Added Gemini Demo

.gitignore

@@ -5,5 +5,12 @@
 /docs/Manifest*.toml
 /docs/build/
 .env
+.env.*
+!.env.example
+demo/JuliaHealthLLM_exp_raw_combined.txt
 .env.example
-JuliaHealthLLM_exp_raw_combined.txt
+.env
+cacert.pem
+JuliaHealthLLM_exp_raw_combined.txt
+FunSQL_combined.txt
+OHDSI_FunSQL_combined.txt

Project.toml

@@ -1,41 +1,53 @@
 name = "HealthLLM"
 uuid = "1de6b779-c1fb-4125-b891-fad447459241"
-authors = ["ParamThakkar123 <paramthakkar864@gmail.com> and TheCedarPrince <jacobszelko@gmail.com>"]
 version = "0.0.1"
+authors = ["ParamThakkar123 <paramthakkar864@gmail.com> and TheCedarPrince <jacobszelko@gmail.com>"]
 
 [deps]
+ConfigEnv = "01234589-554d-41b7-ae5c-7b6ee2db6796"
 DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"
-DrWatson = "634d3b9d-ee7a-5ddf-bec9-22491ea816e1"
 DuckDB = "d2f5444f-75bc-4fdf-ac35-56f514c445e1"
+Embeddings = "c5bfea45-b7f1-5224-a596-15500f5db411"
 FunSQL = "cf6cc811-59f4-4a10-b258-a8547a8f6407"
+GoogleGenAI = "903d41d1-eaca-47dd-943b-fee3930375ab"
 HuggingFaceHub = "d0076355-e2c0-48e6-a044-05906e51b7fc"
 JSON3 = "0f8b85d8-7281-11e9-16c2-39a750bddbf1"
 LibPQ = "194296ae-ab2e-5f79-8cd4-7183a0a5a0d1"
 LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
+MbedTLS = "739be429-bea8-5141-9913-cc70e7f3736d"
+OpenSSL = "4d8831e6-92b7-49fb-bdf8-b643e874388c"
 PromptingTools = "670122d1-24a8-4d70-bfce-740807c42192"
 RAGTools = "16ddad29-bbe8-45a7-857d-3d9514eb0023"
 Serialization = "9e88b42a-f829-5b0c-bbe9-9e923198166b"
 SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
 Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
+Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
+Transformers = "21ca0261-441d-5938-ace7-c90938fde4d4"
 
 [compat]
-DataFrames = "1.8.0"
-DrWatson = "2.19.1"
-DuckDB = "1.3.2"
-FunSQL = "0.15.0"
-HuggingFaceHub = "0.1.2"
-JSON3 = "1.14.3"
+ConfigEnv = "1.0.0"
+DataFrames = "1.8"
+DuckDB = "1.3, 1.4"
+FunSQL = "0.15"
+GoogleGenAI = "0.5"
+HuggingFaceHub = "0.1"
+JSON3 = "1.14"
 LibPQ = "1.18.0"
-LinearAlgebra = "1.10"
+LinearAlgebra = "1.12.0"
 PromptingTools = "0.82.1"
 RAGTools = "0.7.0"
-Serialization = "1.10"
-SparseArrays = "1.10"
-Statistics = "1.10"
+Serialization = "1.11.0"
+SparseArrays = "1.12.0"
+Statistics = "1.11.1"
 julia = "1.10"
 
 [extras]
+DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"
+DuckDB = "d2f5444f-75bc-4fdf-ac35-56f514c445e1"
+FunSQL = "cf6cc811-59f4-4a10-b258-a8547a8f6407"
+HuggingFaceHub = "d0076355-e2c0-48e6-a044-05906e51b7fc"
+JSON3 = "0f8b85d8-7281-11e9-16c2-39a750bddbf1"
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 
 [targets]
-test = ["Test"]
+test = ["DataFrames", "DuckDB", "FunSQL", "HuggingFaceHub", "JSON3", "Test"]

combine_all.jl

@@ -0,0 +1,31 @@
+using Base64
+
+function combine_ohdsi_funsql(ohdsi_file::String, funsql_file::String, output_file::String)
+    open(output_file, "w") do out
+        # Write OHDSI part
+        println(out, "# OHDSI Data")
+        open(ohdsi_file, "r") do f
+            for line in eachline(f)
+                println(out, line)
+            end
+        end
+        println(out, "\n")
+
+        # Write FunSQL part
+        println(out, "# FunSQL Data")
+        open(funsql_file, "r") do f
+            for line in eachline(f)
+                println(out, line)
+            end
+        end
+        println(out, "\n")
+    end
+    println("Combined data written to $(abspath(output_file))")
+end
+
+# Files
+ohdsi_file = "demo/JuliaHealthLLM_exp_raw_combined.txt"
+funsql_file = "FunSQL_combined.txt"
+output_file = "OHDSI_FunSQL_combined.txt"
+
+combine_ohdsi_funsql(ohdsi_file, funsql_file, output_file)

combine_funsql.jl

@@ -0,0 +1,83 @@
+using Pkg
+Pkg.activate(".")
+include("src/HealthLLM.jl")
+
+files = [
+    "FunSQL_repo/LICENSE.md",
+    "FunSQL_repo/NEWS.md",
+    "FunSQL_repo/README.md",
+    "FunSQL_repo/docs/make.jl",
+    "FunSQL_repo/docs/src/index.md",
+    "FunSQL_repo/docs/src/examples/index.md",
+    "FunSQL_repo/docs/src/guide/index.md",
+    "FunSQL_repo/docs/src/reference/index.md",
+    "FunSQL_repo/docs/src/test/clauses.md",
+    "FunSQL_repo/docs/src/test/index.md",
+    "FunSQL_repo/docs/src/test/nodes.md",
+    "FunSQL_repo/docs/src/test/other.md",
+    "FunSQL_repo/docs/src/two-kinds-of-sql-query-builders/index.md",
+    "FunSQL_repo/src/FunSQL.jl",
+    "FunSQL_repo/src/catalogs.jl",
+    "FunSQL_repo/src/connections.jl",
+    "FunSQL_repo/src/dialects.jl",
+    "FunSQL_repo/src/dissect.jl",
+    "FunSQL_repo/src/link.jl",
+    "FunSQL_repo/src/nodes.jl",
+    "FunSQL_repo/src/quote.jl",
+    "FunSQL_repo/src/reflect.jl",
+    "FunSQL_repo/src/render.jl",
+    "FunSQL_repo/src/resolve.jl",
+    "FunSQL_repo/src/serialize.jl",
+    "FunSQL_repo/src/strings.jl",
+    "FunSQL_repo/src/translate.jl",
+    "FunSQL_repo/src/types.jl",
+    "FunSQL_repo/src/clauses/aggregate.jl",
+    "FunSQL_repo/src/clauses/as.jl",
+    "FunSQL_repo/src/clauses/from.jl",
+    "FunSQL_repo/src/clauses/function.jl",
+    "FunSQL_repo/src/clauses/group.jl",
+    "FunSQL_repo/src/clauses/having.jl",
+    "FunSQL_repo/src/clauses/identifier.jl",
+    "FunSQL_repo/src/clauses/internal.jl",
+    "FunSQL_repo/src/clauses/join.jl",
+    "FunSQL_repo/src/clauses/limit.jl",
+    "FunSQL_repo/src/clauses/literal.jl",
+    "FunSQL_repo/src/clauses/note.jl",
+    "FunSQL_repo/src/clauses/order.jl",
+    "FunSQL_repo/src/clauses/partition.jl",
+    "FunSQL_repo/src/clauses/select.jl",
+    "FunSQL_repo/src/clauses/sort.jl",
+    "FunSQL_repo/src/clauses/union.jl",
+    "FunSQL_repo/src/clauses/values.jl",
+    "FunSQL_repo/src/clauses/variable.jl",
+    "FunSQL_repo/src/clauses/where.jl",
+    "FunSQL_repo/src/clauses/window.jl",
+    "FunSQL_repo/src/clauses/with.jl",
+    "FunSQL_repo/src/nodes/aggregate.jl",
+    "FunSQL_repo/src/nodes/append.jl",
+    "FunSQL_repo/src/nodes/as.jl",
+    "FunSQL_repo/src/nodes/bind.jl",
+    "FunSQL_repo/src/nodes/define.jl",
+    "FunSQL_repo/src/nodes/from.jl",
+    "FunSQL_repo/src/nodes/function.jl",
+    "FunSQL_repo/src/nodes/get.jl",
+    "FunSQL_repo/src/nodes/group.jl",
+    "FunSQL_repo/src/nodes/highlight.jl",
+    "FunSQL_repo/src/nodes/internal.jl",
+    "FunSQL_repo/src/nodes/iterate.jl",
+    "FunSQL_repo/src/nodes/join.jl",
+    "FunSQL_repo/src/nodes/limit.jl",
+    "FunSQL_repo/src/nodes/literal.jl",
+    "FunSQL_repo/src/nodes/order.jl",
+    "FunSQL_repo/src/nodes/over.jl",
+    "FunSQL_repo/src/nodes/partition.jl",
+    "FunSQL_repo/src/nodes/select.jl",
+    "FunSQL_repo/src/nodes/sort.jl",
+    "FunSQL_repo/src/nodes/variable.jl",
+    "FunSQL_repo/src/nodes/where.jl",
+    "FunSQL_repo/src/nodes/with.jl",
+    "FunSQL_repo/src/nodes/with_external.jl",
+    "FunSQL_repo/test/runtests.jl"
+]
+
+HealthLLM.write_combined_file(files, "FunSQL_combined.txt")