carrot-transform 0.3.4__py3-none-any.whl → 0.4.0__py3-none-any.whl

carrottransform/cli/subcommands/run_v2.py

@@ -0,0 +1,145 @@
+"""
+Entry point for the v2 processing system
+"""
+
+from pathlib import Path
+from typing import Optional
+import click
+import time
+from carrottransform.tools.click import PathArgs
+from carrottransform.tools.file_helpers import (
+    check_dir_isvalid,
+    resolve_paths,
+    set_omop_filenames,
+)
+from carrottransform.tools.logger import logger_setup
+from carrottransform.tools.orchestrator import V2ProcessingOrchestrator
+
+logger = logger_setup()
+
+
+@click.command()
+@click.option(
+    "--rules-file",
+    type=PathArgs,
+    required=True,
+    help="v2 json file containing mapping rules",
+)
+@click.option(
+    "--output-dir",
+    type=PathArgs,
+    required=True,
+    help="define the output directory for OMOP-format tsv files",
+)
+@click.option(
+    "--write-mode",
+    default="w",
+    type=click.Choice(["w", "a"]),
+    help="force write-mode on output files",
+)
+@click.option(
+    "--person-file",
+    type=PathArgs,
+    required=True,
+    help="File containing person_ids in the first column",
+)
+@click.option(
+    "--omop-ddl-file",
+    type=PathArgs,
+    required=False,
+    help="File containing OHDSI ddl statements for OMOP tables",
+)
+@click.option(
+    "--omop-config-file",
+    type=PathArgs,
+    required=False,
+    help="File containing additional / override json config for omop outputs",
+)
+@click.option(
+    "--omop-version",
+    required=False,
+    help="Quoted string containing omop version - eg '5.3'",
+)
+@click.option("--input-dir", type=PathArgs, required=True, help="Input directories")
+def mapstream_v2(
+    rules_file: Path,
+    output_dir: Path,
+    write_mode: str,
+    person_file: Path,
+    omop_ddl_file: Optional[Path],
+    omop_config_file: Optional[Path],
+    omop_version: Optional[str],
+    input_dir: Path,
+):
+    """Map to OMOP output using v2 format rules - Refactored Implementation"""
+
+    start_time = time.time()
+
+    try:
+        # Resolve paths
+        resolved_paths = resolve_paths(
+            [
+                rules_file,
+                output_dir,
+                person_file,
+                omop_ddl_file,
+                omop_config_file,
+                input_dir,
+            ]
+        )
+        [
+            rules_file,
+            output_dir,
+            person_file,
+            omop_ddl_file,
+            omop_config_file,
+            input_dir,
+        ] = resolved_paths  # type: ignore
+
+        # Validate inputs
+        check_dir_isvalid(input_dir)
+        check_dir_isvalid(output_dir, create_if_missing=True)
+
+        # Set default OMOP file paths when not explicitly provided
+        omop_config_file, omop_ddl_file = set_omop_filenames(
+            omop_ddl_file, omop_config_file, omop_version
+        )
+
+        # Create orchestrator and execute processing
+        orchestrator = V2ProcessingOrchestrator(
+            rules_file=rules_file,
+            output_dir=output_dir,
+            input_dir=input_dir,
+            person_file=person_file,
+            omop_ddl_file=omop_ddl_file,
+            omop_config_file=omop_config_file,
+            write_mode=write_mode,
+        )
+
+        logger.info(
+            f"Loaded v2 mapping rules from: {rules_file} in {time.time() - start_time:.5f} secs"
+        )
+
+        result = orchestrator.execute_processing()
+
+        if result.success:
+            logger.info(
+                f"V2 processing completed successfully in {time.time() - start_time:.5f} secs"
+            )
+        else:
+            logger.error(f"V2 processing failed: {result.error_message}")
+
+    except Exception as e:
+        logger.error(f"V2 processing failed with error: {str(e)}")
+        raise
+
+
+@click.group(help="V2 Commands for mapping data to the OMOP CommonDataModel (CDM).")
+def run_v2():
+    pass
+
+
+run_v2.add_command(mapstream_v2, "mapstream")
+
+if __name__ == "__main__":
+    run_v2()

carrottransform/config/OMOPCDM_postgresql_5.4_ddl.sql

@@ -0,0 +1,550 @@
+--postgresql CDM DDL Specification for OMOP Common Data Model 5.4
+
+--HINT DISTRIBUTE ON KEY (person_id)
+CREATE TABLE @cdmDatabaseSchema.PERSON (
+			person_id integer NOT NULL,
+			gender_concept_id integer NOT NULL,
+			year_of_birth integer NOT NULL,
+			month_of_birth integer NULL,
+			day_of_birth integer NULL,
+			birth_datetime TIMESTAMP NULL,
+			race_concept_id integer NOT NULL,
+			ethnicity_concept_id integer NOT NULL,
+			location_id integer NULL,
+			provider_id integer NULL,
+			care_site_id integer NULL,
+			person_source_value varchar(50) NULL,
+			gender_source_value varchar(50) NULL,
+			gender_source_concept_id integer NULL,
+			race_source_value varchar(50) NULL,
+			race_source_concept_id integer NULL,
+			ethnicity_source_value varchar(50) NULL,
+			ethnicity_source_concept_id integer NULL );
+
+--HINT DISTRIBUTE ON KEY (person_id)
+CREATE TABLE @cdmDatabaseSchema.OBSERVATION_PERIOD (
+			observation_period_id integer NOT NULL,
+			person_id integer NOT NULL,
+			observation_period_start_date date NOT NULL,
+			observation_period_end_date date NOT NULL,
+			period_type_concept_id integer NOT NULL );
+
+--HINT DISTRIBUTE ON KEY (person_id)
+CREATE TABLE @cdmDatabaseSchema.VISIT_OCCURRENCE (
+			visit_occurrence_id integer NOT NULL,
+			person_id integer NOT NULL,
+			visit_concept_id integer NOT NULL,
+			visit_start_date date NOT NULL,
+			visit_start_datetime TIMESTAMP NULL,
+			visit_end_date date NOT NULL,
+			visit_end_datetime TIMESTAMP NULL,
+			visit_type_concept_id Integer NOT NULL,
+			provider_id integer NULL,
+			care_site_id integer NULL,
+			visit_source_value varchar(50) NULL,
+			visit_source_concept_id integer NULL,
+			admitted_from_concept_id integer NULL,
+			admitted_from_source_value varchar(50) NULL,
+			discharged_to_concept_id integer NULL,
+			discharged_to_source_value varchar(50) NULL,
+			preceding_visit_occurrence_id integer NULL );
+
+--HINT DISTRIBUTE ON KEY (person_id)
+CREATE TABLE @cdmDatabaseSchema.VISIT_DETAIL (
+			visit_detail_id integer NOT NULL,
+			person_id integer NOT NULL,
+			visit_detail_concept_id integer NOT NULL,
+			visit_detail_start_date date NOT NULL,
+			visit_detail_start_datetime TIMESTAMP NULL,
+			visit_detail_end_date date NOT NULL,
+			visit_detail_end_datetime TIMESTAMP NULL,
+			visit_detail_type_concept_id integer NOT NULL,
+			provider_id integer NULL,
+			care_site_id integer NULL,
+			visit_detail_source_value varchar(50) NULL,
+			visit_detail_source_concept_id Integer NULL,
+			admitted_from_concept_id Integer NULL,
+			admitted_from_source_value varchar(50) NULL,
+			discharged_to_source_value varchar(50) NULL,
+			discharged_to_concept_id integer NULL,
+			preceding_visit_detail_id integer NULL,
+			parent_visit_detail_id integer NULL,
+			visit_occurrence_id integer NOT NULL );
+
+--HINT DISTRIBUTE ON KEY (person_id)
+CREATE TABLE @cdmDatabaseSchema.CONDITION_OCCURRENCE (
+			condition_occurrence_id integer NOT NULL,
+			person_id integer NOT NULL,
+			condition_concept_id integer NOT NULL,
+			condition_start_date date NOT NULL,
+			condition_start_datetime TIMESTAMP NULL,
+			condition_end_date date NULL,
+			condition_end_datetime TIMESTAMP NULL,
+			condition_type_concept_id integer NOT NULL,
+			condition_status_concept_id integer NULL,
+			stop_reason varchar(20) NULL,
+			provider_id integer NULL,
+			visit_occurrence_id integer NULL,
+			visit_detail_id integer NULL,
+			condition_source_value varchar(50) NULL,
+			condition_source_concept_id integer NULL,
+			condition_status_source_value varchar(50) NULL );
+
+--HINT DISTRIBUTE ON KEY (person_id)
+CREATE TABLE @cdmDatabaseSchema.DRUG_EXPOSURE (
+			drug_exposure_id integer NOT NULL,
+			person_id integer NOT NULL,
+			drug_concept_id integer NOT NULL,
+			drug_exposure_start_date date NOT NULL,
+			drug_exposure_start_datetime TIMESTAMP NULL,
+			drug_exposure_end_date date NOT NULL,
+			drug_exposure_end_datetime TIMESTAMP NULL,
+			verbatim_end_date date NULL,
+			drug_type_concept_id integer NOT NULL,
+			stop_reason varchar(20) NULL,
+			refills integer NULL,
+			quantity NUMERIC NULL,
+			days_supply integer NULL,
+			sig TEXT NULL,
+			route_concept_id integer NULL,
+			lot_number varchar(50) NULL,
+			provider_id integer NULL,
+			visit_occurrence_id integer NULL,
+			visit_detail_id integer NULL,
+			drug_source_value varchar(50) NULL,
+			drug_source_concept_id integer NULL,
+			route_source_value varchar(50) NULL,
+			dose_unit_source_value varchar(50) NULL );
+
+--HINT DISTRIBUTE ON KEY (person_id)
+CREATE TABLE @cdmDatabaseSchema.PROCEDURE_OCCURRENCE (
+			procedure_occurrence_id integer NOT NULL,
+			person_id integer NOT NULL,
+			procedure_concept_id integer NOT NULL,
+			procedure_date date NOT NULL,
+			procedure_datetime TIMESTAMP NULL,
+			procedure_end_date date NULL,
+			procedure_end_datetime TIMESTAMP NULL,
+			procedure_type_concept_id integer NOT NULL,
+			modifier_concept_id integer NULL,
+			quantity integer NULL,
+			provider_id integer NULL,
+			visit_occurrence_id integer NULL,
+			visit_detail_id integer NULL,
+			procedure_source_value varchar(50) NULL,
+			procedure_source_concept_id integer NULL,
+			modifier_source_value varchar(50) NULL );
+
+--HINT DISTRIBUTE ON KEY (person_id)
+CREATE TABLE @cdmDatabaseSchema.DEVICE_EXPOSURE (
+			device_exposure_id integer NOT NULL,
+			person_id integer NOT NULL,
+			device_concept_id integer NOT NULL,
+			device_exposure_start_date date NOT NULL,
+			device_exposure_start_datetime TIMESTAMP NULL,
+			device_exposure_end_date date NULL,
+			device_exposure_end_datetime TIMESTAMP NULL,
+			device_type_concept_id integer NOT NULL,
+			unique_device_id varchar(255) NULL,
+			production_id varchar(255) NULL,
+			quantity integer NULL,
+			provider_id integer NULL,
+			visit_occurrence_id integer NULL,
+			visit_detail_id integer NULL,
+			device_source_value varchar(50) NULL,
+			device_source_concept_id integer NULL,
+			unit_concept_id integer NULL,
+			unit_source_value varchar(50) NULL,
+			unit_source_concept_id integer NULL );
+
+--HINT DISTRIBUTE ON KEY (person_id)
+CREATE TABLE @cdmDatabaseSchema.MEASUREMENT (
+			measurement_id integer NOT NULL,
+			person_id integer NOT NULL,
+			measurement_concept_id integer NOT NULL,
+			measurement_date date NOT NULL,
+			measurement_datetime TIMESTAMP NULL,
+			measurement_time varchar(10) NULL,
+			measurement_type_concept_id integer NOT NULL,
+			operator_concept_id integer NULL,
+			value_as_number NUMERIC NULL,
+			value_as_concept_id integer NULL,
+			unit_concept_id integer NULL,
+			range_low NUMERIC NULL,
+			range_high NUMERIC NULL,
+			provider_id integer NULL,
+			visit_occurrence_id integer NULL,
+			visit_detail_id integer NULL,
+			measurement_source_value varchar(50) NULL,
+			measurement_source_concept_id integer NULL,
+			unit_source_value varchar(50) NULL,
+			unit_source_concept_id integer NULL,
+			value_source_value varchar(50) NULL,
+			measurement_event_id bigint NULL,
+			meas_event_field_concept_id integer NULL );
+
+--HINT DISTRIBUTE ON KEY (person_id)
+CREATE TABLE @cdmDatabaseSchema.OBSERVATION (
+			observation_id integer NOT NULL,
+			person_id integer NOT NULL,
+			observation_concept_id integer NOT NULL,
+			observation_date date NOT NULL,
+			observation_datetime TIMESTAMP NULL,
+			observation_type_concept_id integer NOT NULL,
+			value_as_number NUMERIC NULL,
+			value_as_string varchar(60) NULL,
+			value_as_concept_id Integer NULL,
+			qualifier_concept_id integer NULL,
+			unit_concept_id integer NULL,
+			provider_id integer NULL,
+			visit_occurrence_id integer NULL,
+			visit_detail_id integer NULL,
+			observation_source_value varchar(50) NULL,
+			observation_source_concept_id integer NULL,
+			unit_source_value varchar(50) NULL,
+			qualifier_source_value varchar(50) NULL,
+			value_source_value varchar(50) NULL,
+			observation_event_id bigint NULL,
+			obs_event_field_concept_id integer NULL );
+
+--HINT DISTRIBUTE ON KEY (person_id)
+CREATE TABLE @cdmDatabaseSchema.DEATH (
+			person_id integer NOT NULL,
+			death_date date NOT NULL,
+			death_datetime TIMESTAMP NULL,
+			death_type_concept_id integer NULL,
+			cause_concept_id integer NULL,
+			cause_source_value varchar(50) NULL,
+			cause_source_concept_id integer NULL );
+
+--HINT DISTRIBUTE ON KEY (person_id)
+CREATE TABLE @cdmDatabaseSchema.NOTE (
+			note_id integer NOT NULL,
+			person_id integer NOT NULL,
+			note_date date NOT NULL,
+			note_datetime TIMESTAMP NULL,
+			note_type_concept_id integer NOT NULL,
+			note_class_concept_id integer NOT NULL,
+			note_title varchar(250) NULL,
+			note_text TEXT NOT NULL,
+			encoding_concept_id integer NOT NULL,
+			language_concept_id integer NOT NULL,
+			provider_id integer NULL,
+			visit_occurrence_id integer NULL,
+			visit_detail_id integer NULL,
+			note_source_value varchar(50) NULL,
+			note_event_id bigint NULL,
+			note_event_field_concept_id integer NULL );
+
+--HINT DISTRIBUTE ON RANDOM
+CREATE TABLE @cdmDatabaseSchema.NOTE_NLP (
+			note_nlp_id integer NOT NULL,
+			note_id integer NOT NULL,
+			section_concept_id integer NULL,
+			snippet varchar(250) NULL,
+			"offset" varchar(50) NULL,
+			lexical_variant varchar(250) NOT NULL,
+			note_nlp_concept_id integer NULL,
+			note_nlp_source_concept_id integer NULL,
+			nlp_system varchar(250) NULL,
+			nlp_date date NOT NULL,
+			nlp_datetime TIMESTAMP NULL,
+			term_exists varchar(1) NULL,
+			term_temporal varchar(50) NULL,
+			term_modifiers varchar(2000) NULL );
+
+--HINT DISTRIBUTE ON KEY (person_id)
+CREATE TABLE @cdmDatabaseSchema.SPECIMEN (
+			specimen_id integer NOT NULL,
+			person_id integer NOT NULL,
+			specimen_concept_id integer NOT NULL,
+			specimen_type_concept_id integer NOT NULL,
+			specimen_date date NOT NULL,
+			specimen_datetime TIMESTAMP NULL,
+			quantity NUMERIC NULL,
+			unit_concept_id integer NULL,
+			anatomic_site_concept_id integer NULL,
+			disease_status_concept_id integer NULL,
+			specimen_source_id varchar(50) NULL,
+			specimen_source_value varchar(50) NULL,
+			unit_source_value varchar(50) NULL,
+			anatomic_site_source_value varchar(50) NULL,
+			disease_status_source_value varchar(50) NULL );
+
+--HINT DISTRIBUTE ON RANDOM
+CREATE TABLE @cdmDatabaseSchema.FACT_RELATIONSHIP (
+			domain_concept_id_1 integer NOT NULL,
+			fact_id_1 integer NOT NULL,
+			domain_concept_id_2 integer NOT NULL,
+			fact_id_2 integer NOT NULL,
+			relationship_concept_id integer NOT NULL );
+
+--HINT DISTRIBUTE ON RANDOM
+CREATE TABLE @cdmDatabaseSchema.LOCATION (
+			location_id integer NOT NULL,
+			address_1 varchar(50) NULL,
+			address_2 varchar(50) NULL,
+			city varchar(50) NULL,
+			state varchar(2) NULL,
+			zip varchar(9) NULL,
+			county varchar(20) NULL,
+			location_source_value varchar(50) NULL,
+			country_concept_id integer NULL,
+			country_source_value varchar(80) NULL,
+			latitude NUMERIC NULL,
+			longitude NUMERIC NULL );
+
+--HINT DISTRIBUTE ON RANDOM
+CREATE TABLE @cdmDatabaseSchema.CARE_SITE (
+			care_site_id integer NOT NULL,
+			care_site_name varchar(255) NULL,
+			place_of_service_concept_id integer NULL,
+			location_id integer NULL,
+			care_site_source_value varchar(50) NULL,
+			place_of_service_source_value varchar(50) NULL );
+
+--HINT DISTRIBUTE ON RANDOM
+CREATE TABLE @cdmDatabaseSchema.PROVIDER (
+			provider_id integer NOT NULL,
+			provider_name varchar(255) NULL,
+			npi varchar(20) NULL,
+			dea varchar(20) NULL,
+			specialty_concept_id integer NULL,
+			care_site_id integer NULL,
+			year_of_birth integer NULL,
+			gender_concept_id integer NULL,
+			provider_source_value varchar(50) NULL,
+			specialty_source_value varchar(50) NULL,
+			specialty_source_concept_id integer NULL,
+			gender_source_value varchar(50) NULL,
+			gender_source_concept_id integer NULL );
+
+--HINT DISTRIBUTE ON KEY (person_id)
+CREATE TABLE @cdmDatabaseSchema.PAYER_PLAN_PERIOD (
+			payer_plan_period_id integer NOT NULL,
+			person_id integer NOT NULL,
+			payer_plan_period_start_date date NOT NULL,
+			payer_plan_period_end_date date NOT NULL,
+			payer_concept_id integer NULL,
+			payer_source_value varchar(50) NULL,
+			payer_source_concept_id integer NULL,
+			plan_concept_id integer NULL,
+			plan_source_value varchar(50) NULL,
+			plan_source_concept_id integer NULL,
+			sponsor_concept_id integer NULL,
+			sponsor_source_value varchar(50) NULL,
+			sponsor_source_concept_id integer NULL,
+			family_source_value varchar(50) NULL,
+			stop_reason_concept_id integer NULL,
+			stop_reason_source_value varchar(50) NULL,
+			stop_reason_source_concept_id integer NULL );
+
+--HINT DISTRIBUTE ON RANDOM
+CREATE TABLE @cdmDatabaseSchema.COST (
+			cost_id integer NOT NULL,
+			cost_event_id integer NOT NULL,
+			cost_domain_id varchar(20) NOT NULL,
+			cost_type_concept_id integer NOT NULL,
+			currency_concept_id integer NULL,
+			total_charge NUMERIC NULL,
+			total_cost NUMERIC NULL,
+			total_paid NUMERIC NULL,
+			paid_by_payer NUMERIC NULL,
+			paid_by_patient NUMERIC NULL,
+			paid_patient_copay NUMERIC NULL,
+			paid_patient_coinsurance NUMERIC NULL,
+			paid_patient_deductible NUMERIC NULL,
+			paid_by_primary NUMERIC NULL,
+			paid_ingredient_cost NUMERIC NULL,
+			paid_dispensing_fee NUMERIC NULL,
+			payer_plan_period_id integer NULL,
+			amount_allowed NUMERIC NULL,
+			revenue_code_concept_id integer NULL,
+			revenue_code_source_value varchar(50) NULL,
+			drg_concept_id integer NULL,
+			drg_source_value varchar(3) NULL );
+
+--HINT DISTRIBUTE ON KEY (person_id)
+CREATE TABLE @cdmDatabaseSchema.DRUG_ERA (
+			drug_era_id integer NOT NULL,
+			person_id integer NOT NULL,
+			drug_concept_id integer NOT NULL,
+			drug_era_start_date TIMESTAMP NOT NULL,
+			drug_era_end_date TIMESTAMP NOT NULL,
+			drug_exposure_count integer NULL,
+			gap_days integer NULL );
+
+--HINT DISTRIBUTE ON KEY (person_id)
+CREATE TABLE @cdmDatabaseSchema.DOSE_ERA (
+			dose_era_id integer NOT NULL,
+			person_id integer NOT NULL,
+			drug_concept_id integer NOT NULL,
+			unit_concept_id integer NOT NULL,
+			dose_value NUMERIC NOT NULL,
+			dose_era_start_date TIMESTAMP NOT NULL,
+			dose_era_end_date TIMESTAMP NOT NULL );
+
+--HINT DISTRIBUTE ON KEY (person_id)
+CREATE TABLE @cdmDatabaseSchema.CONDITION_ERA (
+			condition_era_id integer NOT NULL,
+			person_id integer NOT NULL,
+			condition_concept_id integer NOT NULL,
+			condition_era_start_date TIMESTAMP NOT NULL,
+			condition_era_end_date TIMESTAMP NOT NULL,
+			condition_occurrence_count integer NULL );
+
+--HINT DISTRIBUTE ON KEY (person_id)
+CREATE TABLE @cdmDatabaseSchema.EPISODE (
+			episode_id bigint NOT NULL,
+			person_id bigint NOT NULL,
+			episode_concept_id integer NOT NULL,
+			episode_start_date date NOT NULL,
+			episode_start_datetime TIMESTAMP NULL,
+			episode_end_date date NULL,
+			episode_end_datetime TIMESTAMP NULL,
+			episode_parent_id bigint NULL,
+			episode_number integer NULL,
+			episode_object_concept_id integer NOT NULL,
+			episode_type_concept_id integer NOT NULL,
+			episode_source_value varchar(50) NULL,
+			episode_source_concept_id integer NULL );
+
+--HINT DISTRIBUTE ON RANDOM
+CREATE TABLE @cdmDatabaseSchema.EPISODE_EVENT (
+			episode_id bigint NOT NULL,
+			event_id bigint NOT NULL,
+			episode_event_field_concept_id integer NOT NULL );
+
+--HINT DISTRIBUTE ON RANDOM
+CREATE TABLE @cdmDatabaseSchema.METADATA (
+			metadata_id integer NOT NULL,
+			metadata_concept_id integer NOT NULL,
+			metadata_type_concept_id integer NOT NULL,
+			name varchar(250) NOT NULL,
+			value_as_string varchar(250) NULL,
+			value_as_concept_id integer NULL,
+			value_as_number NUMERIC NULL,
+			metadata_date date NULL,
+			metadata_datetime TIMESTAMP NULL );
+
+--HINT DISTRIBUTE ON RANDOM
+CREATE TABLE @cdmDatabaseSchema.CDM_SOURCE (
+			cdm_source_name varchar(255) NOT NULL,
+			cdm_source_abbreviation varchar(25) NOT NULL,
+			cdm_holder varchar(255) NOT NULL,
+			source_description TEXT NULL,
+			source_documentation_reference varchar(255) NULL,
+			cdm_etl_reference varchar(255) NULL,
+			source_release_date date NOT NULL,
+			cdm_release_date date NOT NULL,
+			cdm_version varchar(10) NULL,
+			cdm_version_concept_id integer NOT NULL,
+			vocabulary_version varchar(20) NOT NULL );
+
+--HINT DISTRIBUTE ON RANDOM
+CREATE TABLE @cdmDatabaseSchema.CONCEPT (
+			concept_id integer NOT NULL,
+			concept_name varchar(255) NOT NULL,
+			domain_id varchar(20) NOT NULL,
+			vocabulary_id varchar(20) NOT NULL,
+			concept_class_id varchar(20) NOT NULL,
+			standard_concept varchar(1) NULL,
+			concept_code varchar(50) NOT NULL,
+			valid_start_date date NOT NULL,
+			valid_end_date date NOT NULL,
+			invalid_reason varchar(1) NULL );
+
+--HINT DISTRIBUTE ON RANDOM
+CREATE TABLE @cdmDatabaseSchema.VOCABULARY (
+			vocabulary_id varchar(20) NOT NULL,
+			vocabulary_name varchar(255) NOT NULL,
+			vocabulary_reference varchar(255) NULL,
+			vocabulary_version varchar(255) NULL,
+			vocabulary_concept_id integer NOT NULL );
+
+--HINT DISTRIBUTE ON RANDOM
+CREATE TABLE @cdmDatabaseSchema.DOMAIN (
+			domain_id varchar(20) NOT NULL,
+			domain_name varchar(255) NOT NULL,
+			domain_concept_id integer NOT NULL );
+
+--HINT DISTRIBUTE ON RANDOM
+CREATE TABLE @cdmDatabaseSchema.CONCEPT_CLASS (
+			concept_class_id varchar(20) NOT NULL,
+			concept_class_name varchar(255) NOT NULL,
+			concept_class_concept_id integer NOT NULL );
+
+--HINT DISTRIBUTE ON RANDOM
+CREATE TABLE @cdmDatabaseSchema.CONCEPT_RELATIONSHIP (
+			concept_id_1 integer NOT NULL,
+			concept_id_2 integer NOT NULL,
+			relationship_id varchar(20) NOT NULL,
+			valid_start_date date NOT NULL,
+			valid_end_date date NOT NULL,
+			invalid_reason varchar(1) NULL );
+
+--HINT DISTRIBUTE ON RANDOM
+CREATE TABLE @cdmDatabaseSchema.RELATIONSHIP (
+			relationship_id varchar(20) NOT NULL,
+			relationship_name varchar(255) NOT NULL,
+			is_hierarchical varchar(1) NOT NULL,
+			defines_ancestry varchar(1) NOT NULL,
+			reverse_relationship_id varchar(20) NOT NULL,
+			relationship_concept_id integer NOT NULL );
+
+--HINT DISTRIBUTE ON RANDOM
+CREATE TABLE @cdmDatabaseSchema.CONCEPT_SYNONYM (
+			concept_id integer NOT NULL,
+			concept_synonym_name varchar(1000) NOT NULL,
+			language_concept_id integer NOT NULL );
+
+--HINT DISTRIBUTE ON RANDOM
+CREATE TABLE @cdmDatabaseSchema.CONCEPT_ANCESTOR (
+			ancestor_concept_id integer NOT NULL,
+			descendant_concept_id integer NOT NULL,
+			min_levels_of_separation integer NOT NULL,
+			max_levels_of_separation integer NOT NULL );
+
+--HINT DISTRIBUTE ON RANDOM
+CREATE TABLE @cdmDatabaseSchema.SOURCE_TO_CONCEPT_MAP (
+			source_code varchar(50) NOT NULL,
+			source_concept_id integer NOT NULL,
+			source_vocabulary_id varchar(20) NOT NULL,
+			source_code_description varchar(255) NULL,
+			target_concept_id integer NOT NULL,
+			target_vocabulary_id varchar(20) NOT NULL,
+			valid_start_date date NOT NULL,
+			valid_end_date date NOT NULL,
+			invalid_reason varchar(1) NULL );
+
+--HINT DISTRIBUTE ON RANDOM
+CREATE TABLE @cdmDatabaseSchema.DRUG_STRENGTH (
+			drug_concept_id integer NOT NULL,
+			ingredient_concept_id integer NOT NULL,
+			amount_value NUMERIC NULL,
+			amount_unit_concept_id integer NULL,
+			numerator_value NUMERIC NULL,
+			numerator_unit_concept_id integer NULL,
+			denominator_value NUMERIC NULL,
+			denominator_unit_concept_id integer NULL,
+			box_size integer NULL,
+			valid_start_date date NOT NULL,
+			valid_end_date date NOT NULL,
+			invalid_reason varchar(1) NULL );
+
+--HINT DISTRIBUTE ON RANDOM
+CREATE TABLE @cdmDatabaseSchema.COHORT (
+			cohort_definition_id integer NOT NULL,
+			subject_id integer NOT NULL,
+			cohort_start_date date NOT NULL,
+			cohort_end_date date NOT NULL );
+
+--HINT DISTRIBUTE ON RANDOM
+CREATE TABLE @cdmDatabaseSchema.COHORT_DEFINITION (
+			cohort_definition_id integer NOT NULL,
+			cohort_definition_name varchar(255) NOT NULL,
+			cohort_definition_description TEXT NULL,
+			definition_type_concept_id integer NOT NULL,
+			cohort_definition_syntax TEXT NULL,
+			subject_concept_id integer NOT NULL,
+			cohort_initiation_date date NULL );