updated omop cdm extension

Author: kosuri-indu

Project.toml

@@ -10,11 +10,9 @@ OMOPCommonDataModel = "ba65db9e-6590-4054-ab8a-101ed9124986"
 
 [extensions]
 HealthBaseDrWatsonExt = "DrWatson"
-HealthBaseOMOPExt = ["DataFrames", "OMOPCommonDataModel"]
+HealthBaseOMOPCDMExt = ["DataFrames", "OMOPCommonDataModel"]
 
 [compat]
-DataFrames = "1.7.0"
-OMOPCommonDataModel = "0.1.4"
 julia = "1.10"
 
 [extras]

ext/HealthBaseOMOPCDMExt.jl

@@ -0,0 +1,51 @@
+module HealthBaseOMOPExt
+
+using HealthBase
+using DataFrames
+using OMOPCommonDataModel
+
+__init__() = @info "OMOP CDM extension for HealthBase has been loaded!"
+
+"""
+    HealthTable(df::DataFrame, omop_cdm_version="5.4"; disable_type_enforcement=false)
+
+Validate a DataFrame against the OMOP CDM specification for the given version.
+
+Checks column names/types, attaches OMOP metadata to columns, and returns the DataFrame.
+
+If `disable_type_enforcement` is true, type mismatches emit warnings instead of errors.
+"""
+function HealthBase.HealthTable(df::DataFrame, omop_cdm_version="5.4"; disable_type_enforcement=false)
+    # TODO: have to add logic for version specific fields types
+    omop_fields = Dict{String, Dict{Symbol, Any}}() 
+
+    for t in subtypes(OMOPCommonDataModel.CDMType)
+        for f in fieldnames(t)
+            actual_field_type = fieldtype(t, f)
+            omop_fields[string(f)] = Dict(:type => actual_field_type)
+        end
+    end
+
+    for col in names(df)
+        if haskey(omop_fields, col)
+            fieldinfo = omop_fields[col]
+            expected_type = get(fieldinfo, :type, Any)
+            actual_type = eltype(df[!, col])
+
+            if !(actual_type <: expected_type)
+                msg = "Column '$(col)' has type $(actual_type), expected $(expected_type)"
+                if disable_type_enforcement
+                    @warn msg
+                else
+                    throw(ArgumentError(msg))
+                end
+            end
+
+            for (key, val) in fieldinfo
+                colmetadata!(df, col, string(key), string(val), style=:note)
+            end
+        end
+    end
+
+    return df
+end