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Deprecate observation notice, optional fields, sql writing guide #280

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merged 5 commits into from
Aug 20, 2024
Merged

Deprecate observation notice, optional fields, sql writing guide #280

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f811fb3
optional fields/deprecation docs
dogversioning Aug 14, 2024
dbdf85c
Added sql guide
dogversioning Aug 15, 2024
89821ec
sql regen
dogversioning Aug 20, 2024
45e7ece
PR feedback
dogversioning Aug 20, 2024
29d8f2c
table doc update
dogversioning Aug 20, 2024
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2 changes: 1 addition & 1 deletion .github/pull_request_template.md
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Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@

### Checklist
- [ ] Consider if documentation (like in `docs/`) needs to be updated
- [ ] Consider if documentation (like in `docs/`, or if you've changed the structure of a table) needs to be updated
- [ ] Consider if tests should be added
- [ ] Update template repo if there are changes to study configuration
22 changes: 11 additions & 11 deletions cumulus_library/studies/core/reference_sql/builder_condition.sql
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Original file line number Diff line number Diff line change
Expand Up @@ -25,7 +25,7 @@ CREATE TABLE core__condition_dn_category AS (
s.row,
u.coding.code,
u.coding.display,
u.coding.system AS system,
u.coding.system,
u.coding.userSelected
FROM
flattened_rows AS s,
Expand Down Expand Up @@ -66,7 +66,7 @@ CREATE TABLE core__condition_dn_clinical_status AS (
'0' AS priority,
u.coding.code,
u.coding.display,
u.coding.system AS system,
u.coding.system,
u.coding.userSelected
FROM
condition AS s,
Expand Down Expand Up @@ -131,7 +131,7 @@ CREATE TABLE core__condition_codable_concepts_display AS (
'0' AS priority,
u.coding.code,
u.coding.display,
u.coding.system AS system,
u.coding.system,
u.coding.userSelected
FROM
condition AS s,
Expand All @@ -147,7 +147,7 @@ CREATE TABLE core__condition_codable_concepts_display AS (
'1' AS priority,
u.coding.code,
u.coding.display,
u.coding.system AS system,
u.coding.system,
u.coding.userSelected
FROM
condition AS s,
Expand All @@ -163,7 +163,7 @@ CREATE TABLE core__condition_codable_concepts_display AS (
'2' AS priority,
u.coding.code,
u.coding.display,
u.coding.system AS system,
u.coding.system,
u.coding.userSelected
FROM
condition AS s,
Expand All @@ -179,7 +179,7 @@ CREATE TABLE core__condition_codable_concepts_display AS (
'3' AS priority,
u.coding.code,
u.coding.display,
u.coding.system AS system,
u.coding.system,
u.coding.userSelected
FROM
condition AS s,
Expand All @@ -195,7 +195,7 @@ CREATE TABLE core__condition_codable_concepts_display AS (
'4' AS priority,
u.coding.code,
u.coding.display,
u.coding.system AS system,
u.coding.system,
u.coding.userSelected
FROM
condition AS s,
Expand All @@ -211,7 +211,7 @@ CREATE TABLE core__condition_codable_concepts_display AS (
'5' AS priority,
u.coding.code,
u.coding.display,
u.coding.system AS system,
u.coding.system,
u.coding.userSelected
FROM
condition AS s,
Expand All @@ -227,7 +227,7 @@ CREATE TABLE core__condition_codable_concepts_display AS (
'6' AS priority,
u.coding.code,
u.coding.display,
u.coding.system AS system,
u.coding.system,
u.coding.userSelected
FROM
condition AS s,
Expand Down Expand Up @@ -351,7 +351,7 @@ CREATE TABLE core__condition_codable_concepts_all AS (
0 AS row,
u.coding.code,
u.coding.display,
u.coding.system AS system,
u.coding.system,
u.coding.userSelected
FROM
condition AS s,
Expand Down Expand Up @@ -391,7 +391,7 @@ CREATE TABLE core__condition_dn_verification_status AS (
'0' AS priority,
u.coding.code,
u.coding.display,
u.coding.system AS system,
u.coding.system,
u.coding.userSelected
FROM
condition AS s,
Expand Down
40 changes: 9 additions & 31 deletions cumulus_library/studies/core/reference_sql/builder_documentreference.sql
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Original file line number Diff line number Diff line change
Expand Up @@ -15,7 +15,7 @@ CREATE TABLE core__documentreference_dn_type AS (
0 AS row,
u.coding.code,
u.coding.display,
u.coding.system AS system,
u.coding.system,
u.coding.userSelected
FROM
documentreference AS s,
Expand Down Expand Up @@ -65,7 +65,7 @@ CREATE TABLE core__documentreference_dn_category AS (
'0' AS priority,
u.coding.code,
u.coding.display,
u.coding.system AS system,
u.coding.system,
u.coding.userSelected
FROM
flattened_rows AS s,
Expand Down Expand Up @@ -121,38 +121,16 @@ CREATE TABLE core__documentreference_dn_category AS (

-- ###########################################################

CREATE TABLE core__documentreference_dn_format AS (
WITH

system_format_0 AS (
SELECT DISTINCT
s.id AS id,
u.parent_col.format.code,
u.parent_col.format.display,
u.parent_col.format.system AS system
FROM
documentreference AS s,
UNNEST(s.content) AS u (parent_col)
), --noqa: LT07

union_table AS (
SELECT
id,
system,
code,
display
FROM system_format_0

CREATE TABLE IF NOT EXISTS "cumulus_mhg_dev_db"."core__documentreference_dn_format"
AS (
SELECT * FROM (
VALUES
(cast(NULL AS varchar),cast(NULL AS varchar),cast(NULL AS varchar),cast(NULL AS varchar))
)
SELECT
id,
code,
system,
display
FROM union_table
AS t ("id","code","system","display")
WHERE 1 = 0 -- ensure empty table
);


-- ###########################################################


Expand Down
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