Initial commit

Author: bryanhunter

LICENSE

@@ -186,7 +186,7 @@
       same "printed page" as the copyright notice for easier
       identification within third-party archives.
 
-   Copyright [yyyy] [name of copyright owner]
+   Copyright 2018 HCA Healthcare
 
    Licensed under the Apache License, Version 2.0 (the "License");
    you may not use this file except in compliance with the License.

README.md

@@ -1,2 +1,67 @@
 # elixir-hl7
 An Elixir library for working with HL7 v2.x healthcare data 
+
+Elixir-HL7 provides parsers and data-structures for working with healthcare data that conforms to the HL7 v2.x standards. Elixir-HL7 includes data structures for every HL7 Segment and Datatype defined in HL7 versions 2.1, 2.2, 2.3, 2.3.1, 2.4, 2.5, and 2.5.1. Elixir-HL7 also provides basic support for handling MLLP streams. 
+
+You can learn more about HL7 here:
+* The official HL& website ([hl7.org](http://www.hl7.org/index.cfm))
+* Wikipedia's [HL7 article](https://en.wikipedia.org/wiki/Health_Level_7) 
+
+## Status
+
+This project is at v0.0.1 for a reason. The API and internals will likely quite a bit between now and v1.0. Also, be aware of the details of the license (Apache 2.0). 
+
+## Design goals
+
+### Completeness
+
+The library should contain every segment and datatype defined in the HL7 standard 
+for each supported HL7 version. We used the XSD files found at [hl7.org](http://www.hl7.org/implement/standards/product_brief.cfm?product_id=214) to build our initial set. 
+
+### Speed
+
+For basic reads we are aiming at tens of thousands of messages per second on a typical developer laptop.
+We will include more meaningful benchmarks soon.
+
+### Non-strict evaluation
+
+Non-standard, company-specific data is commonly stored in segments beginning with the letter "Z" such as ZPM (commonly referred to as "Z segments"). Elixir-HL7 stores Z-Segment data as lists of lists in ZSegment structs.
+
+Data for other unknown segments is stored similarly to Z-Segments but in UnknownSegment structs.
+
+Data that overflows the list of fields defined in the specs for segments and datatypes are preserved.
+
+### Flexibility
+
+To access data by ordinal positions or nested named structures 
+
+### Lossless data round-trips
+
+[raw hl7 string] <-> [lists of lists] <-> [data structures]
+
+## Getting started
+
+The Hl7.Example module provides sample data you can use to explore the API. 
+
+```
+iex> raw_hl7 = Hl7.Examples.wikipedia_sample_hl7
+
+"MSH|^~&|MegaReg|XYZHospC|SuperOE|XYZImgCtr|20060529090131-0500||ADT^A01^ADT_A01|01052901|P|2.5\rEVN||200605290901||||200605290900\rPID|||56782445^^^UAReg^PI||KLEINSAMPLE^BARRY^Q^JR||19620910|M||2028-9^^HL70005^RA99113^^XYZ|260 GOODWIN CREST DRIVE^^BIRMINGHAM^AL^35209^^M~NICKELL’S PICKLES^10000 W 100TH AVE^BIRMINGHAM^AL^35200^^O|||||||0105I30001^^^99DEF^AN\rPV1||I|W^389^1^UABH^^^^3||||12345^MORGAN^REX^J^^^MD^0010^UAMC^L||67890^GRAINGER^LUCY^X^^^MD^0010^UAMC^L|MED|||||A0||13579^POTTER^SHERMAN^T^^^MD^0010^UAMC^L|||||||||||||||||||||||||||200605290900\rOBX|1|NM|^Body Height||1.80|m^Meter^ISO+|||||F\rOBX|2|NM|^Body Weight||79|kg^Kilogram^ISO+|||||F\rAL1|1||^ASPIRIN\rDG1|1||786.50^CHEST PAIN, UNSPECIFIED^I9|||A\r"
+```
+
+We can take that sample message and create an `Hl7.Message` like so
+
+```
+iex> raw_hl7 |> Hl7.Message.new() |> Hl7.Message.make_structs()
+```
+
+# Roadmap 
+- [ ] Module docs and function docs
+- [ ] Support adding custom Z-Segments
+- [ ] Once it's a bit less wobbly, publish to hex.pm
+- [ ] Property-based tests and StreamData generators for HL7 segments and datatypes
+- [ ] Support for higher HL7 versions (e.g. 2.8)
+
+# License
+
+Elixir-HL7 source code is released under Apache 2 License. Check LICENSE file for more information.

VERSION

@@ -0,0 +1 @@
+0.0.1

bump_version.exs

@@ -0,0 +1,11 @@
+#! /usr/bin/env elixir
+
+new_version =
+  "VERSION"
+  |> File.read!()
+  |> String.trim()
+  |> Version.parse!()
+  |> (fn ver -> "#{ver.major}.#{ver.minor}.#{ver.patch + 1}" end).()
+
+File.write("VERSION", new_version)
+IO.puts("Version bumped to #{new_version}")

config/config.exs

@@ -0,0 +1,30 @@
+# This file is responsible for configuring your application
+# and its dependencies with the aid of the Mix.Config module.
+use Mix.Config
+
+# This configuration is loaded before any dependency and is restricted
+# to this project. If another project depends on this project, this
+# file won't be loaded nor affect the parent project. For this reason,
+# if you want to provide default values for your application for
+# 3rd-party users, it should be done in your "mix.exs" file.
+
+# You can configure your application as:
+#
+#     config :hl7, key: :value
+#
+# and access this configuration in your application as:
+#
+#     Application.get_env(:hl7, :key)
+#
+# You can also configure a 3rd-party app:
+#
+#     config :logger, level: :info
+#
+
+# It is also possible to import configuration files, relative to this
+# directory. For example, you can emulate configuration per environment
+# by uncommenting the line below and defining dev.exs, test.exs and such.
+# Configuration from the imported file will override the ones defined
+# here (which is why it is important to import them last).
+#
+#     import_config "#{Mix.env}.exs"

lib/hl7.ex

@@ -0,0 +1,27 @@
+defmodule Hl7 do
+  @moduledoc """
+  Functions for reading raw HL7 messages, splitting them into segments, and
+  parsing them into HL7.Segments structures
+  """
+  require Logger
+
+  def open_hl7_file_stream(file_path) do
+    file_ref = File.open!(file_path, [:read])
+    first_three = IO.binread(file_ref, 3)
+    File.close(file_ref)
+
+    case first_three do
+      <<"MSH">> ->
+        File.stream!(file_path)
+
+      <<0x0B, "M", "S">> ->
+        file_path
+        |> File.stream!([], 32768)
+        |> Hl7.MllpStream.raw_to_messages()
+    end
+  end
+
+  def get_separators(<<"MSH", _::binary()>> = raw_message) do
+    Hl7.Separators.new(raw_message)
+  end
+end

lib/hl7/2.1/datatypes/ce.ex

@@ -0,0 +1,15 @@
+defmodule Hl7.V2_1.DataTypes.Ce do
+  @moduledoc """
+  The "CE" (CE) data type
+  """
+
+  use Hl7.DataType,
+    fields: [
+      identifier: nil,
+      text: nil,
+      name_of_coding_system: nil,
+      alternate_identifier: nil,
+      alternate_text: nil,
+      name_of_alternate_coding_system: nil
+    ]
+end

lib/hl7/2.1/segments.ex

@@ -0,0 +1,66 @@
+defmodule Hl7.V2_1.Segments.ZSegment do
+  @moduledoc """
+  HL7 segment data structure for handling non-standard Z-Segments
+  """
+  use Hl7.Segment, fields: [segment: nil, values: nil], undefined_struct: true
+end
+
+defmodule Hl7.V2_1.Segments.UnknownSegment do
+  @moduledoc """
+  HL7 segment data structure for handling unknown segment types
+  """
+  use Hl7.Segment, fields: [segment: nil, values: nil], undefined_struct: true
+end
+
+defmodule Hl7.V2_1.Segments do
+  alias Hl7.V2_1.Segments
+
+  def parse(nested_lists), do: parse(nested_lists |> unlist, nested_lists)
+  def parse("ACC", nested_lists), do: Segments.ACC.new(nested_lists)
+  def parse("ADD", nested_lists), do: Segments.ADD.new(nested_lists)
+  def parse("BHS", nested_lists), do: Segments.BHS.new(nested_lists)
+  def parse("BLG", nested_lists), do: Segments.BLG.new(nested_lists)
+  def parse("BTS", nested_lists), do: Segments.BTS.new(nested_lists)
+  def parse("DG1", nested_lists), do: Segments.DG1.new(nested_lists)
+  def parse("DSC", nested_lists), do: Segments.DSC.new(nested_lists)
+  def parse("DSP", nested_lists), do: Segments.DSP.new(nested_lists)
+  def parse("ERR", nested_lists), do: Segments.ERR.new(nested_lists)
+  def parse("EVN", nested_lists), do: Segments.EVN.new(nested_lists)
+  def parse("FHS", nested_lists), do: Segments.FHS.new(nested_lists)
+  def parse("FT1", nested_lists), do: Segments.FT1.new(nested_lists)
+  def parse("FTS", nested_lists), do: Segments.FTS.new(nested_lists)
+  def parse("GT1", nested_lists), do: Segments.GT1.new(nested_lists)
+  def parse("IN1", nested_lists), do: Segments.IN1.new(nested_lists)
+  def parse("MRG", nested_lists), do: Segments.MRG.new(nested_lists)
+  def parse("MSA", nested_lists), do: Segments.MSA.new(nested_lists)
+  def parse("MSH", nested_lists), do: Segments.MSH.new(nested_lists)
+  def parse("NCK", nested_lists), do: Segments.NCK.new(nested_lists)
+  def parse("NK1", nested_lists), do: Segments.NK1.new(nested_lists)
+  def parse("NPU", nested_lists), do: Segments.NPU.new(nested_lists)
+  def parse("NSC", nested_lists), do: Segments.NSC.new(nested_lists)
+  def parse("NST", nested_lists), do: Segments.NST.new(nested_lists)
+  def parse("NTE", nested_lists), do: Segments.NTE.new(nested_lists)
+  def parse("OBR", nested_lists), do: Segments.OBR.new(nested_lists)
+  def parse("OBX", nested_lists), do: Segments.OBX.new(nested_lists)
+  def parse("ORC", nested_lists), do: Segments.ORC.new(nested_lists)
+  def parse("ORO", nested_lists), do: Segments.ORO.new(nested_lists)
+  def parse("PID", nested_lists), do: Segments.PID.new(nested_lists)
+  def parse("PR1", nested_lists), do: Segments.PR1.new(nested_lists)
+  def parse("PV1", nested_lists), do: Segments.PV1.new(nested_lists)
+  def parse("QRD", nested_lists), do: Segments.QRD.new(nested_lists)
+  def parse("QRF", nested_lists), do: Segments.QRF.new(nested_lists)
+  def parse("RX1", nested_lists), do: Segments.RX1.new(nested_lists)
+  def parse("UB1", nested_lists), do: Segments.UB1.new(nested_lists)
+  def parse("URD", nested_lists), do: Segments.URD.new(nested_lists)
+  def parse("URS", nested_lists), do: Segments.URS.new(nested_lists)
+  def parse(<<"Z", _::binary>>, nested_lists), do: Segments.ZSegment.new(nested_lists)
+  def parse(_, nested_lists), do: Segments.UnknownSegment.new(nested_lists)
+
+  def unlist([h | _]) do
+    unlist(h)
+  end
+
+  def unlist(v) do
+    v
+  end
+end

lib/hl7/2.1/segments/acc.ex

@@ -0,0 +1,15 @@
+defmodule Hl7.V2_1.Segments.ACC do
+  @moduledoc """
+  HL7 segment data structure for "ACC"
+  """
+
+  require Logger
+
+  use Hl7.Segment,
+    fields: [
+      segment: nil,
+      accident_date_time: nil,
+      accident_code: nil,
+      accident_location: nil
+    ]
+end

lib/hl7/2.1/segments/add.ex

@@ -0,0 +1,13 @@
+defmodule Hl7.V2_1.Segments.ADD do
+  @moduledoc """
+  HL7 segment data structure for "ADD"
+  """
+
+  require Logger
+
+  use Hl7.Segment,
+    fields: [
+      segment: nil,
+      addendum_continuation_pointer: nil
+    ]
+end

lib/hl7/2.1/segments/bhs.ex

@@ -0,0 +1,24 @@
+defmodule Hl7.V2_1.Segments.BHS do
+  @moduledoc """
+  HL7 segment data structure for "BHS"
+  """
+
+  require Logger
+
+  use Hl7.Segment,
+    fields: [
+      segment: nil,
+      batch_field_separator: nil,
+      batch_encoding_characters: nil,
+      batch_sending_application: nil,
+      batch_sending_facility: nil,
+      batch_receiving_application: nil,
+      batch_receiving_facility: nil,
+      batch_creation_date_time: nil,
+      batch_security: nil,
+      batch_name_id_type: nil,
+      batch_comment: nil,
+      batch_control_id: nil,
+      reference_batch_control_id: nil
+    ]
+end

lib/hl7/2.1/segments/blg.ex

@@ -0,0 +1,15 @@
+defmodule Hl7.V2_1.Segments.BLG do
+  @moduledoc """
+  HL7 segment data structure for "BLG"
+  """
+
+  require Logger
+
+  use Hl7.Segment,
+    fields: [
+      segment: nil,
+      when_to_charge: nil,
+      charge_type: nil,
+      account_id: nil
+    ]
+end

lib/hl7/2.1/segments/bts.ex

@@ -0,0 +1,15 @@
+defmodule Hl7.V2_1.Segments.BTS do
+  @moduledoc """
+  HL7 segment data structure for "BTS"
+  """
+
+  require Logger
+
+  use Hl7.Segment,
+    fields: [
+      segment: nil,
+      batch_message_count: nil,
+      batch_comment: nil,
+      batch_totals: nil
+    ]
+end

lib/hl7/2.1/segments/dg1.ex

@@ -0,0 +1,26 @@
+defmodule Hl7.V2_1.Segments.DG1 do
+  @moduledoc """
+  HL7 segment data structure for "DG1"
+  """
+
+  require Logger
+
+  use Hl7.Segment,
+    fields: [
+      segment: nil,
+      set_id_diagnosis: nil,
+      diagnosis_coding_method: nil,
+      diagnosis_code: nil,
+      diagnosis_description: nil,
+      diagnosis_date_time: nil,
+      diagnosis_drg_type: nil,
+      major_diagnostic_category: nil,
+      diagnostic_related_group: nil,
+      drg_approval_indicator: nil,
+      drg_grouper_review_code: nil,
+      outlier_type: nil,
+      outlier_days: nil,
+      outlier_cost: nil,
+      grouper_version_and_type: nil
+    ]
+end

lib/hl7/2.1/segments/dsc.ex

@@ -0,0 +1,13 @@
+defmodule Hl7.V2_1.Segments.DSC do
+  @moduledoc """
+  HL7 segment data structure for "DSC"
+  """
+
+  require Logger
+
+  use Hl7.Segment,
+    fields: [
+      segment: nil,
+      continuation_pointer: nil
+    ]
+end

lib/hl7/2.1/segments/dsp.ex

@@ -0,0 +1,17 @@
+defmodule Hl7.V2_1.Segments.DSP do
+  @moduledoc """
+  HL7 segment data structure for "DSP"
+  """
+
+  require Logger
+
+  use Hl7.Segment,
+    fields: [
+      segment: nil,
+      set_id_display_data: nil,
+      display_level: nil,
+      data_line: nil,
+      logical_break_point: nil,
+      result_id: nil
+    ]
+end

lib/hl7/2.1/segments/err.ex

@@ -0,0 +1,13 @@
+defmodule Hl7.V2_1.Segments.ERR do
+  @moduledoc """
+  HL7 segment data structure for "ERR"
+  """
+
+  require Logger
+
+  use Hl7.Segment,
+    fields: [
+      segment: nil,
+      error_code_and_location: nil
+    ]
+end