Dataset required for testing

[Jay-sanjay]

We need to generate a cohort using a cohort definition that can then be used for testing within Eunomia.

[TheCedarPrince]

Hey Jay, here is the code that can be used to build a Cohort. Should also help you with: JuliaHealth/OMOPCDMCohortCreator.jl#61 as we can then build cohorts for testing within the test suit over in OMOPCDMCohortCreator. I actually think this issue should be over in OMOPCDMCohortCreator.jl but we can continue the conversation here. Code:

using JSON3

import DBInterface as DBI

import HealthSampleData: 
       Eunomia
import SQLite: 
        DB
# You'll need to install this via package mode as this has not been added to the general registry yet
# Here is how: pkg> add https://github.com/JuliaHealth/OHDSIAPI.jl 
import OHDSIAPI: 
       ATLAS
import OHDSICohortExpressions: 
	translate, 
	Model

eunomia = Eunomia()
conn = DB(eunomia)

#= 
Step 1: Query ATLAS to get strep throat phenotype definition and read in cohort expression as JSON.
=#

cohort = ATLAS.get_atlas_cohort_definition(
	"1787567" # ATLAS ID
) |> JSON3.read # Parse as JSON

cohort_expression = cohort[:items] |>
	x -> x[1] |> 
	x -> x[:expression] # Get expression

#=
Step 2: Staging creation of cohort tables for the OMOP CDM
=#

model = Model(cdm_version = v"5.3.1",
	cdm_schema = "main",
	vocabulary_schema = "main",
	results_schema = "main",
	target_schema = "main",
	target_table = "cohort"
)

#= 
Step 3: Generating SQL statements for generating strep throat cohorts
=# 

sql = translate(cohort_expression,
	dialect = :sqlite,
	model = model, # Prepared Model
	cohort_definition_id = 1 # ID
)

#= 
Step 4: Executing SQL statements to build strep throat cohort
=# 
for q in split(sql, ";")[1:end – 1]
	DBI.execute(conn, q) 
end

By the end of this, there should now be a cohort generated within the cohort table of Eunomia. You can hopefully use this for testing over in OCC. I think this would actually make a fantastic tutorial for OCC in the future!

Let me know if you have any questions. Thanks @Jay-sanjay !

~ tcp