 'Abdomen (US)') +set abdominal_ultrasound = if(o.concept_id is null, null,'1' ) +; -- index ascending DROP TEMPORARY TABLE IF EXISTS temp_index_asc; CREATE TEMPORARY TABLE temp_index_asc @@ -494,7 +1060,9 @@ FROM (SELECT (SELECT @u:= 0) AS u ORDER BY patient_id, encounter_id DESC ) index_descending ); - + +create index temp_index_asc_ei on temp_index_asc(encounter_id); +create index temp_index_desc_ei on temp_index_desc(encounter_id); #### Final query SELECT @@ -619,4 +1187,4 @@ FROM temp_covid_visit tcv LEFT JOIN temp_index_asc on tcv.encounter_id = temp_index_asc.encounter_id -- index descending LEFT JOIN temp_index_desc on tcv.encounter_id = temp_index_desc.encounter_id -order by tcv.patient_id, tcv.encounter_id ASC; \ No newline at end of file +order by tcv.patient_id, tcv.encounter_id ASC;