pyomop package¶

Submodules¶

pyomop.cdm6_tables module¶

This file is part of PyOMOP.

PyOMOP is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

PyOMOP is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with PyOMOP. If not, see <http://www.gnu.org/licenses/>.

class pyomop.cdm6_tables.AttributeDefinition(**kwargs)[source]¶

Bases: sqlalchemy.orm.decl_api._DynamicAttributesType, sqlalchemy.inspection.Inspectable[sqlalchemy.orm.mapper.Mapper[Any]]

attribute_definition_id¶

attribute_description¶

attribute_name¶

attribute_syntax¶

attribute_type_concept_id¶

class pyomop.cdm6_tables.CareSite(**kwargs)[source]¶

Bases: sqlalchemy.orm.decl_api._DynamicAttributesType, sqlalchemy.inspection.Inspectable[sqlalchemy.orm.mapper.Mapper[Any]]

care_site_id¶

care_site_name¶

care_site_source_value¶

location_id¶

place_of_service_concept_id¶

place_of_service_source_value¶

class pyomop.cdm6_tables.CdmSource(**kwargs)[source]¶

Bases: sqlalchemy.orm.decl_api._DynamicAttributesType, sqlalchemy.inspection.Inspectable[sqlalchemy.orm.mapper.Mapper[Any]]

cdm_etl_reference¶

cdm_holder¶

cdm_release_date¶

cdm_source_abbreviation¶

cdm_source_name¶

cdm_version¶

source_description¶

source_documentation_reference¶

source_release_date¶

vocabulary_version¶

class pyomop.cdm6_tables.Cohort(**kwargs)[source]¶

Bases: sqlalchemy.orm.decl_api._DynamicAttributesType, sqlalchemy.inspection.Inspectable[sqlalchemy.orm.mapper.Mapper[Any]]

cohort_definition_id¶

cohort_end_date¶

cohort_start_date¶

subject_id¶

class pyomop.cdm6_tables.CohortAttribute(**kwargs)[source]¶

Bases: sqlalchemy.orm.decl_api._DynamicAttributesType, sqlalchemy.inspection.Inspectable[sqlalchemy.orm.mapper.Mapper[Any]]

attribute_definition_id¶

cohort_definition_id¶

cohort_end_date¶

cohort_start_date¶

subject_id¶

value_as_concept_id¶

value_as_number¶

class pyomop.cdm6_tables.CohortDefinition(**kwargs)[source]¶

Bases: sqlalchemy.orm.decl_api._DynamicAttributesType, sqlalchemy.inspection.Inspectable[sqlalchemy.orm.mapper.Mapper[Any]]

cohort_definition_description¶

cohort_definition_id¶

cohort_definition_name¶

cohort_definition_syntax¶

cohort_initiation_date¶

definition_type_concept_id¶

subject_concept_id¶

class pyomop.cdm6_tables.Concept(**kwargs)[source]¶

Bases: sqlalchemy.orm.decl_api._DynamicAttributesType, sqlalchemy.inspection.Inspectable[sqlalchemy.orm.mapper.Mapper[Any]]

concept_class_id¶

concept_code¶

concept_id¶

concept_name¶

domain_id¶

invalid_reason¶

standard_concept¶

valid_end_date¶

valid_start_date¶

vocabulary_id¶

class pyomop.cdm6_tables.ConceptAncestor(**kwargs)[source]¶

Bases: sqlalchemy.orm.decl_api._DynamicAttributesType, sqlalchemy.inspection.Inspectable[sqlalchemy.orm.mapper.Mapper[Any]]

ancestor_concept_id¶

descendant_concept_id¶

max_levels_of_separation¶

min_levels_of_separation¶

class pyomop.cdm6_tables.ConceptClass(**kwargs)[source]¶

Bases: sqlalchemy.orm.decl_api._DynamicAttributesType, sqlalchemy.inspection.Inspectable[sqlalchemy.orm.mapper.Mapper[Any]]

concept_class_concept_id¶

concept_class_id¶

concept_class_name¶

class pyomop.cdm6_tables.ConceptRelationship(**kwargs)[source]¶

Bases: sqlalchemy.orm.decl_api._DynamicAttributesType, sqlalchemy.inspection.Inspectable[sqlalchemy.orm.mapper.Mapper[Any]]

concept_id_1¶

concept_id_2¶

invalid_reason¶

relationship_id¶

valid_end_date¶

valid_start_date¶

class pyomop.cdm6_tables.ConceptSynonym(**kwargs)[source]¶

Bases: sqlalchemy.orm.decl_api._DynamicAttributesType, sqlalchemy.inspection.Inspectable[sqlalchemy.orm.mapper.Mapper[Any]]

concept_id¶

concept_synonym_name¶

language_concept_id¶

class pyomop.cdm6_tables.ConditionEra(**kwargs)[source]¶

Bases: sqlalchemy.orm.decl_api._DynamicAttributesType, sqlalchemy.inspection.Inspectable[sqlalchemy.orm.mapper.Mapper[Any]]

condition_concept_id¶

condition_era_end_date¶

condition_era_id¶

condition_era_start_date¶

condition_occurrence_count¶

person_id¶

class pyomop.cdm6_tables.ConditionOccurrence(**kwargs)[source]¶

Bases: sqlalchemy.orm.decl_api._DynamicAttributesType, sqlalchemy.inspection.Inspectable[sqlalchemy.orm.mapper.Mapper[Any]]

condition_concept_id¶

condition_end_date¶

condition_occurrence_id¶

condition_source_concept_id¶

condition_source_value¶

condition_start_date¶

condition_type_concept_id¶

person_id¶

provider_id¶

stop_reason¶

visit_occurrence_id¶

class pyomop.cdm6_tables.Death(**kwargs)[source]¶

Bases: sqlalchemy.orm.decl_api._DynamicAttributesType, sqlalchemy.inspection.Inspectable[sqlalchemy.orm.mapper.Mapper[Any]]

cause_concept_id¶

cause_source_concept_id¶

cause_source_value¶

death_date¶

death_type_concept_id¶

person_id¶

class pyomop.cdm6_tables.DeviceCost(**kwargs)[source]¶

Bases: sqlalchemy.orm.decl_api._DynamicAttributesType, sqlalchemy.inspection.Inspectable[sqlalchemy.orm.mapper.Mapper[Any]]

currency_concept_id¶

device_cost_id¶

device_exposure_id¶

paid_by_coordination_benefits¶

paid_by_payer¶

paid_coinsurance¶

paid_copay¶

paid_toward_deductible¶

payer_plan_period_id¶

total_out_of_pocket¶

total_paid¶

class pyomop.cdm6_tables.DeviceExposure(**kwargs)[source]¶

Bases: sqlalchemy.orm.decl_api._DynamicAttributesType, sqlalchemy.inspection.Inspectable[sqlalchemy.orm.mapper.Mapper[Any]]

device_concept_id¶

device_exposure_end_date¶

device_exposure_id¶

device_exposure_start_date¶

device_source_concept_id¶

device_source_value¶

device_type_concept_id¶

person_id¶

provider_id¶

quantity¶

unique_device_id¶

visit_occurrence_id¶

class pyomop.cdm6_tables.Domain(**kwargs)[source]¶

Bases: sqlalchemy.orm.decl_api._DynamicAttributesType, sqlalchemy.inspection.Inspectable[sqlalchemy.orm.mapper.Mapper[Any]]

domain_concept_id¶

domain_id¶

domain_name¶

class pyomop.cdm6_tables.DoseEra(**kwargs)[source]¶

Bases: sqlalchemy.orm.decl_api._DynamicAttributesType, sqlalchemy.inspection.Inspectable[sqlalchemy.orm.mapper.Mapper[Any]]

dose_era_end_date¶

dose_era_id¶

dose_era_start_date¶

dose_value¶

drug_concept_id¶

person_id¶

unit_concept_id¶

class pyomop.cdm6_tables.DrugCost(**kwargs)[source]¶

Bases: sqlalchemy.orm.decl_api._DynamicAttributesType, sqlalchemy.inspection.Inspectable[sqlalchemy.orm.mapper.Mapper[Any]]

average_wholesale_price¶

currency_concept_id¶

dispensing_fee¶

drug_cost_id¶

drug_exposure_id¶

ingredient_cost¶

paid_by_coordination_benefits¶

paid_by_payer¶

paid_coinsurance¶

paid_copay¶

paid_toward_deductible¶

payer_plan_period_id¶

total_out_of_pocket¶

total_paid¶

class pyomop.cdm6_tables.DrugEra(**kwargs)[source]¶

Bases: sqlalchemy.orm.decl_api._DynamicAttributesType, sqlalchemy.inspection.Inspectable[sqlalchemy.orm.mapper.Mapper[Any]]

drug_concept_id¶

drug_era_end_date¶

drug_era_id¶

drug_era_start_date¶

drug_exposure_count¶

gap_days¶

person_id¶

class pyomop.cdm6_tables.DrugExposure(**kwargs)[source]¶

Bases: sqlalchemy.orm.decl_api._DynamicAttributesType, sqlalchemy.inspection.Inspectable[sqlalchemy.orm.mapper.Mapper[Any]]

days_supply¶

dose_unit_concept_id¶

dose_unit_source_value¶

drug_concept_id¶

drug_exposure_end_date¶

drug_exposure_id¶

drug_exposure_start_date¶

drug_source_concept_id¶

drug_source_value¶

drug_type_concept_id¶

effective_drug_dose¶

lot_number¶

person_id¶

provider_id¶

quantity¶

refills¶

route_concept_id¶

route_source_value¶

sig¶

stop_reason¶

visit_occurrence_id¶

class pyomop.cdm6_tables.DrugStrength(**kwargs)[source]¶

Bases: sqlalchemy.orm.decl_api._DynamicAttributesType, sqlalchemy.inspection.Inspectable[sqlalchemy.orm.mapper.Mapper[Any]]

amount_unit_concept_id¶

amount_value¶

box_size¶

denominator_unit_concept_id¶

denominator_value¶

drug_concept_id¶

ingredient_concept_id¶

invalid_reason¶

numerator_unit_concept_id¶

numerator_value¶

valid_end_date¶

valid_start_date¶

class pyomop.cdm6_tables.FactRelationship(**kwargs)[source]¶

Bases: sqlalchemy.orm.decl_api._DynamicAttributesType, sqlalchemy.inspection.Inspectable[sqlalchemy.orm.mapper.Mapper[Any]]

domain_concept_id_1¶

domain_concept_id_2¶

fact_id_1¶

fact_id_2¶

relationship_concept_id¶

class pyomop.cdm6_tables.Location(**kwargs)[source]¶

Bases: sqlalchemy.orm.decl_api._DynamicAttributesType, sqlalchemy.inspection.Inspectable[sqlalchemy.orm.mapper.Mapper[Any]]

address_1¶

address_2¶

city¶

county¶

location_id¶

location_source_value¶

state¶

zip¶

class pyomop.cdm6_tables.Measurement(**kwargs)[source]¶

Bases: sqlalchemy.orm.decl_api._DynamicAttributesType, sqlalchemy.inspection.Inspectable[sqlalchemy.orm.mapper.Mapper[Any]]

measurement_concept_id¶

measurement_date¶

measurement_id¶

measurement_source_concept_id¶

measurement_source_value¶

measurement_time¶

measurement_type_concept_id¶

operator_concept_id¶

person_id¶

provider_id¶

range_high¶

range_low¶

unit_concept_id¶

unit_source_value¶

value_as_concept_id¶

value_as_number¶

value_source_value¶

visit_occurrence_id¶

class pyomop.cdm6_tables.Note(**kwargs)[source]¶

Bases: sqlalchemy.orm.decl_api._DynamicAttributesType, sqlalchemy.inspection.Inspectable[sqlalchemy.orm.mapper.Mapper[Any]]

note_date¶

note_id¶

note_source_value¶

note_text¶

note_time¶

note_type_concept_id¶

person_id¶

provider_id¶

visit_occurrence_id¶

class pyomop.cdm6_tables.Observation(**kwargs)[source]¶

Bases: sqlalchemy.orm.decl_api._DynamicAttributesType, sqlalchemy.inspection.Inspectable[sqlalchemy.orm.mapper.Mapper[Any]]

observation_concept_id¶

observation_date¶

observation_id¶

observation_source_concept_id¶

observation_source_value¶

observation_time¶

observation_type_concept_id¶

person_id¶

provider_id¶

qualifier_concept_id¶

qualifier_source_value¶

unit_concept_id¶

unit_source_value¶

value_as_concept_id¶

value_as_number¶

value_as_string¶

visit_occurrence_id¶

class pyomop.cdm6_tables.ObservationPeriod(**kwargs)[source]¶

Bases: sqlalchemy.orm.decl_api._DynamicAttributesType, sqlalchemy.inspection.Inspectable[sqlalchemy.orm.mapper.Mapper[Any]]

observation_period_end_date¶

observation_period_id¶

observation_period_start_date¶

period_type_concept_id¶

person_id¶

class pyomop.cdm6_tables.PayerPlanPeriod(**kwargs)[source]¶

Bases: sqlalchemy.orm.decl_api._DynamicAttributesType, sqlalchemy.inspection.Inspectable[sqlalchemy.orm.mapper.Mapper[Any]]

family_source_value¶

payer_plan_period_end_date¶

payer_plan_period_id¶

payer_plan_period_start_date¶

payer_source_value¶

person_id¶

plan_source_value¶

class pyomop.cdm6_tables.Person(**kwargs)[source]¶

Bases: sqlalchemy.orm.decl_api._DynamicAttributesType, sqlalchemy.inspection.Inspectable[sqlalchemy.orm.mapper.Mapper[Any]]

birth_datetime¶

care_site_id¶

day_of_birth¶

death_datetime¶

ethnicity_concept_id¶

ethnicity_source_concept_id¶

ethnicity_source_value¶

gender_concept_id¶

gender_source_concept_id¶

gender_source_value¶

location_id¶

month_of_birth¶

person_id¶

person_source_value¶

provider_id¶

race_concept_id¶

race_source_concept_id¶

race_source_value¶

year_of_birth¶

class pyomop.cdm6_tables.ProcedureCost(**kwargs)[source]¶

Bases: sqlalchemy.orm.decl_api._DynamicAttributesType, sqlalchemy.inspection.Inspectable[sqlalchemy.orm.mapper.Mapper[Any]]

currency_concept_id¶

paid_by_coordination_benefits¶

paid_by_payer¶

paid_coinsurance¶

paid_copay¶

paid_toward_deductible¶

payer_plan_period_id¶

procedure_cost_id¶

procedure_occurrence_id¶

revenue_code_concept_id¶

revenue_code_source_value¶

total_out_of_pocket¶

total_paid¶

class pyomop.cdm6_tables.ProcedureOccurrence(**kwargs)[source]¶

Bases: sqlalchemy.orm.decl_api._DynamicAttributesType, sqlalchemy.inspection.Inspectable[sqlalchemy.orm.mapper.Mapper[Any]]

modifier_concept_id¶

person_id¶

procedure_concept_id¶

procedure_date¶

procedure_occurrence_id¶

procedure_source_concept_id¶

procedure_source_value¶

procedure_type_concept_id¶

provider_id¶

qualifier_source_value¶

quantity¶

visit_occurrence_id¶

class pyomop.cdm6_tables.Provider(**kwargs)[source]¶

Bases: sqlalchemy.orm.decl_api._DynamicAttributesType, sqlalchemy.inspection.Inspectable[sqlalchemy.orm.mapper.Mapper[Any]]

care_site_id¶

dea¶

gender_concept_id¶

gender_source_concept_id¶

gender_source_value¶

npi¶

provider_id¶

provider_name¶

provider_source_value¶

specialty_concept_id¶

specialty_source_concept_id¶

specialty_source_value¶

year_of_birth¶

class pyomop.cdm6_tables.Relationship(**kwargs)[source]¶

Bases: sqlalchemy.orm.decl_api._DynamicAttributesType, sqlalchemy.inspection.Inspectable[sqlalchemy.orm.mapper.Mapper[Any]]

defines_ancestry¶

is_hierarchical¶

relationship_concept_id¶

relationship_id¶

relationship_name¶

reverse_relationship_id¶

class pyomop.cdm6_tables.SourceToConceptMap(**kwargs)[source]¶

Bases: sqlalchemy.orm.decl_api._DynamicAttributesType, sqlalchemy.inspection.Inspectable[sqlalchemy.orm.mapper.Mapper[Any]]

invalid_reason¶

source_code¶

source_code_description¶

source_concept_id¶

source_vocabulary_id¶

target_concept_id¶

target_vocabulary_id¶

valid_end_date¶

valid_start_date¶

class pyomop.cdm6_tables.Speciman(**kwargs)[source]¶

Bases: sqlalchemy.orm.decl_api._DynamicAttributesType, sqlalchemy.inspection.Inspectable[sqlalchemy.orm.mapper.Mapper[Any]]

anatomic_site_concept_id¶

anatomic_site_source_value¶

disease_status_concept_id¶

disease_status_source_value¶

person_id¶

quantity¶

specimen_concept_id¶

specimen_date¶

specimen_id¶

specimen_source_id¶

specimen_source_value¶

specimen_time¶

specimen_type_concept_id¶

unit_concept_id¶

unit_source_value¶

class pyomop.cdm6_tables.VisitCost(**kwargs)[source]¶

Bases: sqlalchemy.orm.decl_api._DynamicAttributesType, sqlalchemy.inspection.Inspectable[sqlalchemy.orm.mapper.Mapper[Any]]

currency_concept_id¶

paid_by_coordination_benefits¶

paid_by_payer¶

paid_coinsurance¶

paid_copay¶

paid_toward_deductible¶

payer_plan_period_id¶

total_out_of_pocket¶

total_paid¶

visit_cost_id¶

visit_occurrence_id¶

class pyomop.cdm6_tables.VisitOccurrence(**kwargs)[source]¶

Bases: sqlalchemy.orm.decl_api._DynamicAttributesType, sqlalchemy.inspection.Inspectable[sqlalchemy.orm.mapper.Mapper[Any]]

care_site_id¶

person_id¶

provider_id¶

visit_concept_id¶

visit_end_date¶

visit_end_time¶

visit_occurrence_id¶

visit_source_concept_id¶

visit_source_value¶

visit_start_date¶

visit_start_time¶

visit_type_concept_id¶

class pyomop.cdm6_tables.Vocabulary(**kwargs)[source]¶

Bases: sqlalchemy.orm.decl_api._DynamicAttributesType, sqlalchemy.inspection.Inspectable[sqlalchemy.orm.mapper.Mapper[Any]]

vocabulary_concept_id¶

vocabulary_id¶

vocabulary_name¶

vocabulary_reference¶

vocabulary_version¶

pyomop.engine_factory module¶

class pyomop.engine_factory.CdmEngineFactory(db='sqlite', host='localhost', port=5432, user='root', pw='pass', name='cdm6.sqlite', schema='public')[source]¶

Bases: object

property async_session¶

property base¶

property db¶

property engine¶

property host¶

async init_models(metadata)[source]¶

property name¶

property port¶

property pw¶

property schema¶

property session¶

property user¶

pyomop.main module¶

pyomop.main.main_routine()[source]¶

pyomop.sqldict module¶

pyomop.vector module¶

class pyomop.vector.CdmVector(result=None)[source]¶

Bases: object

create_df(_names=None)[source]¶

property df¶

query_to_list()[source]¶: List of result Return: columns name, list of result

property result¶

async sql_df(cdm, sqldict=None, query=None, chunksize=1000)[source]¶

pyomop.vocabulary module¶

class pyomop.vocabulary.CdmVocabulary(cdm)[source]¶

Bases: object

property concept_code¶

property concept_id¶

property concept_name¶

create_vocab(folder, sample=None)[source]¶

property domain_id¶

async get_concept(concept_id)[source]¶

async get_concept_by_code(concept_code, vocabulary_id)[source]¶

get_session() → AsyncGenerator[sqlalchemy.ext.asyncio.session.AsyncSession, None][source]¶

set_concept(concept_code, vocabulary_id=None)[source]¶

property vocabulary_id¶

async write_vocab(df, table, if_exists='replace', chunk_size=1000)[source]¶

pyomop package¶

Submodules¶

pyomop.cdm6_tables module¶

pyomop.engine_factory module¶

pyomop.main module¶

pyomop.sqldict module¶

pyomop.vector module¶

pyomop.vocabulary module¶

Module contents¶

pyomop

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