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Fix column declaration and enhance regexp_like support for Snowflake #107

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Fix column declaration and enhance regexp_like support for Snowflake #107

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1a2e6cd
chore: properly declare `Id` column
lawrenceadams Dec 11, 2024
140fd0d
feat: add snowflake+default specific similar to / regexp_like adapter
lawrenceadams Dec 11, 2024
5fdf5d3
refactor: use new regexp_like adapter within measurement model
lawrenceadams Dec 11, 2024
4e473eb
fix: use quote_columns to enable snowflake
lawrenceadams Dec 11, 2024
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9 changes: 5 additions & 4 deletions dbt_project.yml
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Original file line number Diff line number Diff line change
@@ -1,8 +1,8 @@
name: 'synthea_omop_etl'
version: '0.1.0'
name: "synthea_omop_etl"
version: "0.1.0"
config-version: 2

profile: 'synthea_omop_etl'
profile: "synthea_omop_etl"

asset-paths: ["assets"]
docs-paths: ["docs"]
Expand All @@ -13,7 +13,7 @@ seed-paths: ["seeds"]
macro-paths: ["macros"]
snapshot-paths: ["snapshots"]

clean-targets: # directories to be removed by `dbt clean`
clean-targets: # directories to be removed by `dbt clean`
- "target"

vars:
Expand All @@ -34,3 +34,4 @@ seeds:
synthea:
+enabled: true
+schema: synthea_seeds
+quote_columns: true
11 changes: 11 additions & 0 deletions macros/regexp_like.sql
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Original file line number Diff line number Diff line change
@@ -0,0 +1,11 @@
{%- macro regexp_like(subject, pattern) -%}
{{ return(adapter.dispatch("regexp_like")(subject, pattern)) }}
{%- endmacro -%}

{% macro default__regexp_like(subject, pattern) %}
{{ subject }} ~ '{{ pattern }}'
{% endmacro %}

{% macro snowflake__regexp_like(subject, pattern) %}
regexp_like({{ subject }}, '{{ pattern }}')
{% endmacro %}
2 changes: 1 addition & 1 deletion models/omop/measurement.sql
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Expand Up @@ -57,7 +57,7 @@ WITH snomed_measurements AS (
, 32827 AS measurement_type_concept_id
, 0 AS operator_concept_id
, CASE
WHEN o.observation_value ~ '^[-+]?[0-9]+\.?[0-9]*$'
WHEN {{ regexp_like("o.observation_value", "^[-+]?[0-9]+\.?[0-9]*$") }}
THEN {{ dbt.cast("o.observation_value", api.Column.translate_type("decimal")) }}
ELSE {{ dbt.cast("null", api.Column.translate_type("decimal")) }}
END AS value_as_number
Comment on lines 59 to 63
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the new macro is useful and we should keep it for future use (thanks!!!) - but looking at this gross regex, maybe we could use safe_cast here instead? https://docs.getdbt.com/reference/dbt-jinja-functions/cross-database-macros#safe_cast

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@katy-sadowski Had another look through the cross-DB macros and fairly sure there's no regular expression oriented ones sadly - I don't think there is a way around this without using custom dispatchers / macros like this

It raises the question of do we event want to add ❄️ support! I think it is nice to have - just wish they used the ~ operator...

I looked into transpiring with SQLGlot, but I think thats a lot of work for relatively low yield - pulling out the DAG from dbt etc as per here #39 (comment) is quite a lot of work which isn't in the scope of the project (IMHO!)

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ahhh sorry i forgot about what you already said in #68 about safe_cast not being supported on all platforms. let's carry on with the regex approach! agree re: sqlglot.

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18 changes: 9 additions & 9 deletions seeds/synthea/_sources.yml
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Expand Up @@ -20,7 +20,7 @@ seeds:
- name: careplans
config:
column_types:
ID: varchar
Id: varchar
START: date
STOP: date
PATIENT: varchar
Expand All @@ -32,7 +32,7 @@ seeds:
- name: claims
config:
column_types:
ID: varchar
Id: varchar
PATIENTID: varchar
PROVIDERID: varchar
PRIMARYPATIENTINSURANCEID: varchar
Expand Down Expand Up @@ -66,7 +66,7 @@ seeds:
- name: claims_transactions
config:
column_types:
ID: varchar
Id: varchar
CLAIMID: varchar
CHARGEID: integer
PATIENTID: varchar
Expand Down Expand Up @@ -121,7 +121,7 @@ seeds:
- name: encounters
config:
column_types:
ID: varchar
Id: varchar
START: timestamp
STOP: timestamp
PATIENT: varchar
Expand All @@ -139,7 +139,7 @@ seeds:
- name: imaging_studies
config:
column_types:
ID: varchar
Id: varchar
DATE: timestamp
PATIENT: varchar
ENCOUNTER: varchar
Expand Down Expand Up @@ -192,7 +192,7 @@ seeds:
- name: organizations
config:
column_types:
ID: varchar
Id: varchar
NAME: varchar
ADDRESS: varchar
CITY: varchar
Expand All @@ -206,7 +206,7 @@ seeds:
- name: patients
config:
column_types:
ID: varchar
Id: varchar
BIRTHDATE: date
DEATHDATE: date
SSN: varchar
Expand Down Expand Up @@ -245,7 +245,7 @@ seeds:
- name: payers
config:
column_types:
ID: varchar
Id: varchar
NAME: varchar
ADDRESS: varchar
CITY: varchar
Expand Down Expand Up @@ -281,7 +281,7 @@ seeds:
- name: providers
config:
column_types:
ID: varchar
Id: varchar
ORGANIZATION: varchar
NAME: varchar
GENDER: varchar
Expand Down