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fix and add sql queries for the public siorgp dashboard #205

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merged 1 commit into from
Feb 7, 2025
Merged

fix and add sql queries for the public siorgp dashboard #205

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2 changes: 1 addition & 1 deletion resources/sql/SIORGP_PUBLIC_MAIN → resources/sql/SIORGP_PUBLIC_METPREDICT
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Original file line number Diff line number Diff line change
Expand Up @@ -29,7 +29,7 @@ select t.value as pat_pseudonym,
t7.value as location_primary_tumor_precise,
t3.value as therapy,
t4.value as metastases_therapy,
t6.value::integer as age_at_enrollment
t6.value::numeric as age_at_enrollment
from t
left join t t2 on t.pat_ref = t2.pat_ref and t2.code='SIOP_LOCALISATION_PRIMARY_TUMOR'
left join t t3 on t.pat_ref = t3.pat_ref and t3.code='SIOP_NEOADJ_T_RECTAL_CARCINOMA'
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46 changes: 46 additions & 0 deletions resources/sql/SIORGP_PUBLIC_NEOMATCH
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Original file line number Diff line number Diff line change
@@ -0,0 +1,46 @@
/* SIorgP NeoMatch project
The approach chosen here is to minimize the number of tasks generated and thus network traffic via Beam
=> one large query that returns all the most necessary fields over multiple smaller queries
*/
with t as (
select
o.resource->'subject'->>'reference' as pat_ref,
o.resource->'code'->'coding'->0->>'code' as crf,
component->'code'->'coding'->0->>'code' AS code,
COALESCE(
component->'valueCodeableConcept'->'coding'->0->>'code',
component->>'valueDateTime',
component->'valueQuantity'->>'value',
component->>'valueString'
) AS value
FROM
observation o ,
jsonb_array_elements(o.resource->'component') AS component
where o.resource->'code'->'coding'->0->>'code' like 'SIOrgP%'
),
t2 AS (
select t.value as pat_pseudonym,
t2.value as gender,
t6.value::numeric as age_at_enrollment
from t
left join t t2 on t.pat_ref = t2.pat_ref and t2.code='SIOP_GENDER'
left join t t6 on t.pat_ref = t6.pat_ref and t6.code='SIOP_AGE_STUDY_ENROLLMENT'
left join patient p on t.pat_ref = 'Patient/' || (p.resource->>'id')::text
where t.crf like 'SIOrgP - NeoMatch - Visite 1%' and t.code = 'SIOP_PATIENT_PSEUDONYM'
)
-- the total number of patients
select 'NeoMatch' as project, 'n_patients' as field, (select count(distinct pat_pseudonym) from t2) as value
union
select 'NeoMatch' as project, 'gender_male' as field, (select count(distinct pat_pseudonym) from t2 where gender = 'MALE') as value
union
select 'NeoMatch' as project, 'gender_female' as field, (select count(distinct pat_pseudonym) from t2 where gender = 'FEMALE') as value
union
select 'NeoMatch' as project, '<=30' as field, (select count(distinct pat_pseudonym) from t2 where age_at_enrollment <= 30) as value
union
select 'NeoMatch' as project, '31-40' as field, (select count(distinct pat_pseudonym) from t2 where age_at_enrollment >= 31 and age_at_enrollment <= 40) as value
union
select 'NeoMatch' as project, '41-50' as field, (select count(distinct pat_pseudonym) from t2 where age_at_enrollment >= 41 and age_at_enrollment <= 50) as value
union
select 'NeoMatch' as project, '51-60' as field, (select count(distinct pat_pseudonym) from t2 where age_at_enrollment >= 51 and age_at_enrollment <= 60) as value
union
select 'NeoMatch' as project, '>=61' as field, (select count(distinct pat_pseudonym) from t2 where age_at_enrollment >= 61) as value;