ruby_astm 1.1.6 → 1.1.7

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: 97473c3503fe13333b10d72191a32d48e7893885a953059f6e30b13a749e0b18
-  data.tar.gz: db9984ca11f5302743aab7406469925ce2cc223e7c7a0c35131576c94eb5e84e
+  metadata.gz: cc95c55e3f2b580c554e371e52a5280a694a82dc3473ec1e637c82512db728ea
+  data.tar.gz: 97e680a545852f2f4694a8ee3b7574cfe6310f7ec7e419139ed6247d068fe808
 SHA512:
-  metadata.gz: 44e68e846d2d9acdc9580c0b5a5881091f104a68fb894540768bd43b6465fc6c717425775bddee642d8102ee1fdcd5a156042aff22c8a86bd7ae5aef90d14b25
-  data.tar.gz: 54499a0a1880df3c0933878f5bc1af9ba714767cad0ed2038a4cd2704df4ac43cf711e2cb2d4ba265f2a5d65513c8cf18f5f2a0d61048e1c8dad91d56513944a
+  metadata.gz: dd6b39268e00df41b84eb2ef466d4a499436dd9839a0ddbd277678bafb0288226810e76c39cfc2801f0a35cbe3aedace08b0328d111c1d0a38f22a0adcf3ee82
+  data.tar.gz: 1c2635c9fcfb327a58d6e77e1cf96f701ec90b1d3e40eca95d2a8479249aff90a1262f854d76b216e8ad4cf4eff91f8fff5f4fc73a93264a805d3858b4270ebb

data/lib/mappings.json

@@ -191,8 +191,8 @@
 		"TUBE" : "SERUM",
 		"REPORT_NAME" : "SGPT"
 	},
-	"HOMOCY" : {
-		"LIS_CODE" : "HOMOCY",
+	"HOMCY" : {
+		"LIS_CODE" : "HOMCY",
 		"TUBE" : "SERUM",
 		"REPORT_NAME" : "Homocysteine"
 	},

data/lib/ruby_astm/astm_server.rb

@@ -39,6 +39,8 @@ class AstmServer
 
 	def start_server
 		EventMachine.run {
+			serial = EventMachine.open_serial('/dev/ttyS0', 9600, 8,LabInterface)
+			puts "RUNNING SERIAL ON dev/ttyS0 ------------ #{serial.to_s}"
 			self.ethernet_server = EventMachine::start_server self.server_ip, self.server_port, LabInterface
 			AstmServer.log("Running ETHERNET SERVER on #{server_port}")
 			#serial = EventMachine.open_serial('/dev/ttyUSB0', 9600, 8)

data/lib/ruby_astm/header.rb

@@ -45,7 +45,17 @@ class Header
 		puts JSON.pretty_generate(JSON.parse(self.to_json))
 	end
 
-	def build_one_response
+	def get_header_response(options)
+		if (options[:machine_name] && (options[:machine_name] == "cobas-e411"))
+			"1H|\\^&|||host^1|||||cobas-e411|TSDWN^REPLY|P|1\r"
+		else
+			"1H|\`^&||||||||||P|E 1394-97|#{Time.now.strftime("%Y%m%d%H%M%S")}\r"
+		end
+	end
+
+	## depends on the machine code.
+	## if we have that or not.
+	def build_one_response(options)
 		puts "building one response=========="
 		puts "queries are:"
 		puts self.queries.size.to_s
@@ -53,12 +63,11 @@ class Header
 		self.queries.each do |query|
 			puts "doing query"
 			puts query.sample_ids
-			header_response = "1H|\`^&||||||||||P|E 1394-97|#{Time.now.strftime("%Y%m%d%H%M%S")}\r"
-			query.build_response.each do |qresponse|
+			header_response = get_header_response(options)
+			query.build_response(options).each do |qresponse|
 				puts "qresponse is:"
 				puts qresponse
 				header_response += qresponse
-				#responses << (header_response + qresponse)
 			end
 			responses << header_response
 		end

data/lib/ruby_astm/lab_interface.rb

@@ -130,10 +130,10 @@ module LabInterface
       elsif data.bytes.to_a[0] == 6
         puts "GOT ACK --- GENERATING RESPONSE"
         unless self.headers.blank?
-          header_responses = self.headers[-1].build_one_response
+          header_responses = self.headers[-1].build_one_response({machine_name: self.headers[-1].machine_name})
           ## if no queries then, we have to send ack.
           if header_responses.blank?
-            puts "sending ACK since there are queries in the header"
+            puts "sending ACK since there are no queries in the header"
             send_data(ACK)
           end
           header_responses.each_with_index {|response,key|
@@ -204,13 +204,16 @@ module LabInterface
         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"
+        puts "got header"
         header = Header.new({:line => line})
         self.headers ||= []
         self.headers << header
       when "Query"
+        puts "got query"
         query = Query.new({:line => line})
         self.headers[-1].queries << query
       when "Patient"
+        puts "got patient."
         patient = Patient.new({:line => line})
         self.headers[-1].patients << patient
       when "Order"
@@ -221,6 +224,7 @@ module LabInterface
         self.headers[-1].patients[-1].orders[-1].results[result.name] = result
       when "Terminator"
         ## it didn't terminate so there was no commit being called.
+        puts "got terminator."
         self.headers[-1].commit
       end
   end

data/lib/ruby_astm/order.rb

@@ -106,7 +106,7 @@ class Order
 		self.results = {}
 	end
 
-	def build_response
+	def build_response(options)
 		
 		raise "provide a sequence number" if self.sequence_number.blank?
 		raise "provide a specimen id" if self.id.blank?
@@ -117,7 +117,19 @@ class Order
 			#puts "no specimen type has been provided, sending SERUM"
 		end
 
-		"O|#{self.sequence_number}|#{self.id}|#{Time.now.to_i.to_s}|^^^#{self.tests.join('`^^^')}|#{self.priority}||#{Time.now.strftime("%Y%m%d%H%M%S")}||||N||||#{self.specimen_type || 'SERUM'}\r"
+		if (options[:machine_name] && (options[:machine_name] == "cobas-e411"))
+			self.tests = self.tests.map{|c| c = "^^^" + c + "^1"}
+			# ^^0000000387^587^0^2^^S1^SC
+			id_string = options[:sequence_number] + "^" + options[:carrier_number] + "^" + options[:position_number] + "^^" + options[:sample_type] + "^" + options[:container_type]
+
+			"O|1|#{self.id.to_s}|#{id_string}|#{self.tests.join('\\')}|#{self.priority}||#{Time.now.strftime("%Y%m%d%H%M%S")}||||A||||1||||||||||O\r"
+
+		else
+
+			"O|#{self.sequence_number}|#{self.id}|#{Time.now.to_i.to_s}|^^^#{self.tests.join('`^^^')}|#{self.priority}||#{Time.now.strftime("%Y%m%d%H%M%S")}||||N||||#{self.specimen_type || 'SERUM'}\r"
+	
+		end
+
 	end	
 
 end

data/lib/ruby_astm/patient.rb

@@ -24,8 +24,12 @@ class Patient
 	end
 
 	## patient id.
-	def build_response
-		"P|#{self.sequence_number}|#{self.patient_id}|||||||||||||||\r"
+	def build_response(options)
+		if (options[:machine_name] && (options[:machine_name] == "cobas-e411"))
+			"P|1\r"
+		else
+			"P|#{self.sequence_number}|#{self.patient_id}|||||||||||||||\r"
+		end
 	end
 
 	def to_json

data/lib/ruby_astm/query.rb

@@ -6,12 +6,66 @@ class Query
 
 	attr_accessor :sample_ids
 
+
+	###################################################################################################
+	##
+	##
+	## FIELDS SPECIFIC TO ROCHE E411
+	##
+	##
+	###################################################################################################
+
+	attr_accessor :sequence_number
+
+	attr_accessor :carrier_number
+
+	attr_accessor :position_number
+
+	attr_accessor :sample_type
+
+	attr_accessor :container_type
+
+	###################################################################################################
+	##
+	##
+	## ROCHE SPECIFIC FIELDS END.
+	##
+	##
+	###################################################################################################
+
+	def parse_field_for_sample_id(fields,index)
+		return false if fields[index].blank?
+		return false if fields[index].strip.blank?
+		
+		self.sample_ids = fields[index].strip.split(/\'/)
+	
+		return true
+	end
+
 	def initialize(args)
 		line = args[:line]
 		unless line.fields[2].empty?
+			## do the gsub for roche type.
+			## if not successfuul, then parse for one.
+			puts "line fields is:"
+			puts line.fields[2].to_s
+			line.fields[2].scan(/\^{2}(?<sample_id>[A-Za-z0-9]+)\^(?<sequence_number>[0-9]+)\^(?<carrier_number>[a-zA-Z0-9]+)\^(?<position_number>[0-9]+)\^{2}(?<sample_type>[a-zA-Z0-9]+)\^(?<container_type>[a-zA-Z0-9]+)/) { |sample_id,sequence_number,carrier_number,position_number,sample_type,container_type|  
+
+				self.sequence_number = sequence_number
+				self.sample_ids = [sample_id]
+				self.carrier_number = carrier_number
+				self.position_number = position_number
+				self.sample_type = sample_type
+				self.container_type = container_type
+			}
+
+			puts "sequence_number: #{self.sequence_number}, sample id: #{self.sample_id}, carrier number: #{self.carrier_number}, position_number: #{self.position_number}, sample_type: #{self.sample_type}, container_type: #{self.container_type}" 
+
 			fields = line.fields[2].split(/\^/)
-			sample_id = fields[1].strip
-			self.sample_ids = sample_id.split(/\`/)
+			
+			parse_field_for_sample_id(fields,1) if self.container_type.blank?
+				
+
 		end
 	end
 
@@ -26,7 +80,7 @@ class Query
 
 	## each query will build one patient and one order inside it.
 	## the order can have many tests.
-	def build_response(variables=nil)
+	def build_response(options={})
 		
 		responses = []
 
@@ -50,7 +104,7 @@ class Query
 			
 			order = Order.new({:sequence_number => patient.sequence_number, :specimen_id => sid, :tests => tests, :priority => "R"})
 
-			responses << (patient.build_response + order.build_response)
+			responses << (patient.build_response(options) + order.build_response(options.merge({sequence_number: self.sequence_number, carrier_number: self.carrier_number, position_number: self.position_number, sample_type: self.sample_type, container_type: self.container_type})))
 
 		}
 

data/lib/ruby_astm/result.rb

@@ -10,16 +10,33 @@ class Result
 
 	def set_name(args)
 		if line = args[:line]
+			
 			line.fields[2].scan(/\^+(?<name>[A-Za-z0-9\%\#\-\_\?\/]+)\^?(?<dilution>\d+)?/) { |name,dilution|  
 				self.name = lookup_mapping(name)
+				
 				self.report_name = lookup_report_name(name)
+
 			}
+
+			self.name.scan(/(?<test_name>\d+)\/(?<dilution>\d+)\/(?<pre_dilution>[a-zA-Z0-9]+)/) { |test_name,dilution,pre_dilution|
+
+				self.name = lookup_mapping(test_name)
+
+				self.report_name = lookup_report_name(test_name)
+
+				self.dilution = dilution
+
+			}
+
 		end
 	end
 
 	def set_value(args)
 		if line = args[:line]
 			self.value = line.fields[3].strip
+			self.value.scan(/(?<flag>\d+)\^(?<value>\d?\.?\d+)/) {|flag,value|
+				self.value = value
+			}
 			line.fields[2].scan(/\^+(?<name>[A-Za-z0-9\%\#\-\_\?\/]+)\^?(?<dilution>\d+)?/) { |name,dilution|  
 				if transform_expression = lookup_transform(name)
 					self.value = eval(transform_expression)
@@ -57,7 +74,7 @@ class Result
 	def set_dilution(args)
 		if line = args[:line]
 			line.fields[2].scan(/\^+(?<name>[A-Za-z0-9\%\#\-\_\?\/]+)\^?(?<dilution>\d+)?/) { |name,dilution|  
-				self.dilution = dilution
+				self.dilution = dilution unless self.dilution
 			}
 		end
 	end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: ruby_astm
 version: !ruby/object:Gem::Version
-  version: 1.1.6
+  version: 1.1.7
 platform: ruby
 authors:
 - Bhargav Raut