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Merge pull request #474 from njorocs/idsr-enhancements
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Added mode of temperature collection and mode of oxygen saturation co…
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@patryllus
patryllus authored Aug 14, 2024
2 parents e90103e + e61f48e commit 4f58602
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Showing 6 changed files with 22 additions and 4 deletions.
2 changes: 2 additions & 0 deletions omod/src/main/resources/sql/DDL.sql
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Expand Up @@ -1605,9 +1605,11 @@ SELECT "Successfully created etl_ART_preparation table";
systolic_pressure DOUBLE,
diastolic_pressure DOUBLE,
temperature DOUBLE,
temperature_collection_mode INT(11),
pulse_rate DOUBLE,
respiratory_rate DOUBLE,
oxygen_saturation DOUBLE,
oxygen_saturation_collection_mode INT(11),
muac DOUBLE,
z_score_absolute DOUBLE DEFAULT NULL,
z_score INT(11),
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6 changes: 5 additions & 1 deletion omod/src/main/resources/sql/DML.sql
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Expand Up @@ -3440,9 +3440,11 @@ CREATE PROCEDURE sp_populate_etl_patient_triage()
systolic_pressure,
diastolic_pressure,
temperature,
temperature_collection_mode,
pulse_rate,
respiratory_rate,
oxygen_saturation,
oxygen_saturation_collection_mode,
muac,
z_score_absolute,
z_score,
Expand Down Expand Up @@ -3470,9 +3472,11 @@ CREATE PROCEDURE sp_populate_etl_patient_triage()
max(if(o.concept_id=5085,o.value_numeric,null)) as systolic_pressure,
max(if(o.concept_id=5086,o.value_numeric,null)) as diastolic_pressure,
max(if(o.concept_id=5088,o.value_numeric,null)) as temperature,
max(if(o.concept_id=167231,o.value_coded,null)) as temperature_collection_mode,
max(if(o.concept_id=5087,o.value_numeric,null)) as pulse_rate,
max(if(o.concept_id=5242,o.value_numeric,null)) as respiratory_rate,
max(if(o.concept_id=5092,o.value_numeric,null)) as oxygen_saturation,
max(if(o.concept_id=165932,o.value_coded,null)) as oxygen_saturation_collection_mode,
max(if(o.concept_id=1343,o.value_numeric,null)) as muac,
max(if(o.concept_id=162584,o.value_numeric,null)) as z_score_absolute,
max(if(o.concept_id=163515,o.value_coded,null)) as z_score,
Expand All @@ -3489,7 +3493,7 @@ CREATE PROCEDURE sp_populate_etl_patient_triage()
select encounter_type_id, uuid, name from encounter_type where uuid in('d1059fb9-a079-4feb-a749-eedd709ae542','a0034eee-1940-4e35-847f-97537a35d05e','465a92f2-baf8-42e9-9612-53064be868e8')
) et on et.encounter_type_id=e.encounter_type
left outer join obs o on o.encounter_id=e.encounter_id and o.voided=0
and o.concept_id in (160430,1154,159368,5089,5090,5085,5086,5088,5087,5242,5092,1343,163515,167392,1427,160325,162584,163304)
and o.concept_id in (160430,1154,159368,5089,5090,5085,5086,5088,5087,5242,5092,1343,163515,167392,1427,160325,162584,163304,167231,165932)
where e.voided=0
group by e.patient_id, visit_date
;
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2 changes: 2 additions & 0 deletions omod/src/main/resources/sql/DataTools.sql
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Original file line number Diff line number Diff line change
Expand Up @@ -1225,9 +1225,11 @@ SELECT "Successfully created enhanced adherence table";
systolic_pressure,
diastolic_pressure,
temperature,
case temperature_collection_mode when 5112 then 'Axiliary' when 166242 then 'Forehead thermometer gun' when 160240 then 'Oral' end as temperature_collection_mode,
pulse_rate,
respiratory_rate,
oxygen_saturation,
case oxygen_saturation_collection_mode when 162735 then 'Room air' when 162738 then 'On supplemental oxygen' end as oxygen_saturation_collection_mode,
muac,
z_score_absolute,
(case z_score when 1115 then "Normal (Median)" when 123814 then "Mild (-1 SD)" when 123815 then "Moderate (-2 SD)" when 164131 then "Severe (-3 SD and -4 SD)" else "" end) as z_score,
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8 changes: 6 additions & 2 deletions omod/src/main/resources/sql/Scheduled_Updates.sql
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Expand Up @@ -3366,9 +3366,11 @@ CREATE PROCEDURE sp_update_etl_patient_triage(IN last_update_time DATETIME)
systolic_pressure,
diastolic_pressure,
temperature,
temperature_collection_mode,
pulse_rate,
respiratory_rate,
oxygen_saturation,
oxygen_saturation_collection_mode,
muac,
z_score_absolute,
z_score,
Expand Down Expand Up @@ -3396,9 +3398,11 @@ CREATE PROCEDURE sp_update_etl_patient_triage(IN last_update_time DATETIME)
max(if(o.concept_id=5085,o.value_numeric,null)) as systolic_pressure,
max(if(o.concept_id=5086,o.value_numeric,null)) as diastolic_pressure,
max(if(o.concept_id=5088,o.value_numeric,null)) as temperature,
max(if(o.concept_id=167231,o.value_coded,null)) as temperature_collection_mode,
max(if(o.concept_id=5087,o.value_numeric,null)) as pulse_rate,
max(if(o.concept_id=5242,o.value_numeric,null)) as respiratory_rate,
max(if(o.concept_id=5092,o.value_numeric,null)) as oxygen_saturation,
max(if(o.concept_id=165932,o.value_coded,null)) as oxygen_saturation_collection_mode,
max(if(o.concept_id=1343,o.value_numeric,null)) as muac,
max(if(o.concept_id=162584,o.value_numeric,null)) as z_score_absolute,
max(if(o.concept_id=163515,o.value_coded,null)) as z_score,
Expand All @@ -3414,7 +3418,7 @@ CREATE PROCEDURE sp_update_etl_patient_triage(IN last_update_time DATETIME)
select encounter_type_id, uuid, name from encounter_type where uuid in('d1059fb9-a079-4feb-a749-eedd709ae542','a0034eee-1940-4e35-847f-97537a35d05e','465a92f2-baf8-42e9-9612-53064be868e8')
) et on et.encounter_type_id=e.encounter_type
left outer join obs o on o.encounter_id=e.encounter_id and o.voided=0
and o.concept_id in (160430,5089,5090,5085,5086,5088,5087,5242,5092,1343,163515,167392,1427,160325,162584,1154,159368,163304)
and o.concept_id in (160430,5089,5090,5085,5086,5088,5087,5242,5092,1343,163515,167392,1427,160325,162584,1154,159368,163304,167231,165932)
where e.voided=0 and e.date_created >= last_update_time
or e.date_changed >= last_update_time
or e.date_voided >= last_update_time
Expand All @@ -3423,7 +3427,7 @@ CREATE PROCEDURE sp_update_etl_patient_triage(IN last_update_time DATETIME)
group by e.patient_id, visit_date
ON DUPLICATE KEY UPDATE visit_date=VALUES(visit_date),encounter_provider=VALUES(encounter_provider),weight=VALUES(weight),height=VALUES(height),systolic_pressure=VALUES(systolic_pressure),diastolic_pressure=VALUES(diastolic_pressure),
temperature=VALUES(temperature),pulse_rate=VALUES(pulse_rate),respiratory_rate=VALUES(respiratory_rate),complaint_today=VALUES(complaint_today),complaint_duration=VALUES(complaint_duration),
oxygen_saturation=VALUES(oxygen_saturation),muac=VALUES(muac),z_score=VALUES(z_score),nutritional_status=VALUES(nutritional_status),nutritional_intervention=VALUES(nutritional_intervention),last_menstrual_period=VALUES(last_menstrual_period),hpv_vaccinated=VALUES(hpv_vaccinated),voided=VALUES(voided),z_score_absolute=VALUES(z_score_absolute);
oxygen_saturation=VALUES(oxygen_saturation),muac=VALUES(muac),z_score=VALUES(z_score),nutritional_status=VALUES(nutritional_status),nutritional_intervention=VALUES(nutritional_intervention),last_menstrual_period=VALUES(last_menstrual_period),hpv_vaccinated=VALUES(hpv_vaccinated),voided=VALUES(voided),z_score_absolute=VALUES(z_score_absolute),oxygen_saturation_collection_mode=VALUES(oxygen_saturation_collection_mode),temperature_collection_mode=VALUES(temperature_collection_mode);

END $$
-- ------------- populate etl_generalized_anxiety_disorder-------------------------
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2 changes: 2 additions & 0 deletions omod/src/main/resources/sql/dwapi/DDL.sql
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Original file line number Diff line number Diff line change
Expand Up @@ -1580,9 +1580,11 @@ SELECT "Successfully created etl_ART_preparation table";
systolic_pressure DOUBLE,
diastolic_pressure DOUBLE,
temperature DOUBLE,
temperature_collection_mode INT(11),
pulse_rate DOUBLE,
respiratory_rate DOUBLE,
oxygen_saturation DOUBLE,
oxygen_saturation_collection_mode INT(11),
muac DOUBLE,
z_score_absolute DOUBLE DEFAULT NULL,
z_score INT(11),
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6 changes: 5 additions & 1 deletion omod/src/main/resources/sql/dwapi/DML.sql
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Original file line number Diff line number Diff line change
Expand Up @@ -3275,9 +3275,11 @@ CREATE PROCEDURE sp_populate_dwapi_patient_triage()
systolic_pressure,
diastolic_pressure,
temperature,
temperature_collection_mode,
pulse_rate,
respiratory_rate,
oxygen_saturation,
oxygen_saturation_collection_mode,
muac,
z_score_absolute,
z_score,
Expand Down Expand Up @@ -3305,9 +3307,11 @@ CREATE PROCEDURE sp_populate_dwapi_patient_triage()
max(if(o.concept_id=5085,o.value_numeric,null)) as systolic_pressure,
max(if(o.concept_id=5086,o.value_numeric,null)) as diastolic_pressure,
max(if(o.concept_id=5088,o.value_numeric,null)) as temperature,
max(if(o.concept_id=167231,o.value_coded,null)) as temperature_collection_mode,
max(if(o.concept_id=5087,o.value_numeric,null)) as pulse_rate,
max(if(o.concept_id=5242,o.value_numeric,null)) as respiratory_rate,
max(if(o.concept_id=5092,o.value_numeric,null)) as oxygen_saturation,
max(if(o.concept_id=165932,o.value_coded,null)) as oxygen_saturation_collection_mode,
max(if(o.concept_id=1343,o.value_numeric,null)) as muac,
max(if(o.concept_id=162584,o.value_numeric,null)) as z_score_absolute,
max(if(o.concept_id=163515,o.value_coded,null)) as z_score,
Expand All @@ -3324,7 +3328,7 @@ CREATE PROCEDURE sp_populate_dwapi_patient_triage()
select encounter_type_id, uuid, name from encounter_type where uuid in('d1059fb9-a079-4feb-a749-eedd709ae542','a0034eee-1940-4e35-847f-97537a35d05e','465a92f2-baf8-42e9-9612-53064be868e8')
) et on et.encounter_type_id=e.encounter_type
left outer join obs o on o.encounter_id=e.encounter_id and o.voided=0
and o.concept_id in (160430,1154,159368,5089,5090,5085,5086,5088,5087,5242,5092,1343,163515,167392,1427,160325,162584)
and o.concept_id in (160430,1154,159368,5089,5090,5085,5086,5088,5087,5242,5092,1343,163515,167392,1427,160325,162584,163304,167231,165932)
group by e.patient_id, visit_date
;
SELECT "Completed processing Patient Triage data ", CONCAT("Time: ", NOW());
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