From 7bad0a9ef01a48b70750ff28db1e3547e5e818b2 Mon Sep 17 00:00:00 2001 From: Kevin Yee Date: Mon, 19 Mar 2018 17:03:02 -0400 Subject: [PATCH] removed null statements when creating bigquery tables --- BigQuery/OMOP CDM bigquery ddl.txt | 543 +++++++++++++++-------------- 1 file changed, 272 insertions(+), 271 deletions(-) diff --git a/BigQuery/OMOP CDM bigquery ddl.txt b/BigQuery/OMOP CDM bigquery ddl.txt index 2e04b82..837c165 100644 --- a/BigQuery/OMOP CDM bigquery ddl.txt +++ b/BigQuery/OMOP CDM bigquery ddl.txt @@ -1,14 +1,15 @@ +#standardsql create table concept ( concept_id INT64 not null , concept_name STRING not null , domain_id STRING not null , vocabulary_id STRING not null , concept_class_id STRING not null , - standard_concept STRING null , + standard_concept STRING , concept_code STRING not null , valid_start_DATE DATE not null , valid_end_DATE DATE not null , - invalid_reason STRING null + invalid_reason STRING ) ; @@ -17,7 +18,7 @@ create table vocabulary ( vocabulary_id STRING not null, vocabulary_name STRING not null, vocabulary_reference STRING not null, - vocabulary_version STRING null, + vocabulary_version STRING , vocabulary_concept_id INT64 not null ) ; @@ -45,7 +46,7 @@ create table concept_relationship ( relationship_id STRING not null, valid_start_DATE DATE not null, valid_end_DATE DATE not null, - invalid_reason STRING null + invalid_reason STRING ) ; @@ -82,12 +83,12 @@ create table source_to_concept_map ( source_code STRING not null, source_concept_id INT64 not null, source_vocabulary_id STRING not null, - source_code_description STRING null, + source_code_description STRING , target_concept_id INT64 not null, target_vocabulary_id STRING not null, valid_start_DATE DATE not null, valid_end_DATE DATE not null, - invalid_reason STRING null + invalid_reason STRING ) ; @@ -97,16 +98,16 @@ create table source_to_concept_map ( create table drug_strength ( drug_concept_id INT64 not null, ingredient_concept_id INT64 not null, - amount_value FLOAT64 null, - amount_unit_concept_id INT64 null, - numerator_value FLOAT64 null, - numerator_unit_concept_id INT64 null, - denominator_value FLOAT64 null, - denominator_unit_concept_id INT64 null, - box_size INT64 null, - valid_start_DATE DATE not null, - valid_end_DATE DATE not null, - invalid_reason STRING null + amount_value FLOAT64 , + amount_unit_concept_id INT64 , + numerator_value FLOAT64 , + numerator_unit_concept_id INT64 , + denominator_value FLOAT64 , + denominator_unit_concept_id INT64 , + box_size INT64 , + valid_start_DATE DATE not null, + valid_end_DATE DATE not null, + invalid_reason STRING ) ; @@ -115,11 +116,11 @@ create table drug_strength ( create table cohort_definition ( cohort_definition_id INT64 not null, cohort_definition_name STRING not null, - cohort_definition_description STRING null, + cohort_definition_description STRING , definition_type_concept_id INT64 not null, - cohort_definition_syntax STRING null, + cohort_definition_syntax STRING , subject_concept_id INT64 not null, - cohort_initiation_DATE DATE null + cohort_initiation_DATE DATE ) ; @@ -127,9 +128,9 @@ create table cohort_definition ( create table attribute_definition ( attribute_definition_id INT64 not null, attribute_name STRING not null, - attribute_description STRING null, + attribute_description STRING , attribute_type_concept_id INT64 not null, - attribute_syntax STRING null + attribute_syntax STRING ) ; @@ -137,15 +138,15 @@ create table attribute_definition ( create table cdm_source ( cdm_source_name STRING not null , - cdm_source_abbreviation STRING null , - cdm_holder STRING null , - source_description STRING null , - source_documentation_reference STRING null , - cdm_etl_reference STRING null , - source_release_DATE DATE null , - cdm_release_DATE DATE null , - cdm_version STRING null , - vocabulary_version STRING null + cdm_source_abbreviation STRING , + cdm_holder STRING , + source_description STRING , + source_documentation_reference STRING , + cdm_etl_reference STRING , + source_release_DATE DATE , + cdm_release_DATE DATE , + cdm_version STRING , + vocabulary_version STRING ) ; @@ -155,10 +156,10 @@ create table metadata metadata_concept_id INT64 not null , metadata_type_concept_id INT64 not null , name STRING not null , - value_as_string STRING null , - value_as_concept_id INT64 null , - metadata_DATE DATE null , - metadata_DATETIME DATETIME null + value_as_string STRING , + value_as_concept_id INT64 , + metadata_DATE DATE , + metadata_DATETIME DATETIME ) ; @@ -170,21 +171,21 @@ create table person person_id INT64 not null , gender_concept_id INT64 not null , year_of_birth INT64 not null , - month_of_birth INT64 null, - day_of_birth INT64 null, - birth_DATETIME DATETIME null, + month_of_birth INT64 , + day_of_birth INT64 , + birth_DATETIME DATETIME , race_concept_id INT64 not null, ethnicity_concept_id INT64 not null, - location_id INT64 null, - provider_id INT64 null, - care_site_id INT64 null, - person_source_value STRING null, - gender_source_value STRING null, - gender_source_concept_id INT64 null, - race_source_value STRING null, - race_source_concept_id INT64 null, - ethnicity_source_value STRING null, - ethnicity_source_concept_id INT64 null + location_id INT64 , + provider_id INT64 , + care_site_id INT64 , + person_source_value STRING , + gender_source_value STRING , + gender_source_concept_id INT64 , + race_source_value STRING , + race_source_concept_id INT64 , + ethnicity_source_value STRING , + ethnicity_source_concept_id INT64 ) ; @@ -194,8 +195,8 @@ create table observation_period ( observation_period_id INT64 not null , person_id INT64 not null , - observation_period_start_DATE DATE not null , - observation_period_end_DATE DATE not null , + observation_period_start_DATE DATE not null , + observation_period_end_DATE DATE not null , period_type_concept_id INT64 not null ) ; @@ -208,17 +209,17 @@ create table specimen person_id INT64 not null , specimen_concept_id INT64 not null , specimen_type_concept_id INT64 not null , - specimen_DATE DATE not null , - specimen_DATETIME DATETIME null , - quantity FLOAT64 null , - unit_concept_id INT64 null , - anatomic_site_concept_id INT64 null , - disease_status_concept_id INT64 null , - specimen_source_id STRING null , - specimen_source_value STRING null , - unit_source_value STRING null , - anatomic_site_source_value STRING null , - disease_status_source_value STRING null + specimen_DATE DATE not null , + specimen_DATETIME DATETIME , + quantity FLOAT64 , + unit_concept_id INT64 , + anatomic_site_concept_id INT64 , + disease_status_concept_id INT64 , + specimen_source_id STRING , + specimen_source_value STRING , + unit_source_value STRING , + anatomic_site_source_value STRING , + disease_status_source_value STRING ) ; @@ -227,12 +228,12 @@ create table specimen create table death ( person_id INT64 not null , - death_DATE DATE not null , - death_DATETIME DATETIME null , + death_DATE DATE not null , + death_DATETIME DATETIME , death_type_concept_id INT64 not null , - cause_concept_id INT64 null , - cause_source_value STRING null, - cause_source_concept_id INT64 null + cause_concept_id INT64 , + cause_source_value STRING , + cause_source_concept_id INT64 ) ; @@ -243,20 +244,20 @@ create table visit_occurrence visit_occurrence_id INT64 not null , person_id INT64 not null , visit_concept_id INT64 not null , - visit_start_DATE DATE not null , - visit_start_DATETIME DATETIME null , - visit_end_DATE DATE not null , - visit_end_DATETIME DATETIME null , + visit_start_DATE DATE not null , + visit_start_DATETIME DATETIME , + visit_end_DATE DATE not null , + visit_end_DATETIME DATETIME , visit_type_concept_id INT64 not null , - provider_id INT64 null, - care_site_id INT64 null, - visit_source_value STRING null, - visit_source_concept_id INT64 null , - admitting_source_concept_id INT64 null , - admitting_source_value STRING null , - discharge_to_concept_id INT64 null , - discharge_to_source_value STRING null , - preceding_visit_occurrence_id INT64 null + provider_id INT64 , + care_site_id INT64 , + visit_source_value STRING , + visit_source_concept_id INT64 , + admitting_source_concept_id INT64 , + admitting_source_value STRING , + discharge_to_concept_id INT64 , + discharge_to_source_value STRING , + preceding_visit_occurrence_id INT64 ) ; @@ -267,21 +268,21 @@ create table visit_detail visit_detail_id INT64 not null , person_id INT64 not null , visit_detail_concept_id INT64 not null , - visit_start_DATE DATE not null , - visit_start_DATETIME DATETIME null , - visit_end_DATE DATE not null , - visit_end_DATETIME DATETIME null , + visit_start_DATE DATE not null , + visit_start_DATETIME DATETIME , + visit_end_DATE DATE not null , + visit_end_DATETIME DATETIME , visit_type_concept_id INT64 not null , - provider_id INT64 null , - care_site_id INT64 null , - admitting_source_concept_id INT64 null , - discharge_to_concept_id INT64 null , - preceding_visit_detail_id INT64 null , - visit_source_value STRING null , - visit_source_concept_id INT64 null , - admitting_source_value STRING null , - discharge_to_source_value STRING null , - visit_detail_parent_id INT64 null , + provider_id INT64 , + care_site_id INT64 , + admitting_source_concept_id INT64 , + discharge_to_concept_id INT64 , + preceding_visit_detail_id INT64 , + visit_source_value STRING , + visit_source_concept_id INT64 , + admitting_source_value STRING , + discharge_to_source_value STRING , + visit_detail_parent_id INT64 , visit_occurrence_id INT64 not null ) ; @@ -293,17 +294,17 @@ create table procedure_occurrence procedure_occurrence_id INT64 not null , person_id INT64 not null , procedure_concept_id INT64 not null , - procedure_DATE DATE not null , - procedure_DATETIME DATETIME null , + procedure_DATE DATE not null , + procedure_DATETIME DATETIME , procedure_type_concept_id INT64 not null , - modifier_concept_id INT64 null , - quantity INT64 null , - provider_id INT64 null , - visit_occurrence_id INT64 null , - visit_detail_id INT64 null , - procedure_source_value STRING null , - procedure_source_concept_id INT64 null , - modifier_source_value STRING null + modifier_concept_id INT64 , + quantity INT64 , + provider_id INT64 , + visit_occurrence_id INT64 , + visit_detail_id INT64 , + procedure_source_value STRING , + procedure_source_concept_id INT64 , + modifier_source_value STRING ) ; @@ -314,26 +315,26 @@ create table drug_exposure drug_exposure_id INT64 not null , person_id INT64 not null , drug_concept_id INT64 not null , - drug_exposure_start_DATE DATE not null , - drug_exposure_start_DATETIME DATETIME null , - drug_exposure_end_DATE DATE not null , - drug_exposure_end_DATETIME DATETIME null , - verbatim_end_DATE DATE null , + drug_exposure_start_DATE DATE not null , + drug_exposure_start_DATETIME DATETIME , + drug_exposure_end_DATE DATE not null , + drug_exposure_end_DATETIME DATETIME , + verbatim_end_DATE DATE , drug_type_concept_id INT64 not null , - stop_reason STRING null , - refills INT64 null , - quantity FLOAT64 null , - days_supply INT64 null , - sig STRING null , - route_concept_id INT64 null , - lot_number STRING null , - provider_id INT64 null , - visit_occurrence_id INT64 null , - visit_detail_id INT64 null , - drug_source_value STRING null , - drug_source_concept_id INT64 null , - route_source_value STRING null , - dose_unit_source_value STRING null + stop_reason STRING , + refills INT64 , + quantity FLOAT64 , + days_supply INT64 , + sig STRING , + route_concept_id INT64 , + lot_number STRING , + provider_id INT64 , + visit_occurrence_id INT64 , + visit_detail_id INT64 , + drug_source_value STRING , + drug_source_concept_id INT64 , + route_source_value STRING , + dose_unit_source_value STRING ) ; @@ -344,18 +345,18 @@ create table device_exposure device_exposure_id INT64 not null , person_id INT64 not null , device_concept_id INT64 not null , - device_exposure_start_DATE DATE not null , - device_exposure_start_DATETIME DATETIME null , - device_exposure_end_DATE DATE null , - device_exposure_end_DATETIME DATETIME null , + device_exposure_start_DATE DATE not null , + device_exposure_start_DATETIME DATETIME , + device_exposure_end_DATE DATE , + device_exposure_end_DATETIME DATETIME , device_type_concept_id INT64 not null , - unique_device_id STRING null , - quantity INT64 null , - provider_id INT64 null , - visit_occurrence_id INT64 null , - visit_detail_id INT64 null , - device_source_value STRING null , - device_source_concept_id INT64 null + unique_device_id STRING , + quantity INT64 , + provider_id INT64 , + visit_occurrence_id INT64 , + visit_detail_id INT64 , + device_source_value STRING , + device_source_concept_id INT64 ) ; @@ -366,19 +367,19 @@ create table condition_occurrence condition_occurrence_id INT64 not null , person_id INT64 not null , condition_concept_id INT64 not null , - condition_start_DATE DATE not null , - condition_start_DATETIME DATETIME null , - condition_end_DATE DATE null , - condition_end_DATETIME DATETIME null , + condition_start_DATE DATE not null , + condition_start_DATETIME DATETIME , + condition_end_DATE DATE , + condition_end_DATETIME DATETIME , condition_type_concept_id INT64 not null , - stop_reason STRING null , - provider_id INT64 null , - visit_occurrence_id INT64 null , - visit_detail_id INT64 null , - condition_source_value STRING null , - condition_source_concept_id INT64 null , - condition_status_source_value STRING null , - condition_status_concept_id INT64 null + stop_reason STRING , + provider_id INT64 , + visit_occurrence_id INT64 , + visit_detail_id INT64 , + condition_source_value STRING , + condition_source_concept_id INT64 , + condition_status_source_value STRING , + condition_status_concept_id INT64 ) ; @@ -389,23 +390,23 @@ create table measurement measurement_id INT64 not null , person_id INT64 not null , measurement_concept_id INT64 not null , - measurement_DATE DATE not null , - measurement_DATETIME DATETIME null , - measurement_time STRING null , + measurement_DATE DATE not null , + measurement_DATETIME DATETIME , + measurement_time STRING , measurement_type_concept_id INT64 not null , - operator_concept_id INT64 null , - value_as_number FLOAT64 null , - value_as_concept_id INT64 null , - unit_concept_id INT64 null , - range_low FLOAT64 null , - range_high FLOAT64 null , - provider_id INT64 null , - visit_occurrence_id INT64 null , - visit_detail_id INT64 null , - measurement_source_value STRING null , - measurement_source_concept_id INT64 null , - unit_source_value STRING null , - value_source_value STRING null + operator_concept_id INT64 , + value_as_number FLOAT64 , + value_as_concept_id INT64 , + unit_concept_id INT64 , + range_low FLOAT64 , + range_high FLOAT64 , + provider_id INT64 , + visit_occurrence_id INT64 , + visit_detail_id INT64 , + measurement_source_value STRING , + measurement_source_concept_id INT64 , + unit_source_value STRING , + value_source_value STRING ) ; @@ -415,18 +416,18 @@ create table note ( note_id INT64 not null , person_id INT64 not null , - note_DATE DATE not null , - note_DATETIME DATETIME null , + note_DATE DATE not null , + note_DATETIME DATETIME , note_type_concept_id INT64 not null , note_class_concept_id INT64 not null , - note_title STRING null , - note_text STRING null , + note_title STRING , + note_text STRING , encoding_concept_id INT64 not null , language_concept_id INT64 not null , - provider_id INT64 null , - visit_occurrence_id INT64 null , - visit_detail_id INT64 null , - note_source_value STRING null + provider_id INT64 , + visit_occurrence_id INT64 , + visit_detail_id INT64 , + note_source_value STRING ) ; @@ -434,20 +435,20 @@ create table note create table note_nlp ( - note_nlp_id INT64 not null , - note_id INT64 not null , - section_concept_id INT64 null , - snippet STRING null , - "offset" STRING null , + note_nlp_id INT64 , + note_id INT64 , + section_concept_id INT64 , + snippet STRING , + "offset" STRING , lexical_variant STRING not null , - note_nlp_concept_id INT64 null , - note_nlp_source_concept_id INT64 null , - nlp_system STRING null , - nlp_DATE DATE not null , - nlp_DATETIME DATETIME null , - term_exists STRING null , - term_temporal STRING null , - term_modifiers STRING null + note_nlp_concept_id INT64 , + note_nlp_source_concept_id INT64 , + nlp_system STRING , + nlp_DATE DATE not null , + nlp_DATETIME DATETIME , + term_exists STRING , + term_temporal STRING , + term_modifiers STRING ) ; @@ -458,21 +459,21 @@ create table observation observation_id INT64 not null , person_id INT64 not null , observation_concept_id INT64 not null , - observation_DATE DATE not null , - observation_DATETIME DATETIME null , + observation_DATE DATE not null , + observation_DATETIME DATETIME , observation_type_concept_id INT64 not null , - value_as_number FLOAT64 null , - value_as_string STRING null , - value_as_concept_id INT64 null , - qualifier_concept_id INT64 null , - unit_concept_id INT64 null , - provider_id INT64 null , - visit_occurrence_id INT64 null , - visit_detail_id INT64 null , - observation_source_value STRING null , - observation_source_concept_id INT64 null , - unit_source_value STRING null , - qualifier_source_value STRING null + value_as_number FLOAT64 , + value_as_string STRING , + value_as_concept_id INT64 , + qualifier_concept_id INT64 , + unit_concept_id INT64 , + provider_id INT64 , + visit_occurrence_id INT64 , + visit_detail_id INT64 , + observation_source_value STRING , + observation_source_concept_id INT64 , + unit_source_value STRING , + qualifier_source_value STRING ) ; @@ -490,14 +491,14 @@ create table fact_relationship create table location ( - location_id INT64 not null , - address_1 STRING null , - address_2 STRING null , - city STRING null , - state STRING null , - zip STRING null , - county STRING null , - location_source_value STRING null + location_id INT64 not null , + address_1 STRING , + address_2 STRING , + city STRING , + state STRING , + zip STRING , + county STRING , + location_source_value STRING ) ; @@ -505,11 +506,11 @@ create table location create table care_site ( care_site_id INT64 not null , - care_site_name STRING null , - place_of_service_concept_id INT64 null , - location_id INT64 null , - care_site_source_value STRING null , - place_of_service_source_value STRING null + care_site_name STRING , + place_of_service_concept_id INT64 , + location_id INT64 , + care_site_source_value STRING , + place_of_service_source_value STRING ) ; @@ -517,18 +518,18 @@ create table care_site create table provider ( provider_id INT64 not null , - provider_name STRING null , - npi STRING null , - dea STRING null , - specialty_concept_id INT64 null , - care_site_id INT64 null , - year_of_birth INT64 null , - gender_concept_id INT64 null , - provider_source_value STRING null , - specialty_source_value STRING null , - specialty_source_concept_id INT64 null , - gender_source_value STRING null , - gender_source_concept_id INT64 null + provider_name STRING , + npi STRING , + dea STRING , + specialty_concept_id INT64 , + care_site_id INT64 , + year_of_birth INT64 , + gender_concept_id INT64 , + provider_source_value STRING , + specialty_source_value STRING , + specialty_source_concept_id INT64 , + gender_source_value STRING , + gender_source_concept_id INT64 ) ; @@ -536,23 +537,23 @@ create table provider --HINT DISTRIBUTE_ON_KEY(person_id) create table payer_plan_period ( - payer_plan_period_id INT64 not null , - person_id INT64 not null , - payer_plan_period_start_DATE DATE not null , - payer_plan_period_end_DATE DATE not null , - payer_concept_id INT64 null , - payer_source_value STRING null , - payer_source_concept_id INT64 null , - plan_concept_id INT64 null , - plan_source_value STRING null , - plan_source_concept_id INT64 null , - sponsor_concept_id INT64 null , - sponsor_source_value STRING null , - sponsor_source_concept_id INT64 null , - family_source_value STRING null , - stop_reason_concept_id INT64 null , - stop_reason_source_value STRING null , - stop_reason_source_concept_id INT64 null + payer_plan_period_id INT64 not null , + person_id INT64 not null , + payer_plan_period_start_DATE DATE not null , + payer_plan_period_end_DATE DATE not null , + payer_concept_id INT64 , + payer_source_value STRING , + payer_source_concept_id INT64 , + plan_concept_id INT64 , + plan_source_value STRING , + plan_source_concept_id INT64 , + sponsor_concept_id INT64 , + sponsor_source_value STRING , + sponsor_source_concept_id INT64 , + family_source_value STRING , + stop_reason_concept_id INT64 , + stop_reason_source_value STRING , + stop_reason_source_concept_id INT64 ) ; @@ -561,26 +562,26 @@ create table cost ( cost_id INT64 not null , cost_event_id INT64 not null , - cost_domain_id STRING not null , + cost_domain_id STRING not null , cost_type_concept_id INT64 not null , - currency_concept_id INT64 null , - total_charge FLOAT64 null , - total_cost FLOAT64 null , - total_paid FLOAT64 null , - paid_by_payer FLOAT64 null , - paid_by_patient FLOAT64 null , - paid_patient_copay FLOAT64 null , - paid_patient_coinsurance FLOAT64 null , - paid_patient_deductible FLOAT64 null , - paid_by_primary FLOAT64 null , - paid_ingredient_cost FLOAT64 null , - paid_dispensing_fee FLOAT64 null , - payer_plan_period_id INT64 null , - amount_allowed FLOAT64 null , - revenue_code_concept_id INT64 null , - revenue_code_source_value STRING null, - drg_concept_id INT64 null, - drg_source_value STRING null + currency_concept_id INT64 , + total_charge FLOAT64 , + total_cost FLOAT64 , + total_paid FLOAT64 , + paid_by_payer FLOAT64 , + paid_by_patient FLOAT64 , + paid_patient_copay FLOAT64 , + paid_patient_coinsurance FLOAT64 , + paid_patient_deductible FLOAT64 , + paid_by_primary FLOAT64 , + paid_ingredient_cost FLOAT64 , + paid_dispensing_fee FLOAT64 , + payer_plan_period_id INT64 , + amount_allowed FLOAT64 , + revenue_code_concept_id INT64 , + revenue_code_source_value STRING , + drg_concept_id INT64 , + drg_source_value STRING ) ; @@ -599,13 +600,13 @@ create table cohort --HINT DISTRIBUTE_ON_KEY(subject_id) create table cohort_attribute ( - cohort_definition_id INT64 not null , - subject_id INT64 not null , + cohort_definition_id INT64 not null , + subject_id INT64 not null , cohort_start_DATE DATE not null , cohort_end_DATE DATE not null , - attribute_definition_id INT64 not null , - value_as_number FLOAT64 null , - value_as_concept_id INT64 null + attribute_definition_id INT64 not null , + value_as_number FLOAT64 , + value_as_concept_id INT64 ) ; @@ -616,10 +617,10 @@ create table drug_era drug_era_id INT64 not null , person_id INT64 not null , drug_concept_id INT64 not null , - drug_era_start_DATE DATE not null , - drug_era_end_DATE DATE not null , - drug_exposure_count INT64 null , - gap_days INT64 null + drug_era_start_DATE DATE not null , + drug_era_end_DATE DATE not null , + drug_exposure_count INT64 , + gap_days INT64 ) ; @@ -631,9 +632,9 @@ create table dose_era person_id INT64 not null , drug_concept_id INT64 not null , unit_concept_id INT64 not null , - dose_value FLOAT64 not null , - dose_era_start_DATE DATE not null , - dose_era_end_DATE DATE not null + dose_value FLOAT64 not null , + dose_era_start_DATE DATE not null , + dose_era_end_DATE DATE not null ) ; @@ -644,8 +645,8 @@ create table condition_era condition_era_id INT64 not null , person_id INT64 not null , condition_concept_id INT64 not null , - condition_era_start_DATE DATE not null , - condition_era_end_DATE DATE not null , - condition_occurrence_count INT64 null + condition_era_start_DATE DATE not null , + condition_era_end_DATE DATE not null , + condition_occurrence_count INT64 ) ;