example notebooks

examples/exploring-ohdsi-database.jl

@@ -0,0 +1,251 @@
+### A Pluto.jl notebook ###
+# v0.14.2
+
+using Markdown
+using InteractiveUtils
+
+# This Pluto notebook uses @bind for interactivity. When running this notebook outside of Pluto, the following 'mock version' of @bind gives bound variables a default value (instead of an error).
+macro bind(def, element)
+    quote
+        local el = $(esc(element))
+        global $(esc(def)) = Core.applicable(Base.get, el) ? Base.get(el) : missing
+        el
+    end
+end
+
+# ╔═╡ 8bd5e01c-418b-4dd8-ba9f-cb4f932bef03
+begin
+	using FunSQL:
+		SQLTable, Agg, From, Fun, Get, Group, Join, Select, Where, render	
+
+	using PlutoUI
+	using LibPQ
+	using Tables
+	using Plots
+end
+
+# ╔═╡ 32077f7b-90df-445b-b347-8bc9f921ab00
+md"""
+# Exploring OHDSI Database
+"""
+
+# ╔═╡ 4823e73d-1c92-4496-a19e-934891e0568c
+begin
+	DEFAULT_PGHOST = get(ENV, "PGHOST", "/var/run/postgresql")
+	DEFAULT_PGPORT = parse(Int, get(ENV, "PGPORT", "5432"))
+	DEFAULT_PGUSER = get(ENV, "PGUSER", "")
+	DEFAULT_PGPASSWORD = get(ENV, "PGPASSWORD", "")
+
+	md"""
+	## Configure Database Connection
+
+	**Host:**
+	$(@bind PGHOST TextField(default = DEFAULT_PGHOST))
+
+	**Port:**
+	$(@bind PGPORT NumberField(1:65535, default = DEFAULT_PGPORT))
+
+	**Username:**
+	$(@bind PGUSER TextField(default = DEFAULT_PGUSER))
+
+	**Password:**
+	$(@bind PGPASSWORD PasswordField(default = DEFAULT_PGPASSWORD))
+	"""
+end
+
+# ╔═╡ 70b51b71-2da1-49cf-b798-1998592218bc
+md"""
+## Statistics
+"""
+
+# ╔═╡ 0fd29899-809c-4c02-88db-927af32dc6d2
+md"""
+## Appendix
+"""
+
+# ╔═╡ 90701e34-1a2b-4b44-b4dd-33b3de26559e
+function escape_connection_parameter(p)
+	(key, val) = p
+	val = replace(val, '\\' => "\\\\")
+	val = replace(val, '\'' => "\\'")
+	"$key='$val'"
+end
+
+# ╔═╡ 68425c70-5370-4339-900d-83cc9fd9361b
+function connect(db)
+	db != "" || return nothing
+	params = Pair{String, String}[]
+	if PGHOST != ""
+		push!(params, "host" => PGHOST)
+	end
+	push!(params, "port" => string(PGPORT))
+	if PGUSER != ""
+		push!(params, "user" => PGUSER)
+	end
+	if PGPASSWORD != ""
+		push!(params, "password" => PGPASSWORD)
+	end
+	push!(params, "dbname" => db)
+	url = join([escape_connection_parameter(p) for p in params], " ")
+	try
+		LibPQ.Connection(url)
+	catch exc
+		exc isa LibPQ.Errors.LibPQException || rethrow()
+		nothing
+	end
+end
+
+# ╔═╡ 2c2e8c34-aed1-4620-959f-b28a89c693d3
+begin
+	function run(f, c, q; default = nothing)
+		c !== nothing || return default
+		r = LibPQ.execute(c, render(q))
+		f(r)
+	end
+
+	run(c, q; default = nothing) = run(identity, c, q; default = default)
+end
+
+# ╔═╡ 958a0422-06da-4510-a830-21ed6b871cf1
+maintenance_connection = connect("postgres")
+
+# ╔═╡ 004cb1fa-6763-4da6-94a7-ecbd9b6e5345
+begin
+	pg_database =
+		SQLTable(schema = :pg_catalog, :pg_database, :oid, :datname, :datistemplate)
+	pg_namespace =
+		SQLTable(schema = :pg_catalog, :pg_namespace, :oid, :nspname)
+	pg_class =
+		SQLTable(schema = :pg_catalog, :pg_class, :oid, :relname, :relnamespace, :relkind)
+end;
+
+# ╔═╡ aa12fff2-3a62-469f-ab98-d635758bfdf8
+begin
+	AvailableDatabases =
+		From(pg_database) |>
+		Where(
+			Fun.and(
+				Fun.not(Get.datistemplate),
+				Fun.has_database_privilege(Get.oid, "CONNECT")))
+
+	available_databases =
+		run(maintenance_connection, AvailableDatabases, default = []) do rows
+			[row.datname for row in rows]
+		end
+end
+
+# ╔═╡ 9207c58a-1042-4ab9-867e-b1b9e4e8fb99
+begin
+	HasTable(name) =
+		Agg.count(filter = Get.relname .== name) .> 0
+
+	HasTables(names...) =
+		Fun.and(HasTable.(names)...)
+
+	IsEligible =
+		From(pg_class) |>
+		Where(Get.relkind .== "r") |>
+		Join(:nsp => pg_namespace, Get.relnamespace .== Get.nsp.oid) |>
+		Where(Get.nsp.nspname .== "public") |>
+		Group() |>
+		Select(HasTables("concept", "person", "location"))
+
+	function is_eligible(db)
+		c = connect(db)
+		run(c, IsEligible, default = false) do rows
+			rows[1,1]
+		end
+	end
+
+	eligible_databases = filter(is_eligible, available_databases)
+end
+
+# ╔═╡ 827757af-f2c1-4ca4-a4b6-cdb3b50b6bcb
+begin
+	PGDATABASE = ""
+
+	if !isempty(eligible_databases)
+		md"""
+		**Database:**
+		$(@bind PGDATABASE PlutoUI.Select(eligible_databases, default = ""))
+		"""
+	elseif maintenance_connection === nothing
+		md"""
+		!!! danger "Cannot connect to the database server!"
+		"""
+	else
+		md"""
+		!!! danger "Cannot find any OSDSI databases!"
+		"""
+	end
+end
+
+# ╔═╡ 7f3b0bff-e274-4609-8fee-d519e546420b
+connection = connect(PGDATABASE)
+
+# ╔═╡ babeb64c-8d49-4c93-a5bc-1e196681e4cb
+begin
+	concept =
+		SQLTable(:concept, :concept_id, :concept_name, :domain_id, :vocabulary_id, :concept_class_id, :standard_concept, :concept_code, :valid_start_date, :valid_end_date, :invalid_reason)
+	person =
+		SQLTable(:person, :person_id, :gender_concept_id, :year_of_birth, :month_of_birth, :day_of_birth, :time_of_birth, :race_concept_id, :ethnicity_concept_id, :location_id, :provider_id, :care_site_id)
+	location =
+		SQLTable(:location, :location_id, :address_1, :address_2, :city, :state, :zip,  :county)
+end;
+
+# ╔═╡ 946e95bc-b330-42d4-906c-dd55bbdc49d6
+begin
+	PersonTotal = From(person) |> Group() |> Select(Agg.count())
+
+	run(connection, PersonTotal) do rows
+		data = ("Total", rows[1, 1])
+		bar(data, title = "Total # of patients", legend = false, formatter = :plain)
+	end
+end
+
+# ╔═╡ 9f4f069f-0cfe-4837-99a7-be094427e45d
+begin
+	PersonBySex =
+		From(person) |>
+		Group(Get.gender_concept_id) |>
+		Join(concept, Get.gender_concept_id .== Get.concept_id) |>
+		Select(Get.concept_code, Agg.count())
+
+	run(connection, PersonBySex) do rows
+		data = [(row[1], row[2]) for row in rows]
+		bar(data, title = "Patients by Sex",  legend = false, formatter = :plain)
+	end
+end
+
+# ╔═╡ 8a22dd67-610a-449c-a17d-004c8c7cfd61
+begin
+	PersonByYOB =
+		From(person) |>
+		Group(Get.year_of_birth) |>
+		Select(Get.year_of_birth, Agg.count())
+
+	run(connection, PersonByYOB) do rows
+		data = [(row[1], row[2]) for row in rows]
+		bar(data, title = "Patients By Year of Birth", legend = false, formatter = :plain)
+	end
+end
+
+# ╔═╡ Cell order:
+# ╟─32077f7b-90df-445b-b347-8bc9f921ab00
+# ╟─4823e73d-1c92-4496-a19e-934891e0568c
+# ╟─827757af-f2c1-4ca4-a4b6-cdb3b50b6bcb
+# ╟─70b51b71-2da1-49cf-b798-1998592218bc
+# ╠═946e95bc-b330-42d4-906c-dd55bbdc49d6
+# ╠═9f4f069f-0cfe-4837-99a7-be094427e45d
+# ╠═8a22dd67-610a-449c-a17d-004c8c7cfd61
+# ╟─0fd29899-809c-4c02-88db-927af32dc6d2
+# ╠═8bd5e01c-418b-4dd8-ba9f-cb4f932bef03
+# ╠═90701e34-1a2b-4b44-b4dd-33b3de26559e
+# ╠═68425c70-5370-4339-900d-83cc9fd9361b
+# ╠═2c2e8c34-aed1-4620-959f-b28a89c693d3
+# ╠═958a0422-06da-4510-a830-21ed6b871cf1
+# ╠═004cb1fa-6763-4da6-94a7-ecbd9b6e5345
+# ╠═aa12fff2-3a62-469f-ab98-d635758bfdf8
+# ╠═9207c58a-1042-4ab9-867e-b1b9e4e8fb99
+# ╠═7f3b0bff-e274-4609-8fee-d519e546420b
+# ╠═babeb64c-8d49-4c93-a5bc-1e196681e4cb