creating duckdb file for mimic

Author: clarkevans

README.md

@@ -2,6 +2,7 @@
 
 *FunSQL-TestDATA is a set of disparately licensed data sets used for testing FunSQL.*
 
+[mimic-iv-full]: https://physionet.org/content/mimiciv/
 [mimic-iv-demo]: https://physionet.org/content/mimic-iv-demo/
 [odbl-1.0]: https://physionet.org/content/mimic-iv-demo/view-license/2.2/
 [physionet]: https://physionet.org/content/?topic=MIMIC+IV
@@ -26,7 +27,7 @@ from Boston's Beth Israel Deaconess Medical Center electronic health
 records, released though [PhysioNet][physionet] collaborative repository
 under the copyleft [Open Data Commons Open Database License v1.0][odbl-1.0].
 
-The full MIMIC IV dataset is available upon completing [CITI Program][citi]
-"Massachusetts Institute of Technology Affilates" training and executing the
-PhysioNet [Credentialed Health Data License][pchdl]. PhysioNet credentialing
-is available to independent researchers.
+The [full MIMIC IV][mimic-iv-full] dataset is available upon completing
+[CITI Program][citi] "Massachusetts Institute of Technology Affilates" training
+and executing the PhysioNet [Credentialed Health Data License][pchdl].
+PhysioNet credentialing is available to independent researchers.

src/mimic_iv/Makefile

@@ -0,0 +1,2 @@
+demo:
+	julia --project=. mimic_iv.jl

src/mimic_iv/Manifest.toml

@@ -0,0 +1,355 @@
+# This file is machine-generated - editing it directly is not advised
+
+julia_version = "1.11.4"
+manifest_format = "2.0"
+project_hash = "735b286d87c38e8bbc889c4055dfff7a7bac0794"
+
+[[deps.ArgTools]]
+uuid = "0dad84c5-d112-42e6-8d28-ef12dabb789f"
+version = "1.1.2"
+
+[[deps.Artifacts]]
+uuid = "56f22d72-fd6d-98f1-02f0-08ddc0907c33"
+version = "1.11.0"
+
+[[deps.Base64]]
+uuid = "2a0f44e3-6c83-55bd-87e4-b1978d98bd5f"
+version = "1.11.0"
+
+[[deps.BitIntegers]]
+deps = ["Random"]
+git-tree-sha1 = "f98cfeaba814d9746617822032d50a31c9926604"
+uuid = "c3b6d118-76ef-56ca-8cc7-ebb389d030a1"
+version = "0.3.5"
+
+[[deps.CSV]]
+deps = ["CodecZlib", "Dates", "FilePathsBase", "InlineStrings", "Mmap", "Parsers", "PooledArrays", "PrecompileTools", "SentinelArrays", "Tables", "Unicode", "WeakRefStrings", "WorkerUtilities"]
+git-tree-sha1 = "deddd8725e5e1cc49ee205a1964256043720a6c3"
+uuid = "336ed68f-0bac-5ca0-87d4-7b16caf5d00b"
+version = "0.10.15"
+
+[[deps.CodeTracking]]
+deps = ["InteractiveUtils", "UUIDs"]
+git-tree-sha1 = "062c5e1a5bf6ada13db96a4ae4749a4c2234f521"
+uuid = "da1fd8a2-8d9e-5ec2-8556-3022fb5608a2"
+version = "1.3.9"
+
+[[deps.CodecZlib]]
+deps = ["TranscodingStreams", "Zlib_jll"]
+git-tree-sha1 = "962834c22b66e32aa10f7611c08c8ca4e20749a9"
+uuid = "944b1d66-785c-5afd-91f1-9de20f533193"
+version = "0.7.8"
+
+[[deps.Compat]]
+deps = ["TOML", "UUIDs"]
+git-tree-sha1 = "8ae8d32e09f0dcf42a36b90d4e17f5dd2e4c4215"
+uuid = "34da2185-b29b-5c13-b0c7-acf172513d20"
+version = "4.16.0"
+
+    [deps.Compat.extensions]
+    CompatLinearAlgebraExt = "LinearAlgebra"
+
+    [deps.Compat.weakdeps]
+    Dates = "ade2ca70-3891-5945-98fb-dc099432e06a"
+    LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
+
+[[deps.DBInterface]]
+git-tree-sha1 = "a444404b3f94deaa43ca2a58e18153a82695282b"
+uuid = "a10d1c49-ce27-4219-8d33-6db1a4562965"
+version = "2.6.1"
+
+[[deps.DataAPI]]
+git-tree-sha1 = "abe83f3a2f1b857aac70ef8b269080af17764bbe"
+uuid = "9a962f9c-6df0-11e9-0e5d-c546b8b5ee8a"
+version = "1.16.0"
+
+[[deps.DataValueInterfaces]]
+git-tree-sha1 = "bfc1187b79289637fa0ef6d4436ebdfe6905cbd6"
+uuid = "e2d170a0-9d28-54be-80f0-106bbe20a464"
+version = "1.0.0"
+
+[[deps.Dates]]
+deps = ["Printf"]
+uuid = "ade2ca70-3891-5945-98fb-dc099432e06a"
+version = "1.11.0"
+
+[[deps.Downloads]]
+deps = ["ArgTools", "FileWatching", "LibCURL", "NetworkOptions"]
+uuid = "f43a241f-c20a-4ad4-852c-f6b1247861c6"
+version = "1.6.0"
+
+[[deps.DuckDB]]
+deps = ["DBInterface", "Dates", "DuckDB_jll", "FixedPointDecimals", "Tables", "UUIDs", "WeakRefStrings"]
+git-tree-sha1 = "388ccfa7bf0be0d2a07898f385b97bcd6a654403"
+uuid = "d2f5444f-75bc-4fdf-ac35-56f514c445e1"
+version = "1.2.2"
+
+[[deps.DuckDB_jll]]
+deps = ["Artifacts", "JLLWrappers", "Libdl"]
+git-tree-sha1 = "478819e6a40397a9913cf81294559602b8aa67d8"
+uuid = "2cbbab25-fc8b-58cf-88d4-687a02676033"
+version = "1.2.2+0"
+
+[[deps.FilePathsBase]]
+deps = ["Compat", "Dates"]
+git-tree-sha1 = "3bab2c5aa25e7840a4b065805c0cdfc01f3068d2"
+uuid = "48062228-2e41-5def-b9a4-89aafe57970f"
+version = "0.9.24"
+
+    [deps.FilePathsBase.extensions]
+    FilePathsBaseMmapExt = "Mmap"
+    FilePathsBaseTestExt = "Test"
+
+    [deps.FilePathsBase.weakdeps]
+    Mmap = "a63ad114-7e13-5084-954f-fe012c677804"
+    Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
+
+[[deps.FileWatching]]
+uuid = "7b1f6079-737a-58dc-b8bc-7a2ca5c1b5ee"
+version = "1.11.0"
+
+[[deps.FixedPointDecimals]]
+deps = ["BitIntegers", "Parsers"]
+git-tree-sha1 = "cf637cd2d786280d2d4afa59c69294f110e2a28c"
+uuid = "fb4d412d-6eee-574d-9565-ede6634db7b0"
+version = "0.6.3"
+
+[[deps.Future]]
+deps = ["Random"]
+uuid = "9fa8497b-333b-5362-9e8d-4d0656e87820"
+version = "1.11.0"
+
+[[deps.Glob]]
+git-tree-sha1 = "97285bbd5230dd766e9ef6749b80fc617126d496"
+uuid = "c27321d9-0574-5035-807b-f59d2c89b15c"
+version = "1.3.1"
+
+[[deps.InlineStrings]]
+git-tree-sha1 = "6a9fde685a7ac1eb3495f8e812c5a7c3711c2d5e"
+uuid = "842dd82b-1e85-43dc-bf29-5d0ee9dffc48"
+version = "1.4.3"
+
+    [deps.InlineStrings.extensions]
+    ArrowTypesExt = "ArrowTypes"
+    ParsersExt = "Parsers"
+
+    [deps.InlineStrings.weakdeps]
+    ArrowTypes = "31f734f8-188a-4ce0-8406-c8a06bd891cd"
+    Parsers = "69de0a69-1ddd-5017-9359-2bf0b02dc9f0"
+
+[[deps.InteractiveUtils]]
+deps = ["Markdown"]
+uuid = "b77e0a4c-d291-57a0-90e8-8db25a27a240"
+version = "1.11.0"
+
+[[deps.IteratorInterfaceExtensions]]
+git-tree-sha1 = "a3f24677c21f5bbe9d2a714f95dcd58337fb2856"
+uuid = "82899510-4779-5014-852e-03e436cf321d"
+version = "1.0.0"
+
+[[deps.JLLWrappers]]
+deps = ["Artifacts", "Preferences"]
+git-tree-sha1 = "a007feb38b422fbdab534406aeca1b86823cb4d6"
+uuid = "692b3bcd-3c85-4b1f-b108-f13ce0eb3210"
+version = "1.7.0"
+
+[[deps.JuliaInterpreter]]
+deps = ["CodeTracking", "InteractiveUtils", "Random", "UUIDs"]
+git-tree-sha1 = "ad08bbc177bc329888d21a94b37beb6aa919273a"
+uuid = "aa1ae85d-cabe-5617-a682-6adf51b2e16a"
+version = "0.10.2"
+
+[[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 = "8.6.0+0"
+
+[[deps.LibGit2]]
+deps = ["Base64", "LibGit2_jll", "NetworkOptions", "Printf", "SHA"]
+uuid = "76f85450-5226-5b5a-8eaa-529ad045b433"
+version = "1.11.0"
+
+[[deps.LibGit2_jll]]
+deps = ["Artifacts", "LibSSH2_jll", "Libdl", "MbedTLS_jll"]
+uuid = "e37daf67-58a4-590a-8e99-b0245dd2ffc5"
+version = "1.7.2+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"
+version = "1.11.0"
+
+[[deps.LoweredCodeUtils]]
+deps = ["JuliaInterpreter"]
+git-tree-sha1 = "4ef1c538614e3ec30cb6383b9eb0326a5c3a9763"
+uuid = "6f1432cf-f94c-5a45-995e-cdbf5db27b0b"
+version = "3.3.0"
+
+[[deps.Markdown]]
+deps = ["Base64"]
+uuid = "d6f4376e-aef5-505a-96c1-9c027394607a"
+version = "1.11.0"
+
+[[deps.MbedTLS_jll]]
+deps = ["Artifacts", "Libdl"]
+uuid = "c8ffd9c3-330d-5841-b78e-0817d7145fa1"
+version = "2.28.6+0"
+
+[[deps.Mmap]]
+uuid = "a63ad114-7e13-5084-954f-fe012c677804"
+version = "1.11.0"
+
+[[deps.MozillaCACerts_jll]]
+uuid = "14a3606d-f60d-562e-9121-12d972cd8159"
+version = "2023.12.12"
+
+[[deps.NetworkOptions]]
+uuid = "ca575930-c2e3-43a9-ace4-1e988b2c1908"
+version = "1.2.0"
+
+[[deps.OrderedCollections]]
+git-tree-sha1 = "cc4054e898b852042d7b503313f7ad03de99c3dd"
+uuid = "bac558e1-5e72-5ebc-8fee-abe8a469f55d"
+version = "1.8.0"
+
+[[deps.Parsers]]
+deps = ["Dates", "PrecompileTools", "UUIDs"]
+git-tree-sha1 = "7d2f8f21da5db6a806faf7b9b292296da42b2810"
+uuid = "69de0a69-1ddd-5017-9359-2bf0b02dc9f0"
+version = "2.8.3"
+
+[[deps.PooledArrays]]
+deps = ["DataAPI", "Future"]
+git-tree-sha1 = "36d8b4b899628fb92c2749eb488d884a926614d3"
+uuid = "2dfb63ee-cc39-5dd5-95bd-886bf059d720"
+version = "1.4.3"
+
+[[deps.PrecompileTools]]
+deps = ["Preferences"]
+git-tree-sha1 = "5aa36f7049a63a1528fe8f7c3f2113413ffd4e1f"
+uuid = "aea7be01-6a6a-4083-8856-8a6e6704d82a"
+version = "1.2.1"
+
+[[deps.Preferences]]
+deps = ["TOML"]
+git-tree-sha1 = "9306f6085165d270f7e3db02af26a400d580f5c6"
+uuid = "21216c6a-2e73-6563-6e65-726566657250"
+version = "1.4.3"
+
+[[deps.Printf]]
+deps = ["Unicode"]
+uuid = "de0858da-6303-5e67-8744-51eddeeeb8d7"
+version = "1.11.0"
+
+[[deps.REPL]]
+deps = ["InteractiveUtils", "Markdown", "Sockets", "StyledStrings", "Unicode"]
+uuid = "3fa0cd96-eef1-5676-8a61-b3b8758bbffb"
+version = "1.11.0"
+
+[[deps.Random]]
+deps = ["SHA"]
+uuid = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
+version = "1.11.0"
+
+[[deps.Requires]]
+deps = ["UUIDs"]
+git-tree-sha1 = "62389eeff14780bfe55195b7204c0d8738436d64"
+uuid = "ae029012-a4dd-5104-9daa-d747884805df"
+version = "1.3.1"
+
+[[deps.Revise]]
+deps = ["CodeTracking", "FileWatching", "JuliaInterpreter", "LibGit2", "LoweredCodeUtils", "OrderedCollections", "REPL", "Requires", "UUIDs", "Unicode"]
+git-tree-sha1 = "cedc9f9013f7beabd8a9c6d2e22c0ca7c5c2a8ed"
+uuid = "295af30f-e4ad-537b-8983-00126c2a3abe"
+version = "3.7.6"
+
+    [deps.Revise.extensions]
+    DistributedExt = "Distributed"
+
+    [deps.Revise.weakdeps]
+    Distributed = "8ba89e20-285c-5b6f-9357-94700520ee1b"
+
+[[deps.SHA]]
+uuid = "ea8e919c-243c-51af-8825-aaa63cd721ce"
+version = "0.7.0"
+
+[[deps.SentinelArrays]]
+deps = ["Dates", "Random"]
+git-tree-sha1 = "712fb0231ee6f9120e005ccd56297abbc053e7e0"
+uuid = "91c51154-3ec4-41a3-a24f-3f23e20d615c"
+version = "1.4.8"
+
+[[deps.Sockets]]
+uuid = "6462fe0b-24de-5631-8697-dd941f90decc"
+version = "1.11.0"
+
+[[deps.StyledStrings]]
+uuid = "f489334b-da3d-4c2e-b8f0-e476e12c162b"
+version = "1.11.0"
+
+[[deps.TOML]]
+deps = ["Dates"]
+uuid = "fa267f1f-6049-4f14-aa54-33bafae1ed76"
+version = "1.0.3"
+
+[[deps.TableTraits]]
+deps = ["IteratorInterfaceExtensions"]
+git-tree-sha1 = "c06b2f539df1c6efa794486abfb6ed2022561a39"
+uuid = "3783bdb8-4a98-5b6b-af9a-565f29a5fe9c"
+version = "1.0.1"
+
+[[deps.Tables]]
+deps = ["DataAPI", "DataValueInterfaces", "IteratorInterfaceExtensions", "OrderedCollections", "TableTraits"]
+git-tree-sha1 = "598cd7c1f68d1e205689b1c2fe65a9f85846f297"
+uuid = "bd369af6-aec1-5ad0-b16a-f7cc5008161c"
+version = "1.12.0"
+
+[[deps.TranscodingStreams]]
+git-tree-sha1 = "0c45878dcfdcfa8480052b6ab162cdd138781742"
+uuid = "3bb67fe8-82b1-5028-8e26-92a6c54297fa"
+version = "0.11.3"
+
+[[deps.UUIDs]]
+deps = ["Random", "SHA"]
+uuid = "cf7118a7-6976-5b1a-9a39-7adc72f591a4"
+version = "1.11.0"
+
+[[deps.Unicode]]
+uuid = "4ec0a83e-493e-50e2-b9ac-8f72acf5a8f5"
+version = "1.11.0"
+
+[[deps.WeakRefStrings]]
+deps = ["DataAPI", "InlineStrings", "Parsers"]
+git-tree-sha1 = "b1be2855ed9ed8eac54e5caff2afcdb442d52c23"
+uuid = "ea10d353-3f73-51f8-a26c-33c1cb351aa5"
+version = "1.4.2"
+
+[[deps.WorkerUtilities]]
+git-tree-sha1 = "cd1659ba0d57b71a464a29e64dbc67cfe83d54e7"
+uuid = "76eceee3-57b5-4d4a-8e66-0e911cebbf60"
+version = "1.6.1"
+
+[[deps.ZipFile]]
+deps = ["Libdl", "Printf", "Zlib_jll"]
+git-tree-sha1 = "f492b7fe1698e623024e873244f10d89c95c340a"
+uuid = "a5390f91-8eb1-5f08-bee0-b1d1ffed6cea"
+version = "0.10.1"
+
+[[deps.Zlib_jll]]
+deps = ["Libdl"]
+uuid = "83775a58-1f1d-513f-b197-d71354ab007a"
+version = "1.2.13+1"
+
+[[deps.nghttp2_jll]]
+deps = ["Artifacts", "Libdl"]
+uuid = "8e850ede-7688-5339-a07c-302acd2aaf8d"
+version = "1.59.0+0"

src/mimic_iv/Project.toml

@@ -0,0 +1,10 @@
+[deps]
+CSV = "336ed68f-0bac-5ca0-87d4-7b16caf5d00b"
+CodecZlib = "944b1d66-785c-5afd-91f1-9de20f533193"
+DBInterface = "a10d1c49-ce27-4219-8d33-6db1a4562965"
+Downloads = "f43a241f-c20a-4ad4-852c-f6b1247861c6"
+DuckDB = "d2f5444f-75bc-4fdf-ac35-56f514c445e1"
+Glob = "c27321d9-0574-5035-807b-f59d2c89b15c"
+Revise = "295af30f-e4ad-537b-8983-00126c2a3abe"
+Tables = "bd369af6-aec1-5ad0-b16a-f7cc5008161c"
+ZipFile = "a5390f91-8eb1-5f08-bee0-b1d1ffed6cea"