.gitignore

@@ -33,4 +33,3 @@ docs/site/
 data.tsv
 Q*.docx
 Q*.md
-*.log

Manifest.toml

@@ -2,16 +2,7 @@
 
 julia_version = "1.10.5"
 manifest_format = "2.0"
-project_hash = "485bf8850ea9ae7d6a84e8f24d8d02ed87a19c2c"
+project_hash = "7e38425d15a28e7abd87534dcfc793c08d63a4f4"
-
-[[deps.AbstractTrees]]
-git-tree-sha1 = "2d9c9a55f9c93e8887ad391fbae72f8ef55e1177"
-uuid = "1520ce14-60c1-5f80-bbc7-55ef81b5835c"
-version = "0.4.5"
-
-[[deps.ArgTools]]
-uuid = "0dad84c5-d112-42e6-8d28-ef12dabb789f"
-version = "1.1.1"
 
 [[deps.Artifacts]]
 uuid = "56f22d72-fd6d-98f1-02f0-08ddc0907c33"
@@ -19,11 +10,6 @@ uuid = "56f22d72-fd6d-98f1-02f0-08ddc0907c33"
 [[deps.Base64]]
 uuid = "2a0f44e3-6c83-55bd-87e4-b1978d98bd5f"
 
-[[deps.BitFlags]]
-git-tree-sha1 = "0691e34b3bb8be9307330f88d1a3c3f25466c24d"
-uuid = "d1d4a3ce-64b1-5f1a-9ba4-7e7e69966f35"
-version = "0.1.9"
-
 [[deps.CSV]]
 deps = ["CodecZlib", "Dates", "FilePathsBase", "InlineStrings", "Mmap", "Parsers", "PooledArrays", "PrecompileTools", "SentinelArrays", "Tables", "Unicode", "WeakRefStrings", "WorkerUtilities"]
 git-tree-sha1 = "6c834533dc1fabd820c1db03c839bf97e45a3fab"
@@ -51,12 +37,6 @@ deps = ["Artifacts", "Libdl"]
 uuid = "e66e0078-7015-5450-92f7-15fbd957f2ae"
 version = "1.1.1+0"
 
-[[deps.ConcurrentUtilities]]
-deps = ["Serialization", "Sockets"]
-git-tree-sha1 = "ea32b83ca4fefa1768dc84e504cc0a94fb1ab8d1"
-uuid = "f0e56b4a-5159-44fe-b623-3e5288b988bb"
-version = "2.4.2"
-
 [[deps.Crayons]]
 git-tree-sha1 = "249fe38abf76d48563e2f4556bebd215aa317e15"
 uuid = "a8cc5b0e-0ffa-5ad4-8c14-923d3ee1735f"
@@ -88,41 +68,24 @@ version = "1.0.0"
 deps = ["Printf"]
 uuid = "ade2ca70-3891-5945-98fb-dc099432e06a"
 
-[[deps.Downloads]]
-deps = ["ArgTools", "FileWatching", "LibCURL", "NetworkOptions"]
-uuid = "f43a241f-c20a-4ad4-852c-f6b1247861c6"
-version = "1.6.0"
-
-[[deps.ExceptionUnwrapping]]
-deps = ["Test"]
-git-tree-sha1 = "dcb08a0d93ec0b1cdc4af184b26b591e9695423a"
-uuid = "460bff9d-24e4-43bc-9d9f-a8973cb893f4"
-version = "0.1.10"
-
 [[deps.FilePathsBase]]
 deps = ["Compat", "Dates"]
 git-tree-sha1 = "7878ff7172a8e6beedd1dea14bd27c3c6340d361"
 uuid = "48062228-2e41-5def-b9a4-89aafe57970f"
 version = "0.9.22"
-weakdeps = ["Mmap", "Test"]
 
     [deps.FilePathsBase.extensions]
     FilePathsBaseMmapExt = "Mmap"
     FilePathsBaseTestExt = "Test"
 
-[[deps.FileWatching]]
+    [deps.FilePathsBase.weakdeps]
-uuid = "7b1f6079-737a-58dc-b8bc-7a2ca5c1b5ee"
+    Mmap = "a63ad114-7e13-5084-954f-fe012c677804"
+    Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 
 [[deps.Future]]
 deps = ["Random"]
 uuid = "9fa8497b-333b-5362-9e8d-4d0656e87820"
 
-[[deps.HTTP]]
-deps = ["Base64", "CodecZlib", "ConcurrentUtilities", "Dates", "ExceptionUnwrapping", "Logging", "LoggingExtras", "MbedTLS", "NetworkOptions", "OpenSSL", "Random", "SimpleBufferStream", "Sockets", "URIs", "UUIDs"]
-git-tree-sha1 = "d1d712be3164d61d1fb98e7ce9bcbc6cc06b45ed"
-uuid = "cd3eb016-35fb-5094-929b-558a96fad6f3"
-version = "1.10.8"
-
 [[deps.InlineStrings]]
 git-tree-sha1 = "45521d31238e87ee9f9732561bfee12d4eebd52d"
 uuid = "842dd82b-1e85-43dc-bf29-5d0ee9dffc48"
@@ -150,53 +113,11 @@ git-tree-sha1 = "a3f24677c21f5bbe9d2a714f95dcd58337fb2856"
 uuid = "82899510-4779-5014-852e-03e436cf321d"
 version = "1.0.0"
 
-[[deps.JLLWrappers]]
-deps = ["Artifacts", "Preferences"]
-git-tree-sha1 = "f389674c99bfcde17dc57454011aa44d5a260a40"
-uuid = "692b3bcd-3c85-4b1f-b108-f13ce0eb3210"
-version = "1.6.0"
-
-[[deps.JSON3]]
-deps = ["Dates", "Mmap", "Parsers", "PrecompileTools", "StructTypes", "UUIDs"]
-git-tree-sha1 = "eb3edce0ed4fa32f75a0a11217433c31d56bd48b"
-uuid = "0f8b85d8-7281-11e9-16c2-39a750bddbf1"
-version = "1.14.0"
-
-    [deps.JSON3.extensions]
-    JSON3ArrowExt = ["ArrowTypes"]
-
-    [deps.JSON3.weakdeps]
-    ArrowTypes = "31f734f8-188a-4ce0-8406-c8a06bd891cd"
-
 [[deps.LaTeXStrings]]
 git-tree-sha1 = "50901ebc375ed41dbf8058da26f9de442febbbec"
 uuid = "b964fa9f-0449-5b57-a5c2-d3ea65f4040f"
 version = "1.3.1"
 
-[[deps.LibCURL]]
-deps = ["LibCURL_jll", "MozillaCACerts_jll"]
-uuid = "b27032c2-a3e7-50c8-80cd-2d36dbcbfd21"
-version = "0.6.4"
-
-[[deps.LibCURL_jll]]
-deps = ["Artifacts", "LibSSH2_jll", "Libdl", "MbedTLS_jll", "Zlib_jll", "nghttp2_jll"]
-uuid = "deac9b47-8bc7-5906-a0fe-35ac56dc84c0"
-version = "8.4.0+0"
-
-[[deps.LibGit2]]
-deps = ["Base64", "LibGit2_jll", "NetworkOptions", "Printf", "SHA"]
-uuid = "76f85450-5226-5b5a-8eaa-529ad045b433"
-
-[[deps.LibGit2_jll]]
-deps = ["Artifacts", "LibSSH2_jll", "Libdl", "MbedTLS_jll"]
-uuid = "e37daf67-58a4-590a-8e99-b0245dd2ffc5"
-version = "1.6.4+0"
-
-[[deps.LibSSH2_jll]]
-deps = ["Artifacts", "Libdl", "MbedTLS_jll"]
-uuid = "29816b5a-b9ab-546f-933c-edad1886dfa8"
-version = "1.11.0+1"
-
 [[deps.Libdl]]
 uuid = "8f399da3-3557-5675-b5ff-fb832c97cbdb"
 
@@ -204,30 +125,10 @@ uuid = "8f399da3-3557-5675-b5ff-fb832c97cbdb"
 deps = ["Libdl", "OpenBLAS_jll", "libblastrampoline_jll"]
 uuid = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
 
-[[deps.Logging]]
-uuid = "56ddb016-857b-54e1-b83d-db4d58db5568"
-
-[[deps.LoggingExtras]]
-deps = ["Dates", "Logging"]
-git-tree-sha1 = "c1dd6d7978c12545b4179fb6153b9250c96b0075"
-uuid = "e6f89c97-d47a-5376-807f-9c37f3926c36"
-version = "1.0.3"
-
 [[deps.Markdown]]
 deps = ["Base64"]
 uuid = "d6f4376e-aef5-505a-96c1-9c027394607a"
 
-[[deps.MbedTLS]]
-deps = ["Dates", "MbedTLS_jll", "MozillaCACerts_jll", "NetworkOptions", "Random", "Sockets"]
-git-tree-sha1 = "c067a280ddc25f196b5e7df3877c6b226d390aaf"
-uuid = "739be429-bea8-5141-9913-cc70e7f3736d"
-version = "1.1.9"
-
-[[deps.MbedTLS_jll]]
-deps = ["Artifacts", "Libdl"]
-uuid = "c8ffd9c3-330d-5841-b78e-0817d7145fa1"
-version = "2.28.2+1"
-
 [[deps.Missings]]
 deps = ["DataAPI"]
 git-tree-sha1 = "ec4f7fbeab05d7747bdf98eb74d130a2a2ed298d"
@@ -237,37 +138,11 @@ version = "1.2.0"
 [[deps.Mmap]]
 uuid = "a63ad114-7e13-5084-954f-fe012c677804"
 
-[[deps.MozillaCACerts_jll]]
-uuid = "14a3606d-f60d-562e-9121-12d972cd8159"
-version = "2023.1.10"
-
-[[deps.NetworkOptions]]
-uuid = "ca575930-c2e3-43a9-ace4-1e988b2c1908"
-version = "1.2.0"
-
-[[deps.OpenAI]]
-deps = ["Dates", "HTTP", "JSON3"]
-git-tree-sha1 = "c66f597044ac6cd41cbf4b191d59abbaf2003d9f"
-uuid = "e9f21f70-7185-4079-aca2-91159181367c"
-version = "0.9.0"
-
 [[deps.OpenBLAS_jll]]
 deps = ["Artifacts", "CompilerSupportLibraries_jll", "Libdl"]
 uuid = "4536629a-c528-5b80-bd46-f80d51c5b363"
 version = "0.3.23+4"
 
-[[deps.OpenSSL]]
-deps = ["BitFlags", "Dates", "MozillaCACerts_jll", "OpenSSL_jll", "Sockets"]
-git-tree-sha1 = "38cb508d080d21dc1128f7fb04f20387ed4c0af4"
-uuid = "4d8831e6-92b7-49fb-bdf8-b643e874388c"
-version = "1.4.3"
-
-[[deps.OpenSSL_jll]]
-deps = ["Artifacts", "JLLWrappers", "Libdl"]
-git-tree-sha1 = "a028ee3cb5641cccc4c24e90c36b0a4f7707bdf5"
-uuid = "458c3c95-2e84-50aa-8efc-19380b2a3a95"
-version = "3.0.14+0"
-
 [[deps.OrderedCollections]]
 git-tree-sha1 = "dfdf5519f235516220579f949664f1bf44e741c5"
 uuid = "bac558e1-5e72-5ebc-8fee-abe8a469f55d"
@@ -279,11 +154,6 @@ git-tree-sha1 = "8489905bcdbcfac64d1daa51ca07c0d8f0283821"
 uuid = "69de0a69-1ddd-5017-9359-2bf0b02dc9f0"
 version = "2.8.1"
 
-[[deps.Pkg]]
-deps = ["Artifacts", "Dates", "Downloads", "FileWatching", "LibGit2", "Libdl", "Logging", "Markdown", "Printf", "REPL", "Random", "SHA", "Serialization", "TOML", "Tar", "UUIDs", "p7zip_jll"]
-uuid = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f"
-version = "1.10.0"
-
 [[deps.PooledArrays]]
 deps = ["DataAPI", "Future"]
 git-tree-sha1 = "36d8b4b899628fb92c2749eb488d884a926614d3"
@@ -312,28 +182,6 @@ version = "2.3.2"
 deps = ["Unicode"]
 uuid = "de0858da-6303-5e67-8744-51eddeeeb8d7"
 
-[[deps.PromptingTools]]
-deps = ["AbstractTrees", "Base64", "Dates", "HTTP", "JSON3", "Logging", "OpenAI", "Pkg", "PrecompileTools", "Preferences", "REPL", "Random", "Test"]
-git-tree-sha1 = "701d4c30e0af85f7eb685e5930ec85e8810dee37"
-uuid = "670122d1-24a8-4d70-bfce-740807c42192"
-version = "0.51.0"
-
-    [deps.PromptingTools.extensions]
-    FlashRankPromptingToolsExt = ["FlashRank"]
-    GoogleGenAIPromptingToolsExt = ["GoogleGenAI"]
-    MarkdownPromptingToolsExt = ["Markdown"]
-    RAGToolsExperimentalExt = ["SparseArrays", "LinearAlgebra", "Unicode"]
-    SnowballPromptingToolsExt = ["Snowball"]
-
-    [deps.PromptingTools.weakdeps]
-    FlashRank = "22cc3f58-1757-4700-bb45-2032706e5a8d"
-    GoogleGenAI = "903d41d1-eaca-47dd-943b-fee3930375ab"
-    LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
-    Markdown = "d6f4376e-aef5-505a-96c1-9c027394607a"
-    Snowball = "fb8f903a-0164-4e73-9ffe-431110250c3b"
-    SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
-    Unicode = "4ec0a83e-493e-50e2-b9ac-8f72acf5a8f5"
-
 [[deps.REPL]]
 deps = ["InteractiveUtils", "Markdown", "Sockets", "Unicode"]
 uuid = "3fa0cd96-eef1-5676-8a61-b3b8758bbffb"
@@ -360,11 +208,6 @@ version = "1.4.5"
 [[deps.Serialization]]
 uuid = "9e88b42a-f829-5b0c-bbe9-9e923198166b"
 
-[[deps.SimpleBufferStream]]
-git-tree-sha1 = "874e8867b33a00e784c8a7e4b60afe9e037b74e1"
-uuid = "777ac1f9-54b0-4bf8-805c-2214025038e7"
-version = "1.1.0"
-
 [[deps.Sockets]]
 uuid = "6462fe0b-24de-5631-8697-dd941f90decc"
 
@@ -390,12 +233,6 @@ git-tree-sha1 = "a04cabe79c5f01f4d723cc6704070ada0b9d46d5"
 uuid = "892a3eda-7b42-436c-8928-eab12a02cf0e"
 version = "0.3.4"
 
-[[deps.StructTypes]]
-deps = ["Dates", "UUIDs"]
-git-tree-sha1 = "159331b30e94d7b11379037feeb9b690950cace8"
-uuid = "856f2bd8-1eba-4b0a-8007-ebc267875bd4"
-version = "1.11.0"
-
 [[deps.SuiteSparse_jll]]
 deps = ["Artifacts", "Libdl", "libblastrampoline_jll"]
 uuid = "bea87d4a-7f5b-5778-9afe-8cc45184846c"
@@ -418,25 +255,11 @@ git-tree-sha1 = "598cd7c1f68d1e205689b1c2fe65a9f85846f297"
 uuid = "bd369af6-aec1-5ad0-b16a-f7cc5008161c"
 version = "1.12.0"
 
-[[deps.Tar]]
-deps = ["ArgTools", "SHA"]
-uuid = "a4e569a6-e804-4fa4-b0f3-eef7a1d5b13e"
-version = "1.10.0"
-
-[[deps.Test]]
-deps = ["InteractiveUtils", "Logging", "Random", "Serialization"]
-uuid = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
-
 [[deps.TranscodingStreams]]
 git-tree-sha1 = "e84b3a11b9bece70d14cce63406bbc79ed3464d2"
 uuid = "3bb67fe8-82b1-5028-8e26-92a6c54297fa"
 version = "0.11.2"
 
-[[deps.URIs]]
-git-tree-sha1 = "67db6cc7b3821e19ebe75791a9dd19c9b1188f2b"
-uuid = "5c2747f8-b7ea-4ff2-ba2e-563bfd36b1d4"
-version = "1.5.1"
-
 [[deps.UUIDs]]
 deps = ["Random", "SHA"]
 uuid = "cf7118a7-6976-5b1a-9a39-7adc72f591a4"
@@ -464,13 +287,3 @@ version = "1.2.13+1"
 deps = ["Artifacts", "Libdl"]
 uuid = "8e850b90-86db-534c-a0d3-1478176c7d93"
 version = "5.11.0+0"
-
-[[deps.nghttp2_jll]]
-deps = ["Artifacts", "Libdl"]
-uuid = "8e850ede-7688-5339-a07c-302acd2aaf8d"
-version = "1.52.0+1"
-
-[[deps.p7zip_jll]]
-deps = ["Artifacts", "Libdl"]
-uuid = "3f19e933-33d8-53b3-aaab-bd5110c3b7a0"
-version = "17.4.0+2"

Project.toml

@@ -1,5 +1,3 @@
 [deps]
 CSV = "336ed68f-0bac-5ca0-87d4-7b16caf5d00b"
 DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"
-JSON3 = "0f8b85d8-7281-11e9-16c2-39a750bddbf1"
-PromptingTools = "670122d1-24a8-4d70-bfce-740807c42192"

main.jl

@@ -1,15 +1,6 @@
 #!/usr/bin/env julia
 using CSV
 using DataFrames
-using Dates
-using JSON3
-using Logging
-using PromptingTools
-
-# Set logging to file
-log_io = open("antimicrobial-use-survey-analysis_$(now()).log", "w+")
-logger = SimpleLogger(log_io)
-global_logger(logger)
 
 # Import data
 survey_data = DataFrame(CSV.File("data.tsv"; delim='\t', normalizenames=true))
@@ -25,103 +16,8 @@ end #for
 # infer types
 # deleteat!(survey_data, [1,2])
 
-# Compile comments from all questions and analyze
-# We will be offloading the analysis to Ollama running Llama3.1 locally
-questions = [:Q8, :Q16, :Q29, :Q30]
-
-function logged_prompt(prompt)
-    @info "Prompting Llama3.1 with \n```$prompt\n```\n"
-    response = aigenerate(
-        PromptingTools.OllamaSchema(),
-        prompt;
-        model="llama3.1",
-        api_kwargs=(; options=(; num_gpu=99))
-    ).content
-    @info "Llama3.1 responsed with \n```\n$response\n```\n"
-    return response
-end #function
-
-question_dict = Dict()
-
-for q in questions
-    # Summarize the major themes among all answers
-    analysis_prompt = """
-    The following is a list of answers to a survey with one response per paragraph:
-
-    # Antimicrobial usage survey open-ended question: $q
-
-    $(
-        join(
-            [
-                i == 1 ? "**$a**\n" : "$a\n" for (i, a) in enumerate(skipmissing(survey_data[!, q]))
-            ],
-            '\n'
-        )
-    )
-
-    ---
-
-    Summarize the common themes between the survey responses.
-    """
-
-    analysis_response = logged_prompt(analysis_prompt)
-
-
-    # Compile all themes that Llama3 identified.
-    # Llama3 tends to summarize each theme with a bolded statement.
-    # We will extract the bolded statements to compile themes
-    themes = String[]
-    for l in eachline(IOBuffer(analysis_response))
-        m = match(r"^[1-9]+\. \*\*(.+)\*\*:", l)
-        isnothing(m) || push!(themes, first(m))
-    end #for
-    @info "Found themes $themes"
-
-    answer_dict = Dict()
-
-    # Now go back through each answer and check if it is addressing the theme noted
-    for (i, a) in enumerate(skipmissing(survey_data[!, q]))
-        i == 1 && continue #first "answer" is the question
-
-        theme_dict = Dict{String,Union{Bool,Missing}}()
-
-        for t in themes
-            theme_prompt = """
-            The following was answered as a free-response answer on a survey:
-
-            $a
-
-            ---
-
-            Does this answer deal with the theme of $t? Answer yes or no.
-            """
-
-            theme_response = logged_prompt(theme_prompt)
-
-            if startswith(lowercase(theme_response), "yes")
-                theme_dict[t] = true
-            elseif startswith(lowercase(theme_response), "no")
-                theme_dict[t] = false
-            else
-                theme_dict[t] = missing
-            end #if
-        end #for
-
-        answer_dict[a] = theme_dict
-
-    end #for
-
-    question_dict[q] = answer_dict
-
-end #for
-
-
-open("results.json", "w") do io
-    JSON3.write(io, question_dict)
-end
-
-
 # Compile comments from all requested questions
+questions = [:Q8, :Q16, :Q29, :Q30]
 for q in questions
     open("$q.md", "w") do f
         write(f, "# Antimicrobial usage survey open-ended question: $q\n\n")
@@ -137,6 +33,3 @@ for q in questions
     run(`pandoc $q.md -o $q.docx`)
 
 end #for
-
-# Close log file
-close(log_io)