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Merge pull request #1 from JaspreetKhanna/patch-1
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Changed PatientClinicalCourse SQL.
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@avillach
avillach authored Nov 3, 2020
2 parents 8a79d0f + 220355c commit ac09c6b
Showing 1 changed file with 58 additions and 38 deletions.
96 changes: 58 additions & 38 deletions Phase2.1DataExtractionOracle.sql
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Original file line number Diff line number Diff line change
Expand Up @@ -14,6 +14,10 @@
--!!! This is Oracle version of 4CE Phase 2.0 mssql script
--!!! This script has SQL blocks and based on settings in covid_config and config2
--!!! tables selectively they have to be executed.
--!!! Changed PatientClinicalCourse SQL.
--!!! Changed days_since_admission
--!!! Added siteid to all the files extracted
--!!! Fix for the wrong death_date (showing up as a future date) has not been applied in this release
--!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
--------------------------------------------------------------------------------
-- General settings
Expand Down Expand Up @@ -66,6 +70,7 @@ create table PatientSummary (

alter table PatientSummary add primary key (patient_num);

-- Truncate table PatientSummary ;

insert INTO patientsummary (
siteid,
Expand Down Expand Up @@ -130,26 +135,33 @@ create table PatientClinicalCourse (
--select * from PatientClinicalCourse ;
alter table PatientClinicalCourse add primary key (patient_num, days_since_admission);

-- truncate table PatientClinicalCourse ;

insert into PatientClinicalCourse (siteid, patient_num, days_since_admission, calendar_date, in_hospital, severe, deceased)
select distinct '@', p.patient_num,
round(d.d - p.admission_date) days_since_admission,
d.d calendar_date,
max(case when a.patient_num is not null then 1 else 0 end) in_hospital,
max(case when p.severe=1 and d.d>=p.severe_date then 1 else 0 end) severe,
max(case when p.deceased=1 and d.d>=p.death_date then 1 else 0 end) deceased
from PatientSummary p
inner join covid_date_list_temp d --date_list d
on d.d>=p.admission_date and d.d<=p.last_discharge_date
left outer join covid_admissions a
on a.patient_num=p.patient_num
and a.admission_date>=p.admission_date
and a.admission_date<=d.d
and a.discharge_date>=d.d
group by p.patient_num, p.admission_date, d.d
;

commit;
select siteid,patient_num,days_since_admission, calendar_date,
case when in_hospital is not null then 1 else 0 end in_hospital,
severe,
case when death_date is not null then 1 else 0 end DECEASED
from
(select '@' siteid, days_since_admission, patient_num,
count(*) in_hospital,
sum(severe) severe,
max(admission_date) admission_date,
max(death_date) death_date,
max(d) calendar_date
from (
select distinct trunc(d.d)-trunc(c.admission_date) days_since_admission, d.d,c.admission_date,death_date,
c.patient_num, severe
from covid_date_list_temp d
inner join covid_admissions p
on trunc(p.admission_date)<=trunc(d.d) and trunc(p.discharge_date)>=trunc(d.d)
inner join covid_cohort c
on p.patient_num=c.patient_num and trunc(p.admission_date)>=trunc(c.admission_date)
) t
group by days_since_admission,patient_num
) ;
commit;


--------------------------------------------------------------------------------
-- Patient Observations: Selected Data Facts
Expand All @@ -166,11 +178,13 @@ create table PatientObservations (

alter table PatientObservations add primary key (patient_num, concept_type, concept_code, days_since_admission);

-- truncate table PatientObservations ;

-- Diagnoses (3 character ICD9 codes) since 365 days before COVID
insert into PatientObservations (siteid, patient_num, days_since_admission, concept_type, concept_code, value)
select distinct '@',
p.patient_num,
trunc(cast(f.start_date as date) - p.admission_date),
trunc(f.start_date) - trunc(p.admission_date) days_since_admission,
'DIAG-ICD9',
substr(substr(f.concept_cd, length(code_prefix_icd9cm)+1, 999), 1, 3) icd_code_3chars ,
-999
Expand All @@ -186,7 +200,7 @@ insert into PatientObservations (siteid, patient_num, days_since_admission, conc
insert into PatientObservations (siteid, patient_num, days_since_admission, concept_type, concept_code, value)
select distinct '@',
p.patient_num,
trunc(cast(f.start_date as date) - p.admission_date),
trunc(f.start_date) - trunc(p.admission_date) days_since_admission,
'DIAG-ICD10',
substr(substr(f.concept_cd, length(code_prefix_icd10cm)+1, 999), 1, 3) icd_code_3chars,
-999
Expand All @@ -195,14 +209,14 @@ insert into PatientObservations (siteid, patient_num, days_since_admission, conc
inner join covid_cohort p
on f.patient_num=p.patient_num
and f.start_date >= (p.admission_date -365)
where concept_cd like code_prefix_icd10cm||'%' and code_prefix_icd10cm is not null;
where concept_cd like code_prefix_icd10cm||'%' ; --and code_prefix_icd10cm is not null;

commit;
-- Medications (Med Class) since 365 days before COVID
insert into PatientObservations (siteid, patient_num, days_since_admission, concept_type, concept_code, value)
select distinct '@',
p.patient_num,
trunc(cast(f.start_date as date) - p.admission_date),
trunc(f.start_date) - trunc(p.admission_date) days_since_admission,
'MED-CLASS',
m.med_class,
-999
Expand All @@ -218,7 +232,7 @@ insert into PatientObservations (siteid, patient_num, days_since_admission, conc
insert into PatientObservations (siteid, patient_num, days_since_admission, concept_type, concept_code, value)
select '@',
f.patient_num,
trunc(cast(f.start_date as date) - p.admission_date),
trunc(f.start_date) - trunc(p.admission_date) days_since_admission,
'LAB-LOINC',
l.loinc,
avg(f.nval_num*l.scale_factor)
Expand All @@ -232,13 +246,13 @@ insert into PatientObservations (siteid, patient_num, days_since_admission, conc
and f.nval_num >= 0
and f.start_date >= ( p.admission_date -60)
and l.scale_factor is not null
group by f.patient_num,trunc(cast(f.start_date as date) - p.admission_date) , l.loinc;
group by f.patient_num, trunc(f.start_date) - trunc(p.admission_date) , l.loinc;
commit;
-- Procedures (ICD9) each day since COVID (only procedures used in 4CE Phase 1.1 to determine severity)
insert into PatientObservations (siteid, patient_num, days_since_admission, concept_type, concept_code, value)
select distinct '@',
p.patient_num,
trunc(cast(f.start_date as date) - p.admission_date),
trunc(f.start_date) - trunc(p.admission_date) days_since_admission,
'PROC-ICD9',
substr(f.concept_cd, length(code_prefix_icd9proc)+1, 999),
-999
Expand All @@ -259,7 +273,7 @@ commit;

insert into PatientObservations (siteid, patient_num, days_since_admission, concept_type, concept_code, value)
select distinct '@', p.patient_num,
trunc(cast(f.start_date as date) - p.admission_date) ,
trunc(f.start_date) - trunc(p.admission_date) days_since_admission,
'PROC-ICD10',
substr(f.concept_cd, length(code_prefix_icd10pcs)+1, 999) ,
-999
Expand Down Expand Up @@ -296,6 +310,8 @@ create table PatientMapping (

alter table PatientMapping add primary key (patient_num, study_num);

-- truncate table PatientMapping ;

set serveroutput on
declare

Expand Down Expand Up @@ -427,14 +443,15 @@ end;
--To generate data extract files, run listed SQLs

-- File #1: PatientSummary.csv
--spool 'PatientSummary.csv' ;
--spool 'LocalPatientSummary.csv' ;
select s PatientSummaryCSV
from (
select 0 i, 'patient_num,admission_date,days_since_admission,last_discharge_date,still_in_hospital,'
select 0 i, 'siteid,patient_num,admission_date,days_since_admission,last_discharge_date,still_in_hospital,'
||'severe_date,severe,death_date,deceased,sex,age_group,race,race_collected' S FROM DUAL
union all
select row_number() over (order by admission_date, patient_num) i,
cast(patient_num as varchar2(50))
siteid
||','||cast(patient_num as varchar2(50))
||','||to_char(admission_date,'YYYY-MM-DD') --YYYY-MM-DD
||','||to_char(days_since_admission)
||','||to_char(last_discharge_date,'YYYY-MM-DD') --YYYY-MM-DD
Expand All @@ -457,13 +474,14 @@ end;


-- File #2: PatientClinicalCourse.csv
--spool 'PatientClinicalCourse.csv' ;
--spool 'LocalPatientClinicalCourse.csv' ;
select s PatientClinicalCourseCSV
from (
select 0 i, 'patient_num,days_since_admission,calendar_date,in_hospital,severe,deceased' s FROM DUAL
select 0 i, 'siteid,patient_num,days_since_admission,calendar_date,in_hospital,severe,deceased' s FROM DUAL
union all
select row_number() over (order by patient_num, days_since_admission) i,
cast(patient_num as varchar2(50))
siteid
||','||cast(patient_num as varchar2(50))
||','||to_char(days_since_admission)
||','||to_char(calendar_date,'YYYY-MM-DD') --YYYY-MM-DD
||','||to_char(in_hospital)
Expand All @@ -476,13 +494,14 @@ end;
--spool off;
-- File #3: PatientObservations.csv

--spool PatientObservations.csv
--spool LocalPatientObservations.csv
select s PatientObservationsCSV
from (
select 0 i, 'patient_num,days_since_admission,concept_type,concept_code,value' s FROM DUAL
select 0 i, 'siteid,patient_num,days_since_admission,concept_type,concept_code,value' s FROM DUAL
union all
select row_number() over (order by patient_num, concept_type, concept_code, days_since_admission) i,
cast(patient_num as varchar2(50))
siteid
||','||cast(patient_num as varchar2(50))
||','||to_char(days_since_admission)
||','||to_char(concept_type)
||','||to_char(concept_code)
Expand All @@ -495,13 +514,14 @@ end;
--spool off;

-- File #4: PatientMapping.csv
--spool PatientMapping.csv;
--spool LocalPatientMapping.csv;
select s PatientMappingCSV
from (
select 0 i, 'patient_num,study_num' s FROM DUAL
select 0 i, 'siteid,patient_num,study_num' s FROM DUAL
union all
select row_number() over (order by patient_num) i,
to_char(patient_num)
siteid
||','||to_char(patient_num)
||','||to_char(study_num)
from PatientMapping
union all select 9999999, '' FROM DUAL --Add a blank row to make sure the last line in the file with data ends with a line feed.
Expand Down

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