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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.

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