OHDSI · odikia · Feb 7, 2026 · Feb 21, 2026 · Feb 21, 2026 · Feb 21, 2026
diff --git a/.gitignore b/.gitignore
@@ -12,4 +12,4 @@ data/
 .dbt/
 profiles.yml
 .vscode/mcp.json
-.cursor/mcp.json
+.cursor/mcp.json.user.yml
diff --git a/dbt_project.yml b/dbt_project.yml
@@ -396,6 +396,10 @@ models:
       +materialized: table
       +docs:
         node_color: '#EB6622'
+      vocabulary:
+        +schema: vocab
+      clinical:
+        +schema: cdm
     staging:
       synthea:
         +materialized: view

diff --git a/macros/generate_schema_name.sql b/macros/generate_schema_name.sql
@@ -0,0 +1,8 @@
+{% macro generate_schema_name(custom_schema_name, node) -%}
+    {%- set default_schema = target.schema -%}
+    {%- if custom_schema_name is none -%}
+        {{ default_schema }}
+    {%- else -%}
+        {{ default_schema }}_{{ custom_schema_name | trim }}
+    {%- endif -%}
+{%- endmacro %}
diff --git a/macros/get_source.sql b/macros/get_source.sql
@@ -0,0 +1,7 @@
+{%- macro get_source(source_name, table_name) -%}
+    {%- if not var('seed_source', false) and table_name == 'source_to_concept_map_seed' -%}
+        {%- do return(ref('source_to_concept_map_seed')) -%}
+    {%- else -%}
+        {%- do return(source(source_name, table_name)) -%}
+    {%- endif -%}
+{%- endmacro -%}
diff --git a/macros/load_data_duckdb.sql b/macros/load_data_duckdb.sql
@@ -31,7 +31,11 @@
         {% set column_casts = [] %}
         {% for column_name, column_type in columns.items() %}
             {% if column_name in ['valid_start_date', 'valid_end_date'] %}
-                {% do column_casts.append("CAST(strptime(CAST(" ~ column_name ~ " AS VARCHAR), '%Y%m%d') AS DATE) AS " ~ column_name) %}
+                {% if parquet %}
+                    {% do column_casts.append("CAST(" ~ column_name ~ " AS DATE) AS " ~ column_name) %}
+                {% else %}
+                    {% do column_casts.append("CAST(strptime(CAST(" ~ column_name ~ " AS VARCHAR), '%Y%m%d') AS DATE) AS " ~ column_name) %}
+                {% endif %}
             {% elif column_name|lower in ['start', 'stop', 'system', 'type', 'date'] %}
                 {% do column_casts.append("CAST(" ~ adapter.quote(column_name) ~ " AS " ~ api.Column.translate_type(column_type) ~ ") AS " ~ adapter.quote(column_name)) %}
             {% else %}

diff --git a/macros/macros.yml b/macros/macros.yml
@@ -53,6 +53,20 @@ macros:
         type: list[str]
         description: A list of column names
 
+  - name: get_source
+    description: >
+      Wrapper macro around source() that returns a Relation object.
+      Routes source_to_concept_map_seed to ref() when seed_source is false,
+      since this table is not part of the Athena vocabulary download and
+      only exists in the seeds schema.
+    arguments:
+      - name: source_name
+        type: str
+        description: The source name as defined in the sources YAML.
+      - name: table_name
+        type: str
+        description: The table name within the source.
+
   - name: string_truncate
     description: This macro truncates a string to a specified length.
     arguments:

diff --git a/models/omop/_models/care_site.yml → models/omop/clinical/_models/care_site.yml b/models/omop/_models/care_site.yml → models/omop/clinical/_models/care_site.yml
diff --git a/models/omop/_models/cdm_source.yml → models/omop/clinical/_models/cdm_source.yml b/models/omop/_models/cdm_source.yml → models/omop/clinical/_models/cdm_source.yml
diff --git a/models/omop/_models/condition_era.yml → ...s/omop/clinical/_models/condition_era.yml b/models/omop/_models/condition_era.yml → ...s/omop/clinical/_models/condition_era.yml
diff --git a/models/omop/_models/condition_occurrence.yml → ...clinical/_models/condition_occurrence.yml b/models/omop/_models/condition_occurrence.yml → ...clinical/_models/condition_occurrence.yml
diff --git a/models/omop/_models/cost.yml → models/omop/clinical/_models/cost.yml b/models/omop/_models/cost.yml → models/omop/clinical/_models/cost.yml
diff --git a/models/omop/_models/death.yml → models/omop/clinical/_models/death.yml b/models/omop/_models/death.yml → models/omop/clinical/_models/death.yml
diff --git a/models/omop/_models/device_exposure.yml → ...omop/clinical/_models/device_exposure.yml b/models/omop/_models/device_exposure.yml → ...omop/clinical/_models/device_exposure.yml
diff --git a/models/omop/_models/dose_era.yml → models/omop/clinical/_models/dose_era.yml b/models/omop/_models/dose_era.yml → models/omop/clinical/_models/dose_era.yml
diff --git a/models/omop/_models/drug_era.yml → models/omop/clinical/_models/drug_era.yml b/models/omop/_models/drug_era.yml → models/omop/clinical/_models/drug_era.yml
diff --git a/models/omop/_models/drug_exposure.yml → ...s/omop/clinical/_models/drug_exposure.yml b/models/omop/_models/drug_exposure.yml → ...s/omop/clinical/_models/drug_exposure.yml
diff --git a/models/omop/_models/episode.yml → models/omop/clinical/_models/episode.yml b/models/omop/_models/episode.yml → models/omop/clinical/_models/episode.yml
diff --git a/models/omop/_models/episode_event.yml → ...s/omop/clinical/_models/episode_event.yml b/models/omop/_models/episode_event.yml → ...s/omop/clinical/_models/episode_event.yml
diff --git a/models/omop/_models/fact_relationship.yml → ...op/clinical/_models/fact_relationship.yml b/models/omop/_models/fact_relationship.yml → ...op/clinical/_models/fact_relationship.yml
diff --git a/models/omop/_models/location.yml → models/omop/clinical/_models/location.yml b/models/omop/_models/location.yml → models/omop/clinical/_models/location.yml
diff --git a/models/omop/_models/measurement.yml → models/omop/clinical/_models/measurement.yml b/models/omop/_models/measurement.yml → models/omop/clinical/_models/measurement.yml
diff --git a/models/omop/_models/metadata.yml → models/omop/clinical/_models/metadata.yml b/models/omop/_models/metadata.yml → models/omop/clinical/_models/metadata.yml
diff --git a/models/omop/_models/note.yml → models/omop/clinical/_models/note.yml b/models/omop/_models/note.yml → models/omop/clinical/_models/note.yml
diff --git a/models/omop/_models/note_nlp.yml → models/omop/clinical/_models/note_nlp.yml b/models/omop/_models/note_nlp.yml → models/omop/clinical/_models/note_nlp.yml
diff --git a/models/omop/_models/observation.yml → models/omop/clinical/_models/observation.yml b/models/omop/_models/observation.yml → models/omop/clinical/_models/observation.yml
diff --git a/models/omop/_models/observation_period.yml → ...p/clinical/_models/observation_period.yml b/models/omop/_models/observation_period.yml → ...p/clinical/_models/observation_period.yml
diff --git a/models/omop/_models/payer_plan_period.yml → ...op/clinical/_models/payer_plan_period.yml b/models/omop/_models/payer_plan_period.yml → ...op/clinical/_models/payer_plan_period.yml
diff --git a/models/omop/_models/person.yml → models/omop/clinical/_models/person.yml b/models/omop/_models/person.yml → models/omop/clinical/_models/person.yml
diff --git a/models/omop/_models/procedure_occurrence.yml → ...clinical/_models/procedure_occurrence.yml b/models/omop/_models/procedure_occurrence.yml → ...clinical/_models/procedure_occurrence.yml
diff --git a/models/omop/_models/provider.yml → models/omop/clinical/_models/provider.yml b/models/omop/_models/provider.yml → models/omop/clinical/_models/provider.yml
diff --git a/models/omop/_models/specimen.yml → models/omop/clinical/_models/specimen.yml b/models/omop/_models/specimen.yml → models/omop/clinical/_models/specimen.yml
diff --git a/models/omop/_models/visit_detail.yml → ...ls/omop/clinical/_models/visit_detail.yml b/models/omop/_models/visit_detail.yml → ...ls/omop/clinical/_models/visit_detail.yml
diff --git a/models/omop/_models/visit_occurrence.yml → ...mop/clinical/_models/visit_occurrence.yml b/models/omop/_models/visit_occurrence.yml → ...mop/clinical/_models/visit_occurrence.yml
diff --git a/models/omop/care_site.sql → models/omop/clinical/care_site.sql b/models/omop/care_site.sql → models/omop/clinical/care_site.sql
diff --git a/models/omop/cdm_source.sql → models/omop/clinical/cdm_source.sql b/models/omop/cdm_source.sql → models/omop/clinical/cdm_source.sql
diff --git a/models/omop/condition_era.sql → models/omop/clinical/condition_era.sql b/models/omop/condition_era.sql → models/omop/clinical/condition_era.sql
diff --git a/models/omop/condition_occurrence.sql → ...ls/omop/clinical/condition_occurrence.sql b/models/omop/condition_occurrence.sql → ...ls/omop/clinical/condition_occurrence.sql
diff --git a/models/omop/cost.sql → models/omop/clinical/cost.sql b/models/omop/cost.sql → models/omop/clinical/cost.sql
diff --git a/models/omop/death.sql → models/omop/clinical/death.sql b/models/omop/death.sql → models/omop/clinical/death.sql
diff --git a/models/omop/device_exposure.sql → models/omop/clinical/device_exposure.sql b/models/omop/device_exposure.sql → models/omop/clinical/device_exposure.sql
diff --git a/models/omop/dose_era.sql → models/omop/clinical/dose_era.sql b/models/omop/dose_era.sql → models/omop/clinical/dose_era.sql
diff --git a/models/omop/drug_era.sql → models/omop/clinical/drug_era.sql b/models/omop/drug_era.sql → models/omop/clinical/drug_era.sql
diff --git a/models/omop/drug_exposure.sql → models/omop/clinical/drug_exposure.sql b/models/omop/drug_exposure.sql → models/omop/clinical/drug_exposure.sql
diff --git a/models/omop/episode.sql → models/omop/clinical/episode.sql b/models/omop/episode.sql → models/omop/clinical/episode.sql
diff --git a/models/omop/episode_event.sql → models/omop/clinical/episode_event.sql b/models/omop/episode_event.sql → models/omop/clinical/episode_event.sql
diff --git a/models/omop/fact_relationship.sql → models/omop/clinical/fact_relationship.sql b/models/omop/fact_relationship.sql → models/omop/clinical/fact_relationship.sql
diff --git a/models/omop/location.sql → models/omop/clinical/location.sql b/models/omop/location.sql → models/omop/clinical/location.sql
diff --git a/models/omop/measurement.sql → models/omop/clinical/measurement.sql b/models/omop/measurement.sql → models/omop/clinical/measurement.sql
diff --git a/models/omop/metadata.sql → models/omop/clinical/metadata.sql b/models/omop/metadata.sql → models/omop/clinical/metadata.sql
diff --git a/models/omop/note.sql → models/omop/clinical/note.sql b/models/omop/note.sql → models/omop/clinical/note.sql
diff --git a/models/omop/note_nlp.sql → models/omop/clinical/note_nlp.sql b/models/omop/note_nlp.sql → models/omop/clinical/note_nlp.sql
diff --git a/models/omop/observation.sql → models/omop/clinical/observation.sql b/models/omop/observation.sql → models/omop/clinical/observation.sql
diff --git a/models/omop/observation_period.sql → models/omop/clinical/observation_period.sql b/models/omop/observation_period.sql → models/omop/clinical/observation_period.sql
diff --git a/models/omop/payer_plan_period.sql → models/omop/clinical/payer_plan_period.sql b/models/omop/payer_plan_period.sql → models/omop/clinical/payer_plan_period.sql
diff --git a/models/omop/person.sql → models/omop/clinical/person.sql b/models/omop/person.sql → models/omop/clinical/person.sql
diff --git a/models/omop/procedure_occurrence.sql → ...ls/omop/clinical/procedure_occurrence.sql b/models/omop/procedure_occurrence.sql → ...ls/omop/clinical/procedure_occurrence.sql
diff --git a/models/omop/provider.sql → models/omop/clinical/provider.sql b/models/omop/provider.sql → models/omop/clinical/provider.sql
diff --git a/models/omop/specimen.sql → models/omop/clinical/specimen.sql b/models/omop/specimen.sql → models/omop/clinical/specimen.sql
diff --git a/models/omop/visit_detail.sql → models/omop/clinical/visit_detail.sql b/models/omop/visit_detail.sql → models/omop/clinical/visit_detail.sql
diff --git a/models/omop/visit_occurrence.sql → models/omop/clinical/visit_occurrence.sql b/models/omop/visit_occurrence.sql → models/omop/clinical/visit_occurrence.sql
diff --git a/models/omop/_models/concept.yml → models/omop/vocabulary/_models/concept.yml b/models/omop/_models/concept.yml → models/omop/vocabulary/_models/concept.yml
diff --git a/models/omop/_models/concept_ancestor.yml → ...p/vocabulary/_models/concept_ancestor.yml b/models/omop/_models/concept_ancestor.yml → ...p/vocabulary/_models/concept_ancestor.yml
diff --git a/models/omop/_models/concept_class.yml → ...omop/vocabulary/_models/concept_class.yml b/models/omop/_models/concept_class.yml → ...omop/vocabulary/_models/concept_class.yml
diff --git a/models/omop/_models/concept_relationship.yml → ...cabulary/_models/concept_relationship.yml b/models/omop/_models/concept_relationship.yml → ...cabulary/_models/concept_relationship.yml
diff --git a/models/omop/_models/concept_synonym.yml → ...op/vocabulary/_models/concept_synonym.yml b/models/omop/_models/concept_synonym.yml → ...op/vocabulary/_models/concept_synonym.yml
diff --git a/models/omop/_models/domain.yml → models/omop/vocabulary/_models/domain.yml b/models/omop/_models/domain.yml → models/omop/vocabulary/_models/domain.yml
diff --git a/models/omop/_models/drug_strength.yml → ...omop/vocabulary/_models/drug_strength.yml b/models/omop/_models/drug_strength.yml → ...omop/vocabulary/_models/drug_strength.yml
diff --git a/models/omop/_models/relationship.yml → .../omop/vocabulary/_models/relationship.yml b/models/omop/_models/relationship.yml → .../omop/vocabulary/_models/relationship.yml
diff --git a/...ls/omop/_models/source_to_concept_map.yml → ...abulary/_models/source_to_concept_map.yml b/...ls/omop/_models/source_to_concept_map.yml → ...abulary/_models/source_to_concept_map.yml
diff --git a/models/omop/_models/vocabulary.yml → ...ls/omop/vocabulary/_models/vocabulary.yml b/models/omop/_models/vocabulary.yml → ...ls/omop/vocabulary/_models/vocabulary.yml
diff --git a/models/omop/concept.sql → models/omop/vocabulary/concept.sql b/models/omop/concept.sql → models/omop/vocabulary/concept.sql
diff --git a/models/omop/concept_ancestor.sql → models/omop/vocabulary/concept_ancestor.sql b/models/omop/concept_ancestor.sql → models/omop/vocabulary/concept_ancestor.sql
diff --git a/models/omop/concept_class.sql → models/omop/vocabulary/concept_class.sql b/models/omop/concept_class.sql → models/omop/vocabulary/concept_class.sql
diff --git a/models/omop/concept_relationship.sql → .../omop/vocabulary/concept_relationship.sql b/models/omop/concept_relationship.sql → .../omop/vocabulary/concept_relationship.sql
diff --git a/models/omop/concept_synonym.sql → models/omop/vocabulary/concept_synonym.sql b/models/omop/concept_synonym.sql → models/omop/vocabulary/concept_synonym.sql
diff --git a/models/omop/domain.sql → models/omop/vocabulary/domain.sql b/models/omop/domain.sql → models/omop/vocabulary/domain.sql
diff --git a/models/omop/drug_strength.sql → models/omop/vocabulary/drug_strength.sql b/models/omop/drug_strength.sql → models/omop/vocabulary/drug_strength.sql
diff --git a/models/omop/relationship.sql → models/omop/vocabulary/relationship.sql b/models/omop/relationship.sql → models/omop/vocabulary/relationship.sql
diff --git a/models/omop/source_to_concept_map.sql → ...omop/vocabulary/source_to_concept_map.sql b/models/omop/source_to_concept_map.sql → ...omop/vocabulary/source_to_concept_map.sql
diff --git a/models/omop/vocabulary.sql → models/omop/vocabulary/vocabulary.sql b/models/omop/vocabulary.sql → models/omop/vocabulary/vocabulary.sql
diff --git a/models/staging/vocabulary/stg_vocabulary__source_to_concept_map.sql b/models/staging/vocabulary/stg_vocabulary__source_to_concept_map.sql
@@ -1,13 +1,13 @@
-{% set column_names = 
-    dbt_utils.get_filtered_columns_in_relation( source('vocabulary', 'source_to_concept_map_seed') ) 
+{% set column_names =
+    dbt_utils.get_filtered_columns_in_relation( get_source('vocabulary', 'source_to_concept_map_seed') )
 %}
 
 
 WITH cte_stcm_lower AS (
 
     SELECT
         {{ lowercase_columns(column_names) }}
-    FROM {{ source('vocabulary','source_to_concept_map_seed') }}
+    FROM {{ get_source('vocabulary', 'source_to_concept_map_seed') }}
 )
 
 SELECT *

diff --git a/pyproject.toml b/pyproject.toml
@@ -0,0 +1,10 @@
+[project]
+name = "dbt-synthea"
+version = "0.1.0"
+description = "dbt project for transforming Synthea synthetic patient data into OMOP CDM"
+requires-python = ">=3.12,<3.14"
+dependencies = [
+    "dbt-core>=1.9,<2",
+    "dbt-duckdb>=1.9,<2",
+    "duckdb",
+]
diff --git a/uv.lock b/uv.lock