HealthTable: Tables.jl Interface (General)

The HealthTable Struct

The core of the interface is the HealthTable struct.

HealthBase.HealthTable — Type
HealthTable{T}

A lightweight, schema-aware wrapper for OMOP CDM tables, providing a standardized Tables.jl interface and metadata tracking.

The HealthTable struct is designed to wrap OMOP CDM-compliant data sources (such as DataFrames), ensuring that all columns conform to the OMOP CDM specification for a given version. It attaches the OMOP CDM version as metadata and enables seamless integration with the Julia Tables.jl ecosystem.

Fields

  • source::T: The underlying data source (typically a DataFrame) containing the OMOP CDM table data.

Examples

person_df = DataFrame(
    person_id=1:3,
    gender_concept_id=[8507, 8532, 8507],
    year_of_birth=[1990, 1985, 2000]
)
ht = HealthTable(person_df; omop_cdm_version="v5.4.1")
Tables.schema(ht) # Get the schema
DataFrame(ht)     # Materialize as DataFrame
source

Tables.jl API Implementation

The HealthTable wrapper types will implement key Tables.jl methods:

HealthTable implements the Tables.jl interface to ensure compatibility with the Julia data ecosystem:

Tables.istable — Method
Tables.istable(::Type{<:HealthTable})

Signal that HealthTable is a table according to the Tables.jl interface.

This function is part of the Tables.jl interface and is used to identify types that can be treated as tabular data.

Returns

  • Bool: Always returns true for the HealthTable type.
source
Tables.rowaccess — Method
Tables.rowaccess(::Type{<:HealthTable})

Signal that HealthTable supports row-based iteration.

This function is part of the Tables.jl interface. A true return value indicates that Tables.rows can be called on an instance of HealthTable.

Returns

  • Bool: Always returns true for the HealthTable type.
source
Tables.rows — Method
Tables.rows(ht::HealthTable)

Return an iterator over the rows of the HealthTable.

This function implements the row-access part of the Tables.jl interface by delegating to the underlying source object.

Arguments

  • ht::HealthTable: The HealthTable instance.

Returns

  • An iterator object that yields each row of the table.
source
Tables.columnaccess — Method
Tables.columnaccess(::Type{<:HealthTable})

Signal that HealthTable supports column-based access.

This function is part of the Tables.jl interface. A true return value indicates that Tables.columns can be called on an instance of HealthTable.

Returns

  • Bool: Always returns true for the HealthTable type.
source
Tables.columns — Method
Tables.columns(ht::HealthTable)

Return the HealthTable's data as a set of columns.

This function implements the column-access part of the Tables.jl interface by delegating to the underlying source object.

Arguments

  • ht::HealthTable: The HealthTable instance.

Returns

  • A column-accessible object that represents the table's data.
source
Tables.schema — Method
Tables.schema(ht::HealthTable)

Get the schema of the HealthTable.

The schema includes the names and types of the columns. This function delegates the call to the underlying source.

Arguments

  • ht::HealthTable: The HealthTable instance.

Returns

  • Tables.Schema: An object describing the column names and their Julia types.
source
Tables.materializer — Method
Tables.materializer(::Type{<:HealthTable})

Specify the default type to use when materializing a HealthTable.

This function is part of the Tables.jl interface. It allows other packages to convert a HealthTable into a concrete table type like a DataFrame by calling DataFrame(ht).

Returns

  • Type: The DataFrame type, indicating it as the preferred materialization format.
source

Source: https://tables.juliadata.org/stable/implementing-the-interface/