[BUG] AssertionError: c.occurrence !== nothing -- What Does This Mean?

[TheCedarPrince]

I am seeing this error:

ERROR: AssertionError: c.occurrence !== nothing && c.occurr
ence.count_column === nothing
Stacktrace:
  [1] predicate(c::OHDSICohortExpressions.CorrelatedCriteri
a, ctx::OHDSICohortExpressions.TranslateContext)
    @ OHDSICohortExpressions ~/.julia/packages/OHDSICohortE
xpressions/UuDrd/src/translate.jl:725
  [2] predicate(c::OHDSICohortExpressions.CriteriaGroup, ct
x::OHDSICohortExpressions.TranslateContext)
    @ OHDSICohortExpressions ~/.julia/packages/OHDSICohortE
xpressions/UuDrd/src/translate.jl:627
  [3] 
    @ OHDSICohortExpressions ~/.julia/packages/OHDSICohortE
xpressions/UuDrd/src/translate.jl:568
  [4] translate
    @ ~/.julia/packages/OHDSICohortExpressions/UuDrd/src/tr
anslate.jl:554 [inlined]
  [5] translate(c::OHDSICohortExpressions.CohortExpression,
 ctx::OHDSICohortExpressions.TranslateContext)
    @ OHDSICohortExpressions ~/.julia/packages/OHDSICohortE
xpressions/UuDrd/src/translate.jl:141
  [6] translate
    @ ~/.julia/packages/OHDSICohortExpressions/UuDrd/src/tr
anslate.jl:103 [inlined]
  [7] translate(cohort::Dict{String, Any}, dialect::Symbol,
 model::Model, cohort_definition_id::Int64)
    @ OHDSICohortExpressions ~/.julia/packages/OHDSICohortE
xpressions/UuDrd/src/translate.jl:46
  [8] translate(cohort::String, dialect::Symbol, model::Mod
el, cohort_definition_id::Int64)
    @ OHDSICohortExpressions ~/.julia/packages/OHDSICohortE
xpressions/UuDrd/src/translate.jl:41
  [9] #translate#79
    @ ~/.julia/packages/OHDSICohortExpressions/UuDrd/src/tr
anslate.jl:38 [inlined]
 [10] (::var"#32#33")(f::IOStream)
    @ Main ./REPL[99]:23
 [11] open(::var"#32#33", ::String, ::Vararg{String}; kwarg
s::@Kwargs{})
    @ Base ./io.jl:396
 [12] open(::Function, ::String, ::String)
    @ Base ./io.jl:393
 [13] top-level scope
    @ REPL[99]:1
Some type information was truncated. Use `show(err)` to see
 complete types.

When I run this code:

cohort_expression = 
"""
{
     "cdmVersionRange": ">=5.0.0",
     "PrimaryCriteria": {
                                   "CriteriaList": [
                                                     {
                                                        "VisitOccurrence": {
                                                                              "VisitTypeExclude": false
                                                                           }
                                                     }
                                                   ],
                              "ObservationWindow": {
                                                      "PriorDays": 0,
                                                       "PostDays": 0
                                                   },
                           "PrimaryCriteriaLimit": {
                                                      "Type": "First"
                                                   }
                        },
         "ConceptSets": [
                          {
                                     "id": 0,
                                   "name": "Amitriptyline",
                             "expression": {
                                              "items": [
                                                         {
                                                                       "concept": {
                                                                                                   "CONCEPT_ID": 710062,
                                                                                                 "CONCEPT_NAME": "amitriptyline",
                                                                                             "STANDARD_CONCEPT": "S",
                                                                                     "STANDARD_CONCEPT_CAPTION": "Standard",
                                                                                               "INVALID_REASON": "V",
                                                                                       "INVALID_REASON_CAPTION": "Valid",
                                                                                                 "CONCEPT_CODE": "704",
                                                                                                    "DOMAIN_ID": "Drug",
                                                                                                "VOCABULARY_ID": "RxNorm",
                                                                                             "CONCEPT_CLASS_ID": "Ingredient"
                                                                                  },
                                                                    "isExcluded": false,
                                                            "includeDescendants": true,
                                                                 "includeMapped": false
                                                         }
                                                       ]
                                           }
                          }
                        ],
      "QualifiedLimit": {
                           "Type": "First"
                        },
     "ExpressionLimit": {
                           "Type": "First"
                        },
      "InclusionRules": [
                          {
                                   "name": "has Amitriptyline exposure",
                             "expression": {
                                                                 "Type": "ALL",
                                                         "CriteriaList": [
                                                                           {
                                                                                             "Criteria": {
                                                                                                            "DrugExposure": {
                                                                                                                                     "CodesetId": 0,
                                                                                                                               "DrugTypeExclude": false
                                                                                                                            }
                                                                                                         },
                                                                                          "StartWindow": {
                                                                                                                  "Start": {
                                                                                                                              "Coeff": -1
                                                                                                                           },
                                                                                                                    "End": {
                                                                                                                              "Coeff": 1
                                                                                                                           },
                                                                                                            "UseIndexEnd": false,
                                                                                                            "UseEventEnd": false
                                                                                                         },
                                                                                        "RestrictVisit": false,
                                                                              "IgnoreObservationPeriod": false,
                                                                                           "Occurrence": {
                                                                                                                   "Type": 2,
                                                                                                                  "Count": 1,
                                                                                                             "IsDistinct": false,
                                                                                                            "CountColumn": "DOMAIN_CONCEPT"
                                                                                                         }
                                                                           }
                                                                         ],
                                              "DemographicCriteriaList": [],
                                                               "Groups": []
                                           }
                          }
                        ],
   "CensoringCriteria": [],
    "CollapseSettings": {
                           "CollapseType": "ERA",
                                 "EraPad": 0
                        },
        "CensorWindow": {}
}
"""
            model = Model(cdm_version = v"5.3.1", 
                          cdm_schema = "omop",
                          vocabulary_schema = "omop", 
                          results_schema = "omop",
                          target_schema = "omop",
                          target_table = "cohort");

            sql = translate(cohort_expression, 
                            dialect = :postgresql, 
                            model = model,
                            cohort_definition_id = id);

Do you know what is going on here and how I could fix it? Thanks!

[clarkevans]

[BUG] AssertionError: c.occurrence !== nothing -- What Does This Mean?

We did not implement every aspect of the OHDSI cohort expression object, only those that were used in the phenotype library. Why? We would like to ensure that things implemented are actually tested. I think for each case like this, what we need is a cohort definition that would provide some testable result against a given data set, perhaps MIMIC 100. Furthermore, you're welcome to look at the other translation as guidance, and do a pull request, as many of these should be straight-forward enhancements.

[clarkevans]

I've updated the README to discuss this and created an issue template. If this is still unimplemented, could you submit that as a feature request? We would also accept a pull request, but it's important to have test cases.