lis 0.2.1 → 0.2.2

data/lib/lis/messages.rb

@@ -1,6 +1,9 @@
 require 'date'
 
 module LIS::Message
+
+  # declarative definition of message structure
+  #
   module ClassMethods
     CONVERSION_WRITER = {
       :string => lambda { |s| s },
@@ -13,21 +16,6 @@ module LIS::Message
       @field_count
     end
 
-    def from_string(message)
-      type, data = parse(message)
-      klass = (@@messages_by_type || {})[type]
-      raise "unknown message type #{type.inspect}" unless klass
-
-      obj = klass.allocate
-
-      data = data.to_enum(:each_with_index).inject({}) do |h,(elem,idx)|
-        h[idx+2] = elem; h
-      end
-
-      obj.instance_variable_set("@fields", data)
-      obj
-    end
-
     def default_fields
       arr = Array.new(@field_count)
       (0 .. @field_count).inject(arr) do |a,i|
@@ -40,6 +28,8 @@ module LIS::Message
       end
     end
 
+    # define a field of a message at a specific index and an optional type
+    #
     def has_field(idx, name = nil, opts={})
       set_index_for(name, idx) if name
       set_field_attributes(idx, { :name => name,
@@ -65,13 +55,8 @@ module LIS::Message
       end
     end
 
-    def parse(string)
-      type, data = string.scan(/^(.)\|(.*)$/)[0]
-      data = data.split(/\|/)
-
-      return [type, data]
-    end
-
+    # registers a message with a specific type prefix to make {Message::Base.from_string} work
+    #
     def type_id(char = nil)
       return @@messages_by_type.find {|c,klass| klass == self }.first unless char
       @@messages_by_type ||= {}
@@ -100,11 +85,25 @@ module LIS::Message
       @field_names ||= {}
       @field_names[index] = hash
     end
+
+    private
+
+    def class_for_type(type)
+      klass = (@@messages_by_type || {})[type]
+      raise "unknown message type #{type.inspect}" unless klass
+      return klass
+    end
+
+    def parse(string)
+      type, data = string.scan(/^(.)\|(.*)$/)[0]
+      data = data.split(/\|/)
+
+      return [type, data]
+    end
   end
 
   class Base
     extend ClassMethods
-    attr_accessor :frame_number
 
     has_field 2, :sequence_number, :type => :int, :default => 1
 
@@ -112,11 +111,36 @@ module LIS::Message
      self.class.type_id
     end
 
+    # serialize a Message object into a String
+    #
+    #   message = Message.from_string("5L|1|N") #=> <LIS::Message>
+    #   message.to_message #=> "5L|1|N"
+    #
     def to_message
       @fields ||= {}
       arr = Array.new(self.class.default_fields)
       type_id + @fields.inject(arr) { |a,(k,v)| a[k-1] = v; a }.join("|")
     end
-  end
 
+    # instantiate a new Message from a string
+    #
+    #   Message.from_string("5L|1|N") #=> <LIS::Message::Terminator>
+    #
+    # register subclasses by using {ClassMethods#type_id type_id}
+    #
+    def self.from_string(message)
+      type, data = parse(message)
+      klass = class_for_type(type)
+
+      obj = klass.allocate
+
+      data = data.to_enum(:each_with_index).inject({}) do |h,(elem,idx)|
+        h[idx+2] = elem; h
+      end
+
+      obj.instance_variable_set("@fields", data)
+      obj
+    end
+  end
 end
+

data/lib/lis/transfer/application_protocol.rb

@@ -0,0 +1,104 @@
+
+module LIS::Transfer
+  class ApplicationProtocol < ::PacketIO::Base
+    attr_reader :device_name
+
+    def on_result(&block)
+      @on_result_callback = block
+    end
+
+    def on_request(&block)
+      @on_request_callback = block
+    end
+
+    def received_header(message)
+      @patient_information_requests ||= {} # delete the list of patients
+      @device_name = message.sender_name
+    end
+
+    def result_for(patient, order, result)
+      @on_result_callback.call(@device_name, patient, order, result)
+    end
+
+    def received_patient_information(message)
+      @last_order = nil
+      @last_patient = message
+    end
+
+    def received_order_record(message)
+      @last_order = message
+    end
+
+    def received_result(message)
+      result_for(@last_patient, @last_order, message)
+    end
+
+    def received_request_for_information(message)
+      @patient_information_requests ||= {}
+      requests = @on_request_callback.call(@device_name, message.starting_range_id)
+      @patient_information_requests[message.sequence_number] = requests if requests
+    end
+
+    def send_pending_requests
+      sending_session(@patient_information_requests) do |patient_information|
+        patient_information.each do |sequence_nr, 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
+          end
+        end
+      end
+      @patient_information_requests = {}
+    end
+
+    def initialize(*args)
+      super
+
+      @patient_information_requests = {}
+      @last_patient = nil
+      @last_order = nil
+      @handlers = {
+        LIS::Message::Header => :received_header,
+        LIS::Message::Patient => :received_patient_information,
+        LIS::Message::Order => :received_order_record,
+        LIS::Message::Result => :received_result,
+        LIS::Message::Query => :received_request_for_information
+      }
+    end
+
+    def receive(type, message = nil)
+      warn "[R] #{message}" if type == :message and $VERBOSE
+      case type
+        when :begin
+          @last_patient = nil
+          @last_order = nil
+        when :idle
+          send_pending_requests
+        when :message
+          @message = LIS::Message::Base.from_string(message)
+          handler = @handlers[@message.class]
+          send(handler, @message) if handler
+      end
+    end
+
+    def write(type, message=nil)
+      warn "[S] #{message}" if type == :message and $VERBOSE
+      super
+    end
+
+    # @yield data
+    def sending_session(data)
+      # don't send anything if there are no pending requests
+      return if data.nil? or data.empty?
+
+      write :begin
+      write :message, LIS::Message::Header.new("LIS", @device_name).to_message
+      yield data
+      write :message, LIS::Message::Terminator.new.to_message
+      write :idle
+    end
+  end
+end

data/lib/lis/transfer/astm_e1394.rb

@@ -0,0 +1,121 @@
+module LIS::Transfer
+
+  module ASTM
+  end
+
+  # 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
+  #
+  # forwards the following events:
+  #
+  # - :message, String :: when a message is received
+  # - :idle            :: when a transmission is finished (after EOT is received)
+  #
+  class ASTM::E1394 < ::PacketIO::Base
+    ACK = "\006"
+    NAK = "\025"
+    ENQ = "\005"
+    EOT = "\004"
+
+    # format of a message
+    RX = /(?:
+          \005 | # ENQ - start a transaction
+          \004 | # EOT - ends a transaction
+          \005 | # ACK
+          \025 | # NAK
+          (?:\002 (.) (.*?) \015 \003 (.+?) \015 \012) # a message with a checksum
+                #  |   |               `-- checksum
+                #  |   `------------------ message
+                #  `---------------------- frame number
+          )
+        /xm
+
+    def initialize(*args)
+      super(*args)
+      @memo = ""
+      @inside_transmission = false
+    end
+
+    def receive(data)
+      scanner = StringScanner.new(@memo + data)
+      while scanner.scan_until(RX)
+        match = scanner.matched
+        case match
+          when ENQ then transmission_start
+          when EOT then transmission_end
+          when ACK, NAK then nil
+        else
+          received_message(match)
+          write :ack
+        end
+      end
+      @memo = scanner.rest
+      nil
+    end
+
+    def write(type, data = nil)
+      str = case type
+        when :ack then ACK
+        when :nak then NAK
+        when :begin then
+          @frame_number = 0
+          ENQ
+        when :idle then EOT
+        when :message then
+          @frame_number = (@frame_number + 1) % 8
+          self.class.wrap_message(data, @frame_number)
+      else
+        raise ArgumentError
+      end
+      super(str)
+    end
+
+
+    private
+
+    def self.message_from_string(string)
+      match = string.match(RX)
+
+      frame_number, data, checksum = match[1 .. 3]
+
+      expected_checksum = (frame_number + data).each_byte.inject(16) { |a,b| (a+b) % 0x100 }
+      actual_checksum   = checksum.to_i(16)
+
+      raise "checksum mismatch: expected %03x got %03x" % [expected_checksum, actual_checksum] unless expected_checksum == actual_checksum
+      return [frame_number.to_i, data]
+    end
+
+    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 = checksum.to_s(16).upcase.rjust(2,"0")
+
+      "\002#{frame_number}#{string}\015\003#{checksum}\015\012"
+    end
+
+
+    def received_message(message)
+      return false unless @inside_transmission
+      frame_number, message = *self.class.message_from_string(message)
+      forward(:message, message)
+    end
+
+    def transmission_start
+      return false if @inside_transmission
+      write :ack
+      forward :begin
+      @inside_transmission = true
+      true
+    end
+
+    def transmission_end
+      return false unless @inside_transmission
+      forward :idle
+      @inside_transmission = false
+      true
+    end
+  end
+end
+

data/lib/lis/version.rb

@@ -0,0 +1,4 @@
+module LIS
+  VERSION = "0.2.2"
+end
+

data/lib/lis/worklist_manager_interface.rb

@@ -6,6 +6,15 @@ class WorklistManagerInterface
     @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('-')}")
@@ -32,7 +41,7 @@ class WorklistManagerInterface
       "result_timestamp" => result.test_completed_at
     }
 
-    p data
+    # 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

data/lib/lis.rb

@@ -1,16 +1,15 @@
 $:.unshift File.dirname(__FILE__)
 
-module LIS
-  VERSION = "0.2.1"
-end
+require 'packet_io'
 
-require 'lis/io_listener.rb'
-require 'lis/messages.rb'
+require 'lis/version'
 
+require 'lis/messages.rb'
 Dir[File.join(File.dirname(__FILE__), 'lis/messages/**/*.rb')].each { |f| require f }
 
-require 'lis/packetized_protocol.rb'
-require 'lis/application_protocol.rb'
+require 'lis/transfer/astm_e1394.rb'
+require 'lis/transfer/application_protocol.rb'
+
 require 'lis/worklist_manager_interface.rb'
 require 'lis/interface_server.rb'
 

data/lis.gemspec

@@ -1,6 +1,6 @@
 # -*- encoding: utf-8 -*-
 $:.push File.expand_path("../lib", __FILE__)
-require 'lis'
+require 'lis/version'
 
 Gem::Specification.new do |s|
   s.name = %q{lis}
@@ -20,9 +20,12 @@ 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.rc4"
+
   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")
 end
 

data/test/helper.rb

@@ -2,7 +2,6 @@ require 'rubygems'
 require 'test/unit'
 require 'shoulda'
 require 'mocha'
-require 'lib/mock_server'
 
 $LOAD_PATH.unshift(File.join(File.dirname(__FILE__), '..', 'lib'))
 $LOAD_PATH.unshift(File.dirname(__FILE__))

data/test/{test_packetized_protocol.rb → test_astm_e1394.rb}

@@ -17,7 +17,7 @@ class TestPacketizedProtocol < Test::Unit::TestCase
     str = self.class.gsub_nonprintable(str)
     expected = self.class.gsub_nonprintable(expected)
 
-    match = LIS::Transfer::PacketizedProtocol::RX.match(str)
+    match = LIS::Transfer::ASTM::E1394::RX.match(str)
     assert_not_nil match, expected
     assert_equal expected, match[0]
   end
@@ -39,7 +39,7 @@ class TestPacketizedProtocol < Test::Unit::TestCase
     setup do
       @sent = []
       @data = []
-      @protocol = LIS::Transfer::PacketizedProtocol.new(nil, @sent)
+      @protocol = LIS::Transfer::ASTM::E1394.new(nil, @sent)
       @protocol.on_data do |*d|
         @data << d
       end
@@ -95,4 +95,4 @@ class TestPacketizedProtocol < Test::Unit::TestCase
     end
   end
 
-end
+end

metadata

@@ -5,8 +5,8 @@ version: !ruby/object:Gem::Version
   segments: 
   - 0
   - 2
-  - 1
-  version: 0.2.1
+  - 2
+  version: 0.2.2
 platform: ruby
 authors: 
 - Levin Alexander
@@ -14,13 +14,29 @@ autorequire:
 bindir: bin
 cert_chain: []
 
-date: 2011-05-30 00:00:00 +02:00
+date: 2011-06-01 00:00:00 +02:00
 default_executable: 
 dependencies: 
 - !ruby/object:Gem::Dependency 
-  name: shoulda
+  name: packet_io
   prerelease: false
   requirement: &id001 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ~>
+      - !ruby/object:Gem::Version 
+        segments: 
+        - 0
+        - 4
+        - 0
+        - rc4
+        version: 0.4.0.rc4
+  type: :runtime
+  version_requirements: *id001
+- !ruby/object:Gem::Dependency 
+  name: shoulda
+  prerelease: false
+  requirement: &id002 !ruby/object:Gem::Requirement 
     none: false
     requirements: 
     - - ~>
@@ -31,11 +47,11 @@ dependencies:
         - 3
         version: 2.11.3
   type: :development
-  version_requirements: *id001
+  version_requirements: *id002
 - !ruby/object:Gem::Dependency 
   name: mocha
   prerelease: false
-  requirement: &id002 !ruby/object:Gem::Requirement 
+  requirement: &id003 !ruby/object:Gem::Requirement 
     none: false
     requirements: 
     - - ~>
@@ -46,11 +62,11 @@ dependencies:
         - 12
         version: 0.9.12
   type: :development
-  version_requirements: *id002
+  version_requirements: *id003
 - !ruby/object:Gem::Dependency 
   name: yard
   prerelease: false
-  requirement: &id003 !ruby/object:Gem::Requirement 
+  requirement: &id004 !ruby/object:Gem::Requirement 
     none: false
     requirements: 
     - - ~>
@@ -61,11 +77,11 @@ dependencies:
         - 1
         version: 0.7.1
   type: :development
-  version_requirements: *id003
+  version_requirements: *id004
 - !ruby/object:Gem::Dependency 
   name: cucumber
   prerelease: false
-  requirement: &id004 !ruby/object:Gem::Requirement 
+  requirement: &id005 !ruby/object:Gem::Requirement 
     none: false
     requirements: 
     - - ~>
@@ -76,7 +92,20 @@ dependencies:
         - 3
         version: 0.10.3
   type: :development
-  version_requirements: *id004
+  version_requirements: *id005
+- !ruby/object:Gem::Dependency 
+  name: webmock
+  prerelease: false
+  requirement: &id006 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        segments: 
+        - 0
+        version: "0"
+  type: :development
+  version_requirements: *id006
 description: ""
 email: mail@levinalex.net
 executables: 
@@ -86,14 +115,12 @@ extensions: []
 extra_rdoc_files: []
 
 files: 
-- .document
 - .gitignore
 - .yardopts
 - Gemfile
 - LICENSE
 - README.markdown
 - Rakefile
-- VERSION
 - bin/lis2http
 - features/communication basics.feature
 - features/lis.feature
@@ -103,7 +130,6 @@ files:
 - lib/lis/application_protocol.rb
 - lib/lis/commands/application.rb
 - lib/lis/interface_server.rb
-- lib/lis/io_listener.rb
 - lib/lis/messages.rb
 - lib/lis/messages/comment.rb
 - lib/lis/messages/header.rb
@@ -113,6 +139,9 @@ files:
 - lib/lis/messages/result.rb
 - lib/lis/messages/terminator.rb
 - lib/lis/packetized_protocol.rb
+- lib/lis/transfer/application_protocol.rb
+- lib/lis/transfer/astm_e1394.rb
+- lib/lis/version.rb
 - lib/lis/worklist_manager_interface.rb
 - lis.gemspec
 - test/helper.rb
@@ -122,9 +151,8 @@ files:
 - test/messages/test_patients.rb
 - test/messages/test_terminator.rb
 - test/test_application_protocol.rb
-- test/test_io_listener.rb
+- test/test_astm_e1394.rb
 - test/test_messages.rb
-- test/test_packetized_protocol.rb
 has_rdoc: true
 homepage: http://github.com/levinalex/lis
 licenses: []
@@ -169,6 +197,5 @@ test_files:
 - test/messages/test_patients.rb
 - test/messages/test_terminator.rb
 - test/test_application_protocol.rb
-- test/test_io_listener.rb
+- test/test_astm_e1394.rb
 - test/test_messages.rb
-- test/test_packetized_protocol.rb

data/.document

@@ -1,5 +0,0 @@
-README.rdoc
-lib/**/*.rb
-bin/*
-features/**/*.feature
-LICENSE

data/VERSION

@@ -1 +0,0 @@
-0.1.0