OHDSICohortExpressions.jl

OHDSI Cohort Expressions is a re-implementation of OHDSI's Circe

This is a proof-of-concept implementation of a conversion from the JSON cohort definitions used in the OHDSI ecosystem into an SQL transaction.

Project Status

At this time, this implementation is able to convert all 797 cohorts from PhenotypeLibrary v0.1 to generate SQL that works against Amazon RedShift, Microsoft SQL Server, and PostgreSQL.

There are significant gaps in functionality. Many expressions available in the JSON cohort definition have yet to be translated. In these cases, an assertion error should arise. We have yet to write documentation, perform code review, or construct regression tests. The API is in a provisional form and very likely to change.

Example Usage

Following is an example given the demo/ex-10-2.json cohort. This corresponds to excercise 10.2 from the Book of OHDSI. Supported dialects are :redshift, :sqlserver, and :postgresql.

julia> cohort = read("demo/ex-10-2.json", String)

julia> using OHDSICohortExpressions: translate, Model

julia> model = Model(cdm_version=v"5.3.1", cdm_schema="cdm",
                     vocabulary_schema="vcb", results_schema="res",
                     target_schema="res", target_table="cohort");

julia> tsql = translate(cohort, dialect=:sqlserver, model=model,
                         cohort_definition_id=1);

julia> println(tsql)

The return value, tsql is a SQL string with a transaction that populates the cohort table for cohort definition 1.

Usage from "R"

Using JuliaCall library, one could call this function from "R". First, one must install JuliaCall.

> install.packages("JuliaCall")

You could then initialize the Julia environment, and install this library to the Julia environment.

> library("JuliaCall")
> julia_setup(installJulia = TRUE)
> julia_install_package_if_needed("OHDSICohortExpressions")

Construct an "R" proxy, oce, to the Model and translate functions.

> oce <- julia_pkg_import("OHDSICohortExpressions",
                          func_list = c("Model", "translate"))

Construct a model object with data model parameters.

> model = oce$Model(cdm_version="5.3.1", cdm_schema="cdm",
                    vocabulary_schema="vcb", results_schema="res",
                    target_schema="res", target_table="cohort")

Read the cohort file into an R variable.

> library("readr")
> cohort <- read_file("demo/ex-10-2.json")

Translate this cohort definition into the SQL transaction.

> tsql = oce$translate(cohort, dialect="sqlserver", model=model,
                       cohort_definition_id=1)