Create cohort on Eunomia for testing

test/assets/strep_throat.json

@@ -0,0 +1,56 @@
+{
+ "ConceptSets": [
+ {
+ "id": 0,
+ "name": "[jz] Strep Throat Concepts",
+ "expression": {
+ "items": [
+ {
+ "concept": {
+ "CONCEPT_CLASS_ID": "Clinical Finding",
+ "CONCEPT_CODE": "43878008",
+ "CONCEPT_ID": 28060,
+ "CONCEPT_NAME": "Streptococcal sore throat",
+ "DOMAIN_ID": "Condition",
+ "INVALID_REASON": "V",
+ "INVALID_REASON_CAPTION": "Valid",
+ "STANDARD_CONCEPT": "S",
+ "STANDARD_CONCEPT_CAPTION": "Standard",
+ "VOCABULARY_ID": "SNOMED"
+ }
+ }
+ ]
+ }
+ }
+ ],
+ "PrimaryCriteria": {
+ "CriteriaList": [
+ {
+ "ConditionOccurrence": {
+ "CodesetId": 0
+ }
+ }
+ ],
+ "ObservationWindow": {
+ "PriorDays": 0,
+ "PostDays": 0
+ },
+ "PrimaryCriteriaLimit": {
+ "Type": "All"
+ }
+ },
+ "QualifiedLimit": {
+ "Type": "First"
+ },
+ "ExpressionLimit": {
+ "Type": "All"
+ },
+ "InclusionRules": [],
+ "CensoringCriteria": [],
+ "CollapseSettings": {
+ "CollapseType": "ERA",
+ "EraPad": 0
+ },
+ "CensorWindow": {},
+ "cdmVersionRange": ">=5.0.0"
+}

test/runtests.jl

@@ -31,6 +31,19 @@ sqlite_conn = SQLite.DB(Eunomia())
 GenerateDatabaseDetails(:sqlite, "main")
 GenerateTables(sqlite_conn)
 
+cohort = read("./assets/strep_throat.json", String)
+
+#using DBInterface
+
+model = Model(cdm_version=v"5.3.1", cdm_schema="main",
+ vocabulary_schema="main", results_schema="main",
+ target_schema="main", target_table="cohort");
+
+sql = translate(cohort, dialect=:sqlite, model=model,
+ cohort_definition_id=1);
+
+[DBI.execute(sqlite_conn, sub_query) for sub_query in split(sql, ";")[1:end-1]]
+
 @testset "OMOPCDMPathways" begin
  @testset "Data-Preprocessing" begin
  include("Data-Preprocessing/preprocessing.jl")