OHDSI Cohort Expressions is a re-implementation of OHDSI's Circe
This is an alpha-quality implementation of a conversion from the JSON cohort definitions used in the OHDSI ecosystem into an SQL transaction.
This project has only implemented a subset of the OHDSI Circe format
which we are able to verify via the OHDSI PhentotypeLibrary. Other
permutations are left as an assert error. If you encounter one of
these, you could open a gap issue. We've not implemented
these permutations since it's important to have a regression test,
therefore providing an example cohort definition and results is helpful.
First, load or generate a cohort definition in OHDSI Circe format.
In this example, we load the cohort definition from demo/ex-10-2.json,
which corresponds to excercise 10.2 from the Book of OHDSI.
cohort_definition = read("demo/ex-10-2.json", String)Next, use OHDSICohortExpressions.translate() to convert this cohort
definition to a FunSQL query object.
using OHDSICohortExpressions: translate
q = translate(cohort_definition, cohort_definition_id = 1)Run DBInterface.connect() to create a connection to an OMOP CDM database.
The arguments of DBInterface.connect() depend on the database engine and
connection parameters. Consult FunSQL documentation for more information.
using FunSQL, DBInterface
db = DBInterface.connect(FunSQL.SQLConnection{ … }, … )Execute the query to return the corresponding cohort.
using DataFrames
cr = DBInterface.execute(db, q)
df = DataFrame(cr)