lis 0.2.3 → 0.4.3

data/.travis.yml

@@ -0,0 +1,6 @@
+language: ruby
+rvm:
+  - 1.8.7
+  - 1.9.2
+  - 1.9.3
+  - 2.0.0

data/Gemfile

@@ -1,2 +1,2 @@
-source :rubygems
+source "https://rubygems.org"
 gemspec

data/README.markdown

@@ -13,7 +13,52 @@ available][spec])
 [spec]: http://www.google.com/search?q=dpc+lis+immulite+2000+filetype:pdf
 
 
+## Usage
+
+* run the LIS server:
+
+    ```
+    $ gem install lis
+    $ lis help
+    $ lis -l /dev/ttyUSB0 -e http://worklist.example/lis server
+    ```
+
+* now, whenever order requests arrive from the LIS hardware, lis2http will forward them to the specified HTTP endpoint:
+
+    ```
+    GET http://worklist.example/lis/{DEVICE_NAME}-{SPECIMEN_ID}
+    ```
+
+* this should return basic patient information as well as test IDs for all pending requests:
+
+    ```
+    ---
+    id: '1234'
+    patient:
+      id: 98
+      last_name: Sierra
+      first_name: Rudolph
+    types:
+    - TSTID
+    - TSH
+    - FT3
+    - FT4
+    ```
+
+* results are posted to the same URI as soon as they are received:
+
+    ```
+    POST http://worklist.example/lis/{DEVICE_NAME}-{SPECIMEN_ID}/{TEST_NAME}
+
+    ---
+    flags: N
+    result_timestamp: '1993-10-11T09:12:33+00:00'
+    status: F
+    test_name: TSTID
+    unit: mIU/mL
+    value: '8.2'
+    ```
 
 ## Copyright
 
-Copyright (c) 2010-2011 Levin Alexander. See LICENSE for details.
+Copyright (c) 2010-2013 Levin Alexander. See LICENSE for details.

data/Rakefile

@@ -7,9 +7,7 @@ require 'lis'
 
 require 'rake/testtask'
 Rake::TestTask.new(:test) do |test|
-  test.libs << 'lib' << 'test'
-  test.pattern = 'test/**/test_*.rb'
-  test.verbose = true
+  test.libs << 'test'
 end
 
 require 'cucumber/rake/task'

data/bin/lis

@@ -0,0 +1,8 @@
+#!/usr/bin/env ruby
+require 'gli'
+
+require 'lis'
+require 'lis/cli'
+
+exit LIS::CLI.run(ARGV.dup)
+

data/features/lis.feature

@@ -1,8 +1,4 @@
 Feature:
-  In order to diagnose patients correctly
-  As a doctor
-  I want to be able to receive test results via LIS
-
   Scenario: LIS asking for pending requests
     Given LIS Interface listening for messages
     And the following requests are pending for DPC:
@@ -17,7 +13,7 @@ Feature:
     Then LIS should have sent test orders to client:
     """
       1H|\^&|||LIS||||8N1|DPC||P|1|
-      2P|1||||Müller^Rudolph||||||||
+      2P|1|98||98|Müller^Rudolph||||||||
       3O|1|123ABC||^^^TSH
       4O|1|123ABC||^^^FT3
       5O|1|123ABC||^^^FT4

data/features/lis_cli.feature

@@ -0,0 +1,6 @@
+Feature: My bootstrapped app kinda works
+
+  Scenario: App just runs
+    When I get help for "lis"
+    Then the exit status should be 0
+

data/features/step_definitions/lis_cli_steps.rb

@@ -0,0 +1,6 @@
+When /^I get help for "([^"]*)"$/ do |app_name|
+  @app_name = app_name
+  step %(I run `#{app_name} --help`)
+end
+
+# Add more step definitions here

data/features/step_definitions/lis_steps.rb

@@ -1,16 +1,14 @@
 # encoding: UTF-8
 
-require 'mocha'
-require 'yaml'
+
 
 
 Given /^LIS Interface listening for messages$/ do
   @client, @r, @w = PacketIO::Test::MockServer.build
   @io = PacketIO::IOListener.new(@r, @w)
-  @server = LIS::InterfaceServer.create(@io, "http://localhost/lis/")
+  @server = LIS::InterfaceServer.create(@io, "http://localhost/lis")
 
-  stub_request(:post, /http:\/\/localhost\/lis\/result\/.*/).
-    with(:body => /.*/, :headers => {'Accept'=>'*/*', 'Content-Type'=>'application/x-www-form-urlencoded'}).
+  stub_request(:post, /http:\/\/localhost\/lis\/.*?\/.*/).
     to_return(:status => 200, :body => "", :headers => {})
 
   @t = Thread.new do
@@ -36,7 +34,7 @@ end
 Then /^should have posted results:$/ do |table|
   table.hashes.each do |row|
     expected_body = ["test_name", "value", "unit", "status", "flags", "result_timestamp"].inject({}) { |h,k| h[k] = row[k]; h }
-    assert_requested(:post, "http://localhost/lis/result/#{row["id"]}", :times => 1, :body => expected_body)
+    assert_requested(:post, "http://localhost/lis/#{row["id"]}/#{row["test_name"]}", :times => 1, :body => hash_including(expected_body))
   end
 end
 
@@ -53,16 +51,13 @@ Given /^the following requests are pending for (\w+):$/ do |device_name, table|
   table.hashes.each do |patient|
     body = { "patient" => { "last_name" => patient["last_name"],
                             "first_name" => patient["first_name"],
-                            "id" => patient["patient_id"]},
+                            "number" => patient["patient_id"]},
              "id" => patient["id"],
              "types" => patient["test_names"].strip.split(/\s+/) }
 
-    stub_request(:get, "http://localhost/lis/find_requests/#{device_name}-#{patient["id"]}").
-      with(:headers => {'Accept'=>'*/*'}).
+    stub_request(:get, "http://localhost/lis/#{device_name}-#{patient["id"]}").
       to_return(:status => 200, :body => body.to_yaml, :headers => {})
-
   end
-
 end
 
 

data/features/support/env.rb

@@ -1,9 +1,16 @@
 $LOAD_PATH.unshift(File.dirname(__FILE__) + '/../../lib')
+
 require 'lis'
 
+require 'mocha'
+require 'yaml'
+require 'aruba/cucumber'
+
 require 'packet_io/test/mock_server'
 require 'test/unit/assertions'
 require 'webmock/cucumber'
 
+WebMock.disable_net_connect!
+
 World(Test::Unit::Assertions)
 

data/lib/lis.rb

@@ -1,15 +1,16 @@
-$:.unshift File.dirname(__FILE__)
-
 require 'packet_io'
+require 'yaml'
 
 require 'lis/version'
-
 require 'lis/messages.rb'
+require 'lis/data'
+
 Dir[File.join(File.dirname(__FILE__), 'lis/messages/**/*.rb')].each { |f| require f }
 
 require 'lis/transfer/astm_e1394.rb'
 require 'lis/transfer/application_protocol.rb'
+require 'lis/transfer/logging'
+require 'lis/http_interface.rb'
 
-require 'lis/worklist_manager_interface.rb'
 require 'lis/interface_server.rb'
 

data/lib/lis/cli.rb

@@ -0,0 +1,47 @@
+module LIS
+  module CLI
+    extend GLI::App
+    program_desc "LIS interface to Siemens Immulite 2000XPi or other similar analyzers"
+    version LIS::VERSION
+
+    flag ["config","c"], :default_value => File.join(ENV['HOME'],'.lis'),
+                   :desc => "stores configuration and authentication data",
+                   :arg_name => "FILE"
+
+    flag ["listen", "l"], :arg_name => "PORT", :desc => "which port to listen on", :default_value => "/dev/ttyUSB0"
+    flag ["endpoint", "e"], :arg_name => "URI", :desc => "HTTP endpoint", :default_value => "http://localhost/api/lis"
+    switch ["verbose", "v"], :desc => "Increase verbosity"
+
+    pre do |global_options,command,options,args|
+      $VERBOSE = global_options[:verbose]
+      true
+    end
+
+    desc "run the LIS server"
+    command "server" do |c|
+      c.action do |global_options,options,args|
+        port = global_options[:listen]
+        warn "configuring #{port}"
+        `stty -echo raw ospeed 9600 ispeed 9600 < #{port}`
+        warn "listening on: #{port}"
+        port = File.open(port, "w+")
+
+        LIS::InterfaceServer.listen(port, global_options[:endpoint]).run!
+      end
+    end
+
+    desc "load a list of test requests"
+    arg_name "DEVICE_NAME REQUEST_ID"
+    command "requests" do |c|
+      c.action do |global_options,options,args|
+
+        req = LIS::HTTPInterface.new(global_options[:endpoint]).load_requests(*args)
+        puts req.types
+      end
+
+
+    end
+
+
+  end
+end

data/lib/lis/data.rb

@@ -0,0 +1,45 @@
+module LIS
+  module Data
+    class Request
+      def initialize(data={})
+        @data = data
+      end
+
+      def patient_id
+        @data["patient"]["number"]
+      end
+      def patient_last_name
+        @data["patient"]["last_name"]
+      end
+      def patient_first_name
+        @data["patient"]["first_name"]
+      end
+      def id
+        @data["id"]
+      end
+
+      def types
+        @data["types"]
+      end
+
+
+      def each_type
+        @data["types"].each do |t|
+          yield id, t
+        end
+      end
+
+      def to_hash
+        @data
+      end
+
+      def self.from_yaml(text, barcode)
+        data = YAML.load(text)
+        data["id"] = barcode
+
+        new(data)
+      end
+    end
+  end
+end
+

data/lib/lis/http_interface.rb

@@ -0,0 +1,74 @@
+# encoding: UTF-8
+
+require 'rest-client'
+
+class LIS::HTTPInterface
+  def initialize(endpoint)
+    @endpoint = endpoint
+  end
+
+  # expects all pending requests for the given device and barcode
+  #
+  #   { "id" => "1234",
+  #     "patient" => { "id" => 98,
+  #                    "last_name" => "Sierra",
+  #                    "first_name" => "Rudolph" },
+  #     "types" => [ "TSH", "FT3", "FT4" ] }
+  #
+  def load_requests(device_name, barcode)
+    begin
+      result = RestClient.get(uri(device_name, barcode))
+      data = LIS::Data::Request.from_yaml(result.body, barcode)
+    rescue Exception => e
+      puts e
+      puts e.backtrace
+      data = nil
+    end
+
+    warn "data: #{data.inspect}" if $VERBOSE
+
+    data
+  end
+
+
+  def set_request_status(device_name, data)
+    # uri = URI.join(@endpoint, "result_status/#{[device_name, data.id].join('-')}")
+    # Net::HTTP.post_form(uri, data.to_hash)
+  end
+
+  def send_result(device_name, order, result)
+    barcode = order.specimen_id
+
+    data = {
+      "test_name" => order.universal_test_id,
+      "value" => result.result_value,
+      "unit" => result.unit,
+      "status" => result.result_status,
+      "flags" => result.abnormal_flags,
+      "result_timestamp" => result.test_completed_at,
+      "raw" => result.raw_data
+    }
+
+    # FIXME: WTF: should not just catch everything
+    begin
+      res = RestClient.post(uri(device_name, barcode, order.universal_test_id), data)
+    rescue Exception => e
+      puts "EXCEPTION"
+      p e
+    end
+  end
+
+
+  private
+
+  def uri(device_name, barcode, test_name = nil)
+    id = [device_name, barcode].join("-")
+
+    s = [@endpoint, id, test_name].compact.join("/")
+    warn "uri: #{s}" if $VERBOSE
+
+    s
+  end
+
+end
+

data/lib/lis/interface_server.rb

@@ -10,17 +10,21 @@ module LIS
     end
 
 
-    def initialize(server, http_endpoint, protocol_stack = [LIS::Transfer::ASTM::E1394, LIS::Transfer::ApplicationProtocol])
+    def initialize(server, http_endpoint)
       @server = server
-      protocol = protocol_stack.inject(server) { |i,klass| klass.new(i) }
-      interface = WorklistManagerInterface.new(http_endpoint)
 
+      protocol = LIS::Transfer::ApplicationProtocol.new(LIS::Transfer::Logging.new(LIS::Transfer::ASTM::E1394.new(server)))
+      interface = HTTPInterface.new(http_endpoint)
 
       protocol.on_request do |device_name, barcode|
+        warn "loading requests" if $VERBOSE
         interface.load_requests(device_name, barcode)
       end
-      protocol.on_result do |*args|
-        interface.send_result(*args)
+      protocol.on_result do |device_name, patient, order, result|
+        interface.send_result(device_name, order, result)
+      end
+      protocol.on_request_sent do |device_name, data|
+        interface.set_request_status(device_name, data)
       end
     end
 

data/lib/lis/messages/result.rb

@@ -38,6 +38,10 @@ module LIS::Message
     has_field 12, :test_started_at, :type => :timestamp
     has_field 13, :test_completed_at, :type => :timestamp
 
+    def raw_data
+      to_message
+    end
+
     def universal_test_id
       universal_test_id_internal.gsub(/\^/,"")
     end

data/lib/lis/transfer/application_protocol.rb

@@ -12,6 +12,10 @@ module LIS::Transfer
       @on_request_callback = block
     end
 
+    def on_request_sent(&block)
+      @on_request_sent_callback = block
+    end
+
     def received_header(message)
       @patient_information_requests ||= {} # delete the list of patients
       @device_name = message.sender_name
@@ -42,14 +46,16 @@ module LIS::Transfer
 
     def send_pending_requests
       sending_session(@patient_information_requests) do |patient_information|
-        patient_information.each do |sequence_nr, data|
+        patient_information.each do |sequence_nr, request_data|
           write :message, LIS::Message::Patient.new(sequence_nr,
-                                                    data["patient"]["number"],
-                                                    data["patient"]["last_name"],
-                                                    data["patient"]["first_name"]).to_message
-          data["types"].each do |request|
-            write :message, LIS::Message::Order.new(sequence_nr, data["id"], request).to_message
+                                                    request_data.patient_id,
+                                                    request_data.patient_last_name,
+                                                    request_data.patient_first_name).to_message
+          request_data.each_type do |id, request|
+            write :message, LIS::Message::Order.new(sequence_nr, id, request).to_message
           end
+
+          @on_request_sent_callback.call(@device_name, request_data) if @on_request_sent_callback
         end
       end
       @patient_information_requests = {}
@@ -71,7 +77,6 @@ module LIS::Transfer
     end
 
     def receive(type, message = nil)
-      warn "[R] #{message}" if type == :message and $VERBOSE
       case type
         when :begin
           @last_patient = nil

data/lib/lis/transfer/astm_e1394.rb

@@ -8,7 +8,7 @@ module LIS::Transfer
   # splits a stream into lis packets and only lets packets through
   # that are inside a session delimited by ENQ .. EOT
   #
-  # check the checksum and do acknowledgement of messages
+  # checks the checksum and does acknowledgement of messages
   #
   # forwards the following events:
   #
@@ -81,7 +81,7 @@ module LIS::Transfer
 
       frame_number, data, checksum = match[1 .. 3]
 
-      expected_checksum = (frame_number + data).each_byte.inject(16) { |a,b| (a+b) % 0x100 }
+      expected_checksum = compute_checksum(frame_number + data)
       actual_checksum   = checksum.to_i(16)
 
       raise "checksum mismatch: expected %03x got %03x" % [expected_checksum, actual_checksum] unless expected_checksum == actual_checksum
@@ -90,12 +90,16 @@ module LIS::Transfer
 
     def self.wrap_message(string, frame_number)
       frame_number = (frame_number % 8).to_s
-      checksum = (frame_number + string).each_byte.inject(16) { |a,b| (a+b) % 0x100 }
+      checksum = compute_checksum(frame_number + string)
       checksum = checksum.to_s(16).upcase.rjust(2,"0")
 
       "\002#{frame_number}#{string}\015\003#{checksum}\015\012"
     end
 
+    def self.compute_checksum(str)
+      str.each_byte.inject(16) { |a,b| (a+b) % 0x100 }
+    end
+
 
     def received_message(message)
       return false unless @inside_transmission

data/lib/lis/transfer/logging.rb

@@ -0,0 +1,27 @@
+
+module LIS::Transfer
+  class Logging < ::PacketIO::Base
+    def initialize(*args)
+      @verbose = $VERBOSE
+      super
+    end
+
+    def receive(type, message=nil)
+      output("<", type, message)
+      super
+    end
+
+    def write(type, message=nil)
+      output(">", type, message)
+      super
+    end
+
+
+    private
+
+    def output(direction, type, message)
+      warn [direction, type.to_s, message].join(" ") if @verbose
+    end
+  end
+end
+

data/lib/lis/version.rb

@@ -1,6 +1,6 @@
 # encoding: UTF-8
 
 module LIS
-  VERSION = "0.2.3"
+  VERSION = "0.4.3"
 end
 

data/lis.gemspec

@@ -20,12 +20,16 @@ Gem::Specification.new do |s|
   s.require_paths = ["lib"]
   s.summary = %q{LIS interface to Siemens Immulite 2000XPi or other similar analyzers}
 
-  s.add_dependency "packet_io", "~> 0.4.0"
+  s.add_dependency "packet_io", ">= 0.4.2"
+  s.add_dependency "rest-client"
+  s.add_dependency "rake"
+  s.add_dependency "gli", ">= 2.0.0.rc5"
 
-  s.add_development_dependency("shoulda", "~> 2.11.3")
-  s.add_development_dependency("mocha", "~> 0.9.12")
-  s.add_development_dependency("yard", "~> 0.7.1")
-  s.add_development_dependency("cucumber", "~> 0.10.3")
-  s.add_development_dependency("webmock", "~> 1.6.4")
+  s.add_development_dependency("shoulda", ">= 3.1.0")
+  s.add_development_dependency("mocha", ">= 0.12.0")
+  s.add_development_dependency("yard")
+  s.add_development_dependency("cucumber", ">= 1.2.0")
+  s.add_development_dependency("webmock", ">= 1.8.7")
+  s.add_development_dependency('aruba')
 end
 

data/test/helper.rb

@@ -1,12 +1,15 @@
 require 'rubygems'
 require 'test/unit'
+require 'webmock/test_unit'
 require 'shoulda'
-require 'mocha'
+require 'mocha/setup'
 
 $LOAD_PATH.unshift(File.join(File.dirname(__FILE__), '..', 'lib'))
 $LOAD_PATH.unshift(File.dirname(__FILE__))
 require 'lis'
 
+WebMock.disable_net_connect!
+
 class Test::Unit::TestCase
 end
 

data/test/test_http_interface.rb

@@ -0,0 +1,61 @@
+require 'helper'
+
+class TestHTTPInterface < Test::Unit::TestCase
+
+  def setup
+    @interface = LIS::HTTPInterface.new("http://localhost/lis")
+    @device_name = "LIS1"
+  end
+
+
+  context "posting a result" do
+    setup do
+      @order = LIS::Message::Order.new(13, 12345, "TSTID")
+      @string = "R|1|^^^LH|8.2|mIU/mL|.7\.7^400\400|N|N|F||test|19931011091233|19931011091233|DPCCIRRUS"
+      @result = LIS::Message::Result.from_string(@string)
+    end
+
+    should "should post correct format to the HTTP endpoint" do
+      result_stub = stub_request(:post, "http://localhost/lis/LIS1-12345/TSTID").
+        with(:body => { "flags"=>"N",
+                        "result_timestamp"=>"1993-10-11T09:12:33+00:00",
+                        "status"=>"F",
+                        "test_name"=>"TSTID",
+                        "unit"=>"mIU/mL",
+                        "value"=>"8.2",
+                        "raw"=>@string}).
+        to_return(:status => 200, :body => "", :headers => {})
+
+      @interface.send_result(@device_name, @order, @result)
+      assert_requested(result_stub)
+    end
+  end
+
+  context "requesting test" do
+    setup do
+      @http_result = { "id" => "1234",
+                        "patient" => { "number" => 98,
+                                       "last_name" => "Sierra",
+                                       "first_name" => "Rudolph" },
+                        "types" => [ "TSH", "FT3", "FT4" ] }.to_yaml
+    end
+
+
+    should "return patient information and requests" do
+      stub_request( :get, "http://localhost/lis/LIS1-SOMETHING").to_return(:status => 301, :headers => { 'Location' => "http://localhost/lis/LIS1-1234" } )
+
+      result_stub = stub_request(:get, "http://localhost/lis/LIS1-1234")
+      result_stub.to_return( :status => 200, :body => @http_result, :headers => {})
+      data = @interface.load_requests(@device_name, "SOMETHING")
+
+      expected = { "id" => "SOMETHING",
+                   "patient" => { "number" => 98,
+                                  "last_name" => "Sierra",
+                                  "first_name" => "Rudolph" },
+                   "types" => [ "TSH", "FT3", "FT4" ] }
+
+      assert_equal expected, data.to_hash
+    end
+  end
+end
+

data/test/test_messages.rb

@@ -70,4 +70,4 @@ class TestMessages < Test::Unit::TestCase
     end
   end
 
-end
+end

metadata

@@ -1,141 +1,201 @@
---- !ruby/object:Gem::Specification 
+--- !ruby/object:Gem::Specification
 name: lis
-version: !ruby/object:Gem::Version 
-  hash: 17
-  prerelease: false
-  segments: 
-  - 0
-  - 2
-  - 3
-  version: 0.2.3
+version: !ruby/object:Gem::Version
+  version: 0.4.3
+  prerelease: 
 platform: ruby
-authors: 
+authors:
 - Levin Alexander
 autorequire: 
 bindir: bin
 cert_chain: []
-
-date: 2011-06-11 00:00:00 +02:00
-default_executable: 
-dependencies: 
-- !ruby/object:Gem::Dependency 
+date: 2013-03-05 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
   name: packet_io
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 0.4.2
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 0.4.2
+- !ruby/object:Gem::Dependency
+  name: rest-client
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :runtime
   prerelease: false
-  requirement: &id001 !ruby/object:Gem::Requirement 
-    none: false
-    requirements: 
-    - - ~>
-      - !ruby/object:Gem::Version 
-        hash: 15
-        segments: 
-        - 0
-        - 4
-        - 0
-        version: 0.4.0
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: rake
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
   type: :runtime
-  version_requirements: *id001
-- !ruby/object:Gem::Dependency 
-  name: shoulda
   prerelease: false
-  requirement: &id002 !ruby/object:Gem::Requirement 
-    none: false
-    requirements: 
-    - - ~>
-      - !ruby/object:Gem::Version 
-        hash: 37
-        segments: 
-        - 2
-        - 11
-        - 3
-        version: 2.11.3
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: gli
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 2.0.0.rc5
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 2.0.0.rc5
+- !ruby/object:Gem::Dependency
+  name: shoulda
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 3.1.0
   type: :development
-  version_requirements: *id002
-- !ruby/object:Gem::Dependency 
-  name: mocha
   prerelease: false
-  requirement: &id003 !ruby/object:Gem::Requirement 
-    none: false
-    requirements: 
-    - - ~>
-      - !ruby/object:Gem::Version 
-        hash: 35
-        segments: 
-        - 0
-        - 9
-        - 12
-        version: 0.9.12
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 3.1.0
+- !ruby/object:Gem::Dependency
+  name: mocha
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 0.12.0
   type: :development
-  version_requirements: *id003
-- !ruby/object:Gem::Dependency 
-  name: yard
   prerelease: false
-  requirement: &id004 !ruby/object:Gem::Requirement 
-    none: false
-    requirements: 
-    - - ~>
-      - !ruby/object:Gem::Version 
-        hash: 1
-        segments: 
-        - 0
-        - 7
-        - 1
-        version: 0.7.1
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 0.12.0
+- !ruby/object:Gem::Dependency
+  name: yard
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
   type: :development
-  version_requirements: *id004
-- !ruby/object:Gem::Dependency 
-  name: cucumber
   prerelease: false
-  requirement: &id005 !ruby/object:Gem::Requirement 
-    none: false
-    requirements: 
-    - - ~>
-      - !ruby/object:Gem::Version 
-        hash: 49
-        segments: 
-        - 0
-        - 10
-        - 3
-        version: 0.10.3
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: cucumber
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 1.2.0
   type: :development
-  version_requirements: *id005
-- !ruby/object:Gem::Dependency 
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 1.2.0
+- !ruby/object:Gem::Dependency
   name: webmock
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 1.8.7
+  type: :development
   prerelease: false
-  requirement: &id006 !ruby/object:Gem::Requirement 
-    none: false
-    requirements: 
-    - - ~>
-      - !ruby/object:Gem::Version 
-        hash: 7
-        segments: 
-        - 1
-        - 6
-        - 4
-        version: 1.6.4
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 1.8.7
+- !ruby/object:Gem::Dependency
+  name: aruba
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
   type: :development
-  version_requirements: *id006
-description: ""
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+description: ''
 email: mail@levinalex.net
-executables: 
-- lis2http
+executables:
+- lis
 extensions: []
-
 extra_rdoc_files: []
-
-files: 
+files:
 - .gitignore
+- .travis.yml
 - .yardopts
 - Gemfile
 - LICENSE
 - README.markdown
 - Rakefile
-- bin/lis2http
+- bin/lis
 - features/communication basics.feature
 - features/lis.feature
+- features/lis_cli.feature
+- features/step_definitions/lis_cli_steps.rb
 - features/step_definitions/lis_steps.rb
 - features/support/env.rb
 - lib/lis.rb
-- lib/lis/commands/application.rb
+- lib/lis/cli.rb
+- lib/lis/data.rb
+- lib/lis/http_interface.rb
 - lib/lis/interface_server.rb
 - lib/lis/messages.rb
 - lib/lis/messages/comment.rb
@@ -147,63 +207,60 @@ files:
 - lib/lis/messages/terminator.rb
 - lib/lis/transfer/application_protocol.rb
 - lib/lis/transfer/astm_e1394.rb
+- lib/lis/transfer/logging.rb
 - lib/lis/version.rb
-- lib/lis/worklist_manager_interface.rb
 - lis.gemspec
 - test/helper.rb
-- test/lib/mock_server.rb
 - test/messages/test_header.rb
 - test/messages/test_order.rb
 - test/messages/test_patients.rb
 - test/messages/test_terminator.rb
 - test/test_application_protocol.rb
 - test/test_astm_e1394.rb
+- test/test_http_interface.rb
 - test/test_messages.rb
-has_rdoc: true
 homepage: http://github.com/levinalex/lis
 licenses: []
-
 post_install_message: 
-rdoc_options: 
+rdoc_options:
 - --charset=UTF-8
-require_paths: 
+require_paths:
 - lib
-required_ruby_version: !ruby/object:Gem::Requirement 
+required_ruby_version: !ruby/object:Gem::Requirement
   none: false
-  requirements: 
-  - - ">="
-    - !ruby/object:Gem::Version 
-      hash: 3
-      segments: 
+  requirements:
+  - - ! '>='
+    - !ruby/object:Gem::Version
+      version: '0'
+      segments:
       - 0
-      version: "0"
-required_rubygems_version: !ruby/object:Gem::Requirement 
+      hash: 4116448878207311103
+required_rubygems_version: !ruby/object:Gem::Requirement
   none: false
-  requirements: 
-  - - ">="
-    - !ruby/object:Gem::Version 
-      hash: 3
-      segments: 
-      - 0
-      version: "0"
+  requirements:
+  - - ! '>='
+    - !ruby/object:Gem::Version
+      version: '0'
 requirements: []
-
 rubyforge_project: 
-rubygems_version: 1.3.7
+rubygems_version: 1.8.25
 signing_key: 
 specification_version: 3
 summary: LIS interface to Siemens Immulite 2000XPi or other similar analyzers
-test_files: 
+test_files:
 - features/communication basics.feature
 - features/lis.feature
+- features/lis_cli.feature
+- features/step_definitions/lis_cli_steps.rb
 - features/step_definitions/lis_steps.rb
 - features/support/env.rb
 - test/helper.rb
-- test/lib/mock_server.rb
 - test/messages/test_header.rb
 - test/messages/test_order.rb
 - test/messages/test_patients.rb
 - test/messages/test_terminator.rb
 - test/test_application_protocol.rb
 - test/test_astm_e1394.rb
+- test/test_http_interface.rb
 - test/test_messages.rb
+has_rdoc: 

data/bin/lis2http

@@ -1,6 +0,0 @@
-#!/usr/bin/env ruby
-
-require 'lis'
-require 'lis/commands/application.rb'
-
-LIS::Application.new(ARGV).run!

data/lib/lis/commands/application.rb

@@ -1,57 +0,0 @@
-# encoding: UTF-8
-
-require 'optparse'
-
-module LIS
-  class Options < Hash
-    attr_reader :opts
-
-    def initialize(args)
-      super()
-
-      default_options = { :port => "/dev/ttyUSB0", :uri => "http://localhost/lis/" }
-      self.merge!(default_options)
-
-      @opts = OptionParser.new do |o|
-        appname = File.basename($0)
-        o.banner = "Usage: #{appname} [options]"
-
-        o.on('-l, --listen PORT', 'which port to listen on (default: "/dev/ttyUSB0")') do |port|
-          self[:port] = port
-        end
-        o.on('-e, --endpoint URI', 'HTTP endpoint (default: "http://localhost/lis/")') do |endpoint|
-          self[:uri] = endpoint
-        end
-        o.on("-v", "--[no-]verbose", "Run verbosely") do |v|
-          $VERBOSE = v
-          self[:verbose] = v
-        end
-      end
-
-      begin
-        @opts.parse!(args)
-        self[:project_name] = args.shift
-      rescue OptionParser::ParseError => e
-        self[:invalid_argument] = e.message
-      end
-    end
-  end
-
-  class Application
-    def initialize(opts)
-      @options = Options.new(opts)
-
-      if @options[:invalid_argument]
-        warn @options.opts
-        exit 1
-      end
-    end
-
-    def run!
-      warn "listening on: #{@options[:port]}"
-      port = File.open(@options[:port], "w+")
-      LIS::InterfaceServer.listen(port, @options[:uri]).run!
-    end
-  end
-
-end

data/lib/lis/worklist_manager_interface.rb

@@ -1,69 +0,0 @@
-# encoding: UTF-8
-
-require 'net/http'
-require 'yaml'
-
-class WorklistManagerInterface
-  def initialize(endpoint)
-    @endpoint = endpoint
-  end
-
-  # expects all pending requests for the given device and barcode
-  #
-  #   { "id" => "1234",
-  #     "patient" => { "number" => 98,
-  #                    "last_name" => "Sierra",
-  #                    "first_name" => "Rudolph" },
-  #     "types" => [ "TSH", "FT3", "FT4" ] }
-  #
-  #
-  def load_requests(device_name, barcode)
-    begin
-      uri = URI.join(@endpoint,"find_requests/#{[device_name, barcode].join('-')}")
-      result = fetch_with_redirect(uri.to_s)
-      data = YAML.load(result.body)
-      data["id"] = barcode
-    rescue Exception => e
-      puts e
-      puts e.backtrace
-      data = nil
-    end
-
-    data
-  end
-
-  def send_result(device_name, patient, order, result)
-    barcode = order.specimen_id
-    data = {
-      "test_name" => order.universal_test_id,
-      "value" => result.result_value,
-      "unit" => result.unit,
-      "status" => result.result_status,
-      "flags" => result.abnormal_flags,
-      "result_timestamp" => result.test_completed_at
-    }
-
-    # FIXME: WTF: should not just catch everything
-    begin
-      res = Net::HTTP.post_form(URI.join(@endpoint, "result/#{[device_name, barcode].join('-')}"), data.to_hash)
-    rescue Exception => e
-      puts "EXCEPTION"
-      p e
-    end
-  end
-
-
-  private
-
-  def fetch_with_redirect(uri_str, limit = 10)
-    raise ArgumentError, 'too many HTTP redirects' if limit == 0
-
-    response = Net::HTTP.get_response(URI.parse(uri_str))
-    case response
-      when Net::HTTPSuccess     then response
-      when Net::HTTPRedirection then fetch_with_redirect(response['location'], limit - 1)
-    else
-      response.error!
-    end
-  end
-end

data/test/lib/mock_server.rb

@@ -1,50 +0,0 @@
-module Mock
-end
-
-class Mock::Server
-  def initialize(read, write)
-    @read, @write = read, write
-    @queue = Queue.new
-    @thread = Thread.new do
-      parse_commands
-    end
-  end
-
-  def write(string)
-    @queue.push [:write, string]
-    self
-  end
-
-  def read_all
-    @read.readpartial(4096)
-  end
-
-  def wait(seconds = 0.02)
-    @queue.push [:wait, seconds]
-    self
-  end
-
-  def eof
-    @queue.push [:close]
-  end
-
-
-  private
-
-  def parse_commands
-    loop do
-      action, data = @queue.pop
-
-      case action
-        when :close
-          @write.close
-          break
-        when :write
-          @write.write(data)
-          @write.flush
-        when :wait
-          sleep data
-      end
-    end
-  end
-end