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Data quality updates (#133)
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* Data quality updates

* changed delimiter character

* trim comment

* docstatus check

* ref update
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@dogversioning
dogversioning authored Oct 18, 2023
1 parent eae81c1 commit 73f3b1d
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Showing 25 changed files with 5,168 additions and 5,795 deletions.
152 changes: 73 additions & 79 deletions cumulus_library/studies/core/builder_encounter_coding.sql
View file
Original file line number Diff line number Diff line change
Expand Up @@ -15,12 +15,10 @@ CREATE TABLE core__encounter_dn_type AS (
u.codeable_concept.system AS code_system
FROM
encounter AS s,

UNNEST(s.type) AS cc (cc_row),
UNNEST(cc.cc_row.coding) AS u (codeable_concept)

WHERE
u.codeable_concept.system = 'http://hl7.org/fhir/ValueSet/encounter-type'
u.codeable_concept.system = 'http://terminology.hl7.org/CodeSystem/encounter-type'
), --noqa: LT07
system_type_1 AS (
SELECT DISTINCT
Expand All @@ -31,12 +29,10 @@ CREATE TABLE core__encounter_dn_type AS (
u.codeable_concept.system AS code_system
FROM
encounter AS s,

UNNEST(s.type) AS cc (cc_row),
UNNEST(cc.cc_row.coding) AS u (codeable_concept)

WHERE
u.codeable_concept.system = 'http://terminology.hl7.org/CodeSystem/encounter-type'
u.codeable_concept.system = 'http://terminology.hl7.org/CodeSystem/v2-0004'
), --noqa: LT07
system_type_2 AS (
SELECT DISTINCT
Expand All @@ -47,12 +43,10 @@ CREATE TABLE core__encounter_dn_type AS (
u.codeable_concept.system AS code_system
FROM
encounter AS s,

UNNEST(s.type) AS cc (cc_row),
UNNEST(cc.cc_row.coding) AS u (codeable_concept)

WHERE
u.codeable_concept.system = 'http://terminology.hl7.org/CodeSystem/v2-0004'
u.codeable_concept.system = 'urn:oid:2.16.840.1.113883.4.642.3.248'
), --noqa: LT07
system_type_3 AS (
SELECT DISTINCT
Expand All @@ -63,26 +57,8 @@ CREATE TABLE core__encounter_dn_type AS (
u.codeable_concept.system AS code_system
FROM
encounter AS s,

UNNEST(s.type) AS cc (cc_row),
UNNEST(cc.cc_row.coding) AS u (codeable_concept)

WHERE
u.codeable_concept.system = 'urn:oid:2.16.840.1.113883.4.642.3.248'
), --noqa: LT07
system_type_4 AS (
SELECT DISTINCT
s.id AS id,
'4' AS priority,
u.codeable_concept.code AS code,
u.codeable_concept.display AS display,
u.codeable_concept.system AS code_system
FROM
encounter AS s,

UNNEST(s.type) AS cc (cc_row),
UNNEST(cc.cc_row.coding) AS u (codeable_concept)

WHERE
u.codeable_concept.system = 'http://snomed.info/sct'
), --noqa: LT07
Expand Down Expand Up @@ -119,14 +95,6 @@ CREATE TABLE core__encounter_dn_type AS (
code,
display
FROM system_type_3
UNION
SELECT
id,
priority,
code_system,
code,
display
FROM system_type_4
),

partitioned_table AS (
Expand Down Expand Up @@ -165,10 +133,9 @@ CREATE TABLE core__encounter_dn_servicetype AS (
u.codeable_concept.system AS code_system
FROM
encounter AS s,

UNNEST(s.servicetype.coding) AS u (codeable_concept)
WHERE
u.codeable_concept.system = 'http://hl7.org/fhir/ValueSet/service-type'
u.codeable_concept.system = 'http://terminology.hl7.org/CodeSystem/service-type'
), --noqa: LT07
system_servicetype_1 AS (
SELECT DISTINCT
Expand All @@ -179,10 +146,9 @@ CREATE TABLE core__encounter_dn_servicetype AS (
u.codeable_concept.system AS code_system
FROM
encounter AS s,

UNNEST(s.servicetype.coding) AS u (codeable_concept)
WHERE
u.codeable_concept.system = 'http://terminology.hl7.org/CodeSystem/service-type'
u.codeable_concept.system = 'urn:oid:2.16.840.1.113883.4.642.3.518'
), --noqa: LT07
system_servicetype_2 AS (
SELECT DISTINCT
Expand All @@ -193,21 +159,6 @@ CREATE TABLE core__encounter_dn_servicetype AS (
u.codeable_concept.system AS code_system
FROM
encounter AS s,

UNNEST(s.servicetype.coding) AS u (codeable_concept)
WHERE
u.codeable_concept.system = 'urn:oid:2.16.840.1.113883.4.642.3.518'
), --noqa: LT07
system_servicetype_3 AS (
SELECT DISTINCT
s.id AS id,
'3' AS priority,
u.codeable_concept.code AS code,
u.codeable_concept.display AS display,
u.codeable_concept.system AS code_system
FROM
encounter AS s,

UNNEST(s.servicetype.coding) AS u (codeable_concept)
WHERE
u.codeable_concept.system = 'http://snomed.info/sct'
Expand Down Expand Up @@ -237,14 +188,6 @@ CREATE TABLE core__encounter_dn_servicetype AS (
code,
display
FROM system_servicetype_2
UNION
SELECT
id,
priority,
code_system,
code,
display
FROM system_servicetype_3
),

partitioned_table AS (
Expand Down Expand Up @@ -283,10 +226,9 @@ CREATE TABLE core__encounter_dn_priority AS (
u.codeable_concept.system AS code_system
FROM
encounter AS s,

UNNEST(s.priority.coding) AS u (codeable_concept)
WHERE
u.codeable_concept.system = 'http://terminology.hl7.org/ValueSet/v3-ActPriority'
u.codeable_concept.system = 'http://terminology.hl7.org/CodeSystem/v3-ActPriority'
), --noqa: LT07
system_priority_1 AS (
SELECT DISTINCT
Expand All @@ -297,22 +239,81 @@ CREATE TABLE core__encounter_dn_priority AS (
u.codeable_concept.system AS code_system
FROM
encounter AS s,

UNNEST(s.priority.coding) AS u (codeable_concept)
WHERE
u.codeable_concept.system = 'http://snomed.info/sct'
), --noqa: LT07

union_table AS (
SELECT
id,
priority,
code_system,
code,
display
FROM system_priority_0
UNION
SELECT
id,
priority,
code_system,
code,
display
FROM system_priority_1
),

partitioned_table AS (
SELECT
id,
code,
code_system,
display,
priority,
ROW_NUMBER()
OVER (
PARTITION BY id
) AS available_priority
FROM union_table
GROUP BY id, priority, code_system, code, display
ORDER BY priority ASC
)

SELECT
id,
code,
code_system,
display
FROM partitioned_table
WHERE available_priority = 1
);

CREATE TABLE core__encounter_dn_reasoncode AS (
WITH
system_reasoncode_0 AS (
SELECT DISTINCT
s.id AS id,
'0' AS priority,
u.codeable_concept.code AS code,
u.codeable_concept.display AS display,
u.codeable_concept.system AS code_system
FROM
encounter AS s,
UNNEST(s.reasoncode) AS cc (cc_row),
UNNEST(cc.cc_row.coding) AS u (codeable_concept)
WHERE
u.codeable_concept.system = 'http://terminology.hl7.org/CodeSystem/v3-ActPriority'
), --noqa: LT07
system_priority_2 AS (
system_reasoncode_1 AS (
SELECT DISTINCT
s.id AS id,
'2' AS priority,
'1' AS priority,
u.codeable_concept.code AS code,
u.codeable_concept.display AS display,
u.codeable_concept.system AS code_system
FROM
encounter AS s,

UNNEST(s.priority.coding) AS u (codeable_concept)
UNNEST(s.reasoncode) AS cc (cc_row),
UNNEST(cc.cc_row.coding) AS u (codeable_concept)
WHERE
u.codeable_concept.system = 'http://snomed.info/sct'
), --noqa: LT07
Expand All @@ -324,23 +325,15 @@ CREATE TABLE core__encounter_dn_priority AS (
code_system,
code,
display
FROM system_priority_0
UNION
SELECT
id,
priority,
code_system,
code,
display
FROM system_priority_1
FROM system_reasoncode_0
UNION
SELECT
id,
priority,
code_system,
code,
display
FROM system_priority_2
FROM system_reasoncode_1
),

partitioned_table AS (
Expand All @@ -367,3 +360,4 @@ CREATE TABLE core__encounter_dn_priority AS (
FROM partitioned_table
WHERE available_priority = 1
);

1 change: 1 addition & 0 deletions cumulus_library/studies/core/builder_patient_extension.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -34,5 +34,6 @@ def prepare_queries(self, cursor: object, schema: str):
extension["name"],
extension["fhirpath"],
["ombCategory", "detailed", "text"],
is_array=True,
)
self.queries.append(get_extension_denormalize_query(config))
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