ruby_astm 1.0.5 → 1.0.6

checksums.yaml

@@ -1,7 +1,7 @@
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-  data.tar.gz: f6e234ae0f2e806c74f331a1e544de7c83ff754d
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+  data.tar.gz: 40b5a1d881488650d4fe3c12ae558b33f27d8767
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data/lib/mappings.json

@@ -193,5 +193,53 @@
 	"ESR" : {
 		"LIS_CODE" : "ESR",
 		"TUBE" : "ESR"
+	},
+	"GLU" : {
+		"LIS_CODE" : "GLU",
+		"TUBE" : "URINE_CONTAINER"
+	},
+	"BIL" : {
+		"LIS_CODE" : "BIL",
+		"TUBE" : "URINE_CONTAINER"
+	},
+	"KET" : {
+		"LIS_CODE" : "KET",
+		"TUBE" : "URINE_CONTAINER"
+	},
+	"SG" : {
+		"LIS_CODE" : "SG",
+		"TUBE" : "URINE_CONTAINER"
+	},
+	"BLO" : {
+		"LIS_CODE" : "BLO",
+		"TUBE" : "URINE_CONTAINER"
+	},
+	"pH" : {
+		"LIS_CODE" : "pH",
+		"TUBE" : "URINE_CONTAINER"
+	},
+	"PRO" : {
+		"LIS_CODE" : "PRO",
+		"TUBE" : "URINE_CONTAINER"
+	},
+	"URO" : {
+		"LIS_CODE" : "URO",
+		"TUBE" : "URINE_CONTAINER"
+	},
+	"NIT" : {
+		"LIS_CODE" : "NIT",
+		"TUBE" : "URINE_CONTAINER"
+	},
+	"LEU" : {
+		"LIS_CODE" : "LEU",
+		"TUBE" : "URINE_CONTAINER"
+	},
+	"COL" : {
+		"LIS_CODE" : "COL",
+		"TUBE" : "URINE_CONTAINER"
+	},
+	"CLA" : {
+		"LIS_CODE" : "CLA",
+		"TUBE" : "URINE_CONTAINER"
 	}
 }

data/lib/ruby_astm/HL7/hl7_header.rb

@@ -5,13 +5,16 @@ class Hl7Header < Header
 	attr_accessor :message_type
 	attr_accessor :message_control_id
 
+	def set_protocol(args)
+		self.protocol = "HL7"
+	end	
+
 	def initialize(args)
-		super.tap do |r|
-			set_machine_name(args)
-			set_date_time(args)
-			set_message_type(args)
-			set_message_control_id(args)
-		end
+		super
+		set_machine_name(args)
+		set_date_time(args)
+		set_message_type(args)
+		set_message_control_id(args)
 	end
 
 	def set_machine_name(args)
@@ -46,8 +49,76 @@ class Hl7Header < Header
 		end
 	end
 
+	################################################################################
+	##
+	##
+	## METHODS FOR generating the acknowledgement to an HL7 Message
+	##
+	##
+	################################################################################
+
+	def seperator
+		"|"
+	end
+
+	def header
+		"MSH"
+	end
+
+	def field_seperators
+		"^~\\&"
+	end
+
+	def sending_application_name
+		"Pathofast_LIS"
+	end
+
+	def sending_facility_name
+		"Pathofast"
+	end
+
+	def sending_date_time
+		Time.now.strftime("%Y%m%d%H%M%S")		
+	end
+
+	def ack_message
+		"ACK"
+	end
+
+	def nack_message
+		"NACK"
+	end
+
+	def hl7_version
+		"2.4"
+	end
+
 	def generate_ack_success_response
 		
+		ack_msg = ""
+		ack_msg += header + seperator
+		ack_msg += field_seperators + seperator
+		ack_msg += sending_application_name + seperator
+		ack_msg += sending_facility_name + seperator
+		ack_msg += seperator
+		ack_msg += seperator
+		ack_msg += sending_date_time + seperator
+		ack_msg += seperator
+		ack_msg += ack_msg + seperator
+		ack_msg += self.message_control_id + seperator
+		ack_msg += seperator
+		ack_msg += hl7_version + seperator
+		ack_msg += seperator
+		ack_msg += seperator
+		ack_msg += seperator
+		ack_msg += seperator
+		ack_msg += seperator
+		ack_msg += seperator
+		ack_msg += seperator
+		ack_msg += "AA" + seperator
+		ack_msg += sending_date_time + seperator
+		ack_msg
+
 	end
 
 	def generate_ack_failure_response

data/lib/ruby_astm/HL7/hl7_order.rb

@@ -0,0 +1,6 @@
+require "ruby_astm/order"
+class Hl7Order < Order
+	def set_id(args)
+		self.id = args[:patient_id]
+	end
+end

data/lib/ruby_astm/HL7/hl7_patient.rb

@@ -0,0 +1,14 @@
+require "ruby_astm/patient"
+class Hl7Patient < Patient
+	def set_sequence_number(args)
+		
+	end
+
+	def set_patient_id(args)
+		if line = args[:line]
+			unless line.fields[3].blank?
+				self.patient_id = line.fields[3].strip
+			end
+		end
+	end
+end

data/lib/ruby_astm/header.rb

@@ -3,30 +3,46 @@ class Header
 	attr_accessor :patients
 	attr_accessor :queries
 	attr_accessor :response_sent
+	attr_accessor :protocol
+
+	def is_astm?
+		self.protocol == "ASTM"
+	end		
+
+	def is_hl7?
+		self.protocol == "HL7"
+	end
+
+
+	def set_protocol(args)
+		self.protocol = "ASTM"
+	end	
 
 	def initialize(args)
 		self.patients = []
 		self.queries = []
 		self.response_sent = false
-		if args[:line]
-			line = args[:line]
-			line
+		if line = args[:line]
+			set_machine_name(args)
+			set_protocol(args)
 		else
 			super
 		end
 	end
 
-	def set_machine_name(line)
-		unless line.fields[4].empty?
-			fields = line.fields[4].split(/\^/)
-			self.machine_name = fields[0].strip
+	def set_machine_name(args)
+		if line = args[:line]
+			unless line.fields[4].empty?
+				fields = line.fields[4].split(/\^/)
+				self.machine_name = fields[0].strip
+			end
 		end
 	end
 
 	## pushes each patient into a redis list called "patients"
 	def commit
 		self.patients.map{|patient| $redis.lpush("patients",patient.to_json)}
-		#puts JSON.pretty_generate(JSON.parse(self.to_json))
+		puts JSON.pretty_generate(JSON.parse(self.to_json))
 	end
 
 	## used to respond to queries.

data/lib/ruby_astm/lab_interface.rb

@@ -29,7 +29,9 @@ module LabInterface
   def process_text_file(full_file_path)
     #full_file_path ||= File.join root,'../test','resources','sysmex_550_sample.txt'
     IO.read(full_file_path).each_line do |line|
-      process_text(line)
+      line.split('\\r').each do |txt| 
+        process_text(txt)
+      end
     end
   end
 
@@ -98,7 +100,15 @@ module LabInterface
       else
         ## send the header 
         puts "--------- SENT ACK -----------"
-        send_data(ACK)
+        if self.headers[-1].is_astm?
+          send_data(ACK)
+        elsif self.headers[-1].is_hl7?
+          if self.headers.size > 0
+            ## commit should return the jsonified thing, if possible.
+            self.headers[-1].commit
+            send_data(self.headers[-1].generate_ack_success_response)
+          end
+        end
       end
   end
 
@@ -109,6 +119,8 @@ module LabInterface
   end
 
   def process_text(text)
+      ## should replace carriage returns with new lines, before processing any file.
+      ## or text.
       text.split("\n").each do |l|
 		    line = Line.new({:text => l})
         process_type(line)
@@ -125,9 +137,11 @@ module LabInterface
         hl7_observation = Hl7Observation.new({:line => line})
         self.headers[-1].patients[-1].orders[-1].results[hl7_observation.name] = hl7_observation
       when "Hl7_Patient"
-        ## like a patient
-      when "Hl7_Patient_Visti"
-        ## like an order.
+        hl7_patient = Hl7Patient.new({:line => line})
+        self.headers[-1].patients << hl7_patient
+      when "Hl7_Order"
+        hl7_order = Hl7Order.new({:line => line, :patient_id => self.headers[-1].patients[-1].patient_id})
+        self.headers[-1].patients[-1].orders << hl7_order
       when "Header"
         header = Header.new({:line => line})
         self.headers ||= []
@@ -145,6 +159,7 @@ module LabInterface
         result = Result.new({:line => line})
         self.headers[-1].patients[-1].orders[-1].results[result.name] = result
       when "Terminator"
+        ## it didn't terminate so there was no commit being called.
         self.headers[-1].commit
       end
   end

data/lib/ruby_astm/line.rb

@@ -4,6 +4,8 @@ class Line
 		"H" => "Header",
 		"MSH" => "Hl7_Header",
 		"OBX" => "Hl7_Observation",
+		"PID" => "Hl7_Patient",
+		"OBR" => "Hl7_Order",
 		"P" => "Patient",
 		"Q" => "Query",
 		"O" => "Order",

data/lib/ruby_astm/order.rb

@@ -34,7 +34,55 @@ class Order
 	## index (11)
 	attr_accessor :action_code
 
+	def set_id(args)
+		if line = args[:line]
+			if !line.fields[2].strip.blank?
+				line.fields[2].strip.scan(/(?<specimen_id>[^\^]+)/) { |specimen_id|
+					self.id ||= specimen_id
+				}
+			elsif !line.fields[3].strip.blank?
+				## for the sysmex xn-550 this is the regex.
+				line.fields[3].strip.scan(/(?<tube_rack>\d+\^)+(?<patient_id>.+)\^/) { |tube_rack,patient_id|  self.id = patient_id.strip}
+			end
+		else
+			self.id = args[:specimen_id]
+		end
+	end
+
+	def set_sequence_number(args)
+		self.sequence_number = args[:sequence_number]
+	end
+
+	def set_tests(args)
+		self.tests = args[:tests]
+	end
+
+	def set_specimen_type(args)
+		self.specimen_type = args[:specimen_type]
+	end
+
+	def set_date_time(args)		
+		self.date_time = args[:date_time]
+	end
+
+	def set_priority(args)
+		self.priority = args[:priority]
+	end
+
+	def set_action_Code(args)
+		self.action_code = args[:args]
+	end
+
 	def initialize(args)
+		set_id(args)
+		set_priority(args)
+		set_sequence_number(args)
+		set_tests(args)
+		set_specimen_type(args)
+		set_date_time(args)
+		set_priority(args)
+		set_action_Code(args)
+=begin		
 		if args[:line]
 			line = args[:line]
 			if !line.fields[2].strip.blank?
@@ -50,11 +98,11 @@ class Order
 			self.tests = args[:tests]
 			self.id = args[:specimen_id]
 			self.specimen_type = args[:specimen_type]
-			self.tests = args[:tests]
 			self.date_time = args[:date_time]
 			self.priority = args[:priority]
 			self.action_code = args[:action_code]
 		end
+=end
 		self.results = {}
 	end
 

data/lib/ruby_astm/patient.rb

@@ -5,17 +5,24 @@ class Patient
 	attr_accessor :patient_id
 	attr_accessor :orders
 	
-	def initialize(args)
-		if args[:line]
-			line = args[:line]
-			self.sequence_number = line.fields[1].to_i
-			self.orders = []
+	def set_sequence_number(args)
+		if line = args[:line]
+			self.sequence_number = line.fields[-1].to_i
 		else
 			self.sequence_number = args[:sequence_number]
-			self.patient_id = args[:patient_id]
 		end
 	end
 
+	def set_patient_id(args)
+		self.patient_id = args[:patient_id]
+	end
+
+	def initialize(args)
+		set_sequence_number(args)
+		set_patient_id(args)
+		self.orders = []
+	end
+
 	## patient id.
 	def build_response
 		"P|#{self.sequence_number}|#{self.patient_id}|||||||||||||||\r"

data/lib/ruby_astm.rb

@@ -10,4 +10,7 @@ require "ruby_astm/astm_server"
 require "publisher/adapter"
 require "publisher/google_lab_interface"
 require "publisher/poller"
-require "ruby_astm/HL7/hl7_header"
+require "ruby_astm/HL7/hl7_header"
+require "ruby_astm/HL7/hl7_patient"
+require "ruby_astm/HL7/hl7_order"
+require "ruby_astm/HL7/hl7_observation"

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: ruby_astm
 version: !ruby/object:Gem::Version
-  version: 1.0.5
+  version: 1.0.6
 platform: ruby
 authors:
 - Bhargav Raut
@@ -122,6 +122,8 @@ files:
 - lib/ruby_astm.rb
 - lib/ruby_astm/HL7/hl7_header.rb
 - lib/ruby_astm/HL7/hl7_observation.rb
+- lib/ruby_astm/HL7/hl7_order.rb
+- lib/ruby_astm/HL7/hl7_patient.rb
 - lib/ruby_astm/astm_server.rb
 - lib/ruby_astm/frame.rb
 - lib/ruby_astm/header.rb
@@ -155,4 +157,6 @@ rubygems_version: 2.6.14.1
 signing_key: 
 specification_version: 4
 summary: A Ruby gem to interface with Medical instruments that work on the ASTM protocol
+  and HL7 protocol. Offers limited bidirectionality for ASTM. Bidirectionality is
+  currently not supported for HL7
 test_files: []