eds_scikit.io.settings

default_tables_to_save module-attribute

default_tables_to_save = ['person', 'visit_occurrence', 'visit_detail', 'condition_occurrence', 'procedure_occurrence', 'care_site', 'concept']

The default tables loaded when instanciating a HiveData or a PostgresData

tables_to_load module-attribute

tables_to_load = {'person': ['person_id', 'location_id', 'year_of_birth', 'month_of_birth', 'day_of_birth', 'birth_datetime', 'death_datetime', 'gender_source_value', 'gender_source_concept_id', 'cdm_source'], 'visit_occurrence': ['visit_occurrence_id', 'person_id', 'visit_occurrence_source_value', 'preceding_visit_occurrence_id', 'care_site_id', 'visit_start_datetime', 'visit_end_datetime', 'visit_source_value', 'visit_source_concept_id', 'visit_type_source_value', 'visit_type_source_concept_id', 'admitted_from_source_value', 'admitted_from_source_concept_id', 'discharge_to_source_value', 'discharge_to_source_concept_id', 'row_status_source_value', 'stay_source_value', 'stay_source_concept_id', 'cdm_source'], 'care_site': ['care_site_id', 'care_site_source_value', 'care_site_name', 'care_site_short_name', 'place_of_service_source_value', 'care_site_type_source_value', 'valid_start_date', 'valid_end_date'], 'visit_detail': ['visit_detail_id', 'visit_occurrence_id', 'person_id', 'preceding_visit_detail_id', 'visit_detail_parent_id', 'care_site_id', 'visit_detail_start_date', 'visit_detail_start_datetime', 'visit_detail_end_date', 'visit_detail_end_datetime', 'visit_detail_source_value', 'visit_detail_source_concept_id', 'visit_detail_type_source_value', 'visit_detail_type_source_concept_id', 'admitted_from_source_value', 'admitted_from_source_concept_id', 'discharge_to_source_value', 'discharge_to_source_concept_id', 'cdm_source'], 'condition_occurrence': ['condition_occurrence_id', 'person_id', 'visit_occurrence_id', 'visit_detail_id', 'condition_start_datetime', 'condition_source_value', 'condition_source_concept_id', 'condition_status_source_value', 'condition_status_source_concept_id', 'cdm_source'], 'procedure_occurrence': ['procedure_occurrence_id', 'person_id', 'visit_occurrence_id', 'visit_detail_id', 'procedure_datetime', 'procedure_source_value', 'procedure_source_concept_id', 'cdm_source'], 'concept': ['concept_id', 'concept_name', 'domain_id', 'vocabulary_id', 'concept_class_id', 'standard_concept', 'concept_code', 'valid_start_date', 'valid_end_date', 'invalid_reason']}

The default columns loaded when instanciating a HiveData or a PostgresData

measurement_config module-attribute

measurement_config = dict(standard_terminologies=['LOINC', 'AnaBio', 'ANABIO', 'ANALYSES_LABORATOIRE'], standard_concept_regex={'LOINC': '[0-9]{2,5}[-][0-9]', 'AnaBio': '[A-Z][0-9]{4}', 'ANABIO': '[A-Z][0-9]{4}'}, source_terminologies={'ANALYSES_LABORATOIRE': 'Analyses Laboratoire', 'GLIMS_ANABIO': 'GLIMS.{0,20}Anabio', 'GLIMS_LOINC': 'GLIMS.{0,20}LOINC', 'ITM_ANABIO': 'ITM - ANABIO', 'ITM_LOINC': 'ITM - LOINC'}, mapping=[('ANALYSES_LABORATOIRE', 'GLIMS_ANABIO', 'Maps to'), ('ANALYSES_LABORATOIRE', 'GLIMS_LOINC', 'Maps to'), ('GLIMS_ANABIO', 'ITM_ANABIO', 'Mapped from'), ('ITM_ANABIO', 'ITM_LOINC', 'Maps to')])

AP-HP specific configuration. ITM and GLIMS do not share the same ANABIO-to-LOINC mapping. ITM referential is more reliable but covers less ANABIO codes the GLIMS referential.