carrot-transform 0.3__py3-none-any.whl

carrottransform/config/OMOPCDM_postgresql_5.3_ddl.sql

@@ -0,0 +1,508 @@
+--postgresql CDM DDL Specification for OMOP Common Data Model 5.3
+
+--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,
+			admitting_source_concept_id integer NULL,
+			admitting_source_value varchar(50) NULL,
+			discharge_to_concept_id integer NULL,
+			discharge_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,
+			admitting_source_value Varchar(50) NULL,
+			admitting_source_concept_id Integer NULL,
+			discharge_to_source_value Varchar(50) NULL,
+			discharge_to_concept_id integer NULL,
+			preceding_visit_detail_id integer NULL,
+			visit_detail_parent_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_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(50) 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 );
+
+--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,
+			value_source_value varchar(50) 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 );
+
+--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 );
+
+--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 );
+
+--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 date NOT NULL,
+			drug_era_end_date date 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 date NOT NULL,
+			dose_era_end_date date 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 date NOT NULL,
+			condition_era_end_date date NOT NULL,
+			condition_occurrence_count integer NULL );
+
+--HINT DISTRIBUTE ON RANDOM
+CREATE TABLE @cdmDatabaseSchema.METADATA (
+			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,
+			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) NULL,
+			cdm_holder varchar(255) NULL,
+			source_description TEXT NULL,
+			source_documentation_reference varchar(255) NULL,
+			cdm_etl_reference varchar(255) NULL,
+			source_release_date date NULL,
+			cdm_release_date date NULL,
+			cdm_version varchar(10) NULL,
+			vocabulary_version varchar(20) 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) NOT 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_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 );
+
+--HINT DISTRIBUTE ON RANDOM
+CREATE TABLE @cdmDatabaseSchema.ATTRIBUTE_DEFINITION (
+			attribute_definition_id integer NOT NULL,
+			attribute_name varchar(255) NOT NULL,
+			attribute_description TEXT NULL,
+			attribute_type_concept_id integer NOT NULL,
+			attribute_syntax TEXT NULL );

carrottransform/config/omop.json

@@ -0,0 +1,61 @@
+{
+  "datetime_linked_fields": {
+    "condition_occurrence": {
+	    "condition_start_datetime": "condition_start_date", 
+	    "condition_end_datetime": "condition_end_date"
+    },
+    "death": {
+	    "death_datetime": "death_date"
+    },
+    "drug_exposure": {
+	    "drug_exposure_start_datetime": "drug_exposure_start_date", 
+	    "drug_exposure_end_datetime": "drug_exposure_end_date"
+    },
+    "measurement": {
+	    "measurement_datetime": "measurement_date"
+    },
+    "observation": {
+	    "observation_datetime": "observation_date"
+    },
+    "procedure_occurrence": {
+	    "procedure_datetime": "procedure_date"
+    },
+    "specimen": {
+	    "specimen_datetime": "specimen_date"
+    },
+    "visit_occurrence": {
+	    "visit_start_datetime": "visit_start_date", 
+	    "visit_end_datetime": "visit_end_date"
+    }
+  },
+  "date_field_components": {
+    "person": {
+	    "birth_datetime": {
+		    "year":"year_of_birth", 
+		    "month":"month_of_birth", 
+		    "day":"day_of_birth"
+	    }
+    }
+  },
+  "person_id_field": {
+    "condition_occurrence": "person_id",
+    "death": "person_id",
+    "drug_exposure": "person_id",
+    "measurement": "person_id",
+    "observation": "person_id",
+    "person": "person_id",
+    "procedure_occurrence": "person_id",
+    "specimen": "person_id",
+    "visit_occurrence": "person_id"
+  },
+  "auto_number_field": {
+    "condition_occurrence": "condition_occurrence_id",
+    "death": "death_id",
+    "drug_exposure": "drug_exposure_id",
+    "measurement": "measurement_id",
+    "observation": "observation_id",
+    "procedure_occurrence": "procedure_occurrence_id",
+    "specimen": "specimen_id",
+    "visit_occurrence": "visit_occurrence_id"
+  }
+}

carrottransform/tools/__init__.py

@@ -0,0 +1,17 @@
+import carrottransform
+import os
+import sys
+import json
+import time
+
+from .file_helpers import (
+  load_json
+)
+
+from .metrics import (
+  Metrics
+)
+from . import mappingrules
+
+from . import omopcdm
+

carrottransform/tools/file_helpers.py

@@ -0,0 +1,14 @@
+import os
+import json
+    
+def load_json(f_in):
+  if os.path.exists(f_in):
+    data = json.load(open(f_in))
+  else:
+    try:
+      data = json.loads(f_in)
+    except Exception as err:
+      raise FileNotFoundError(f"{f_in} not found. Or cannot parse as json")
+
+  return data
+