ruby_astm 1.5.0 → 1.5.2

checksums.yaml

@@ -1,7 +1,7 @@
 ---
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-  data.tar.gz: 607c8eb219d2bb4d0ecb4d84de0d953372929e3d090af61c9337118418b6ae79
+SHA1:
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+  data.tar.gz: d803f0319f91c825ab9fa560c7dfe3ae7e08f9a7
 SHA512:
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+  data.tar.gz: 0dfbc2aad3bfac163e3121a0d501895775c1eec7f4c5d8f72b19df4fd8922e225bc01bd2f9b9a87af1560ed98972dbcbbad3d209feefcc2aacba475dad6f7951

data/lib/mappings.json

@@ -2,6 +2,7 @@
 	"_comment" : "key -> code sent by analyzer, eg sysmex sends WBC count under the code 'WBC'. value -> object. Object structure: 'LIS_CODE': in the google lab interface, this code is present in two places on google drive. one) in the name of the file, two) inside the file, where the test result value should be added. For eg in the hemogram report, TLCparam, is present in the name of the file, as well as inside the file, so the google script will update it with the relevant value. 'TUBE' stands for the type of tube in which this test has to be performed. This should match the constants in the Google Lab Interface.rb file. Now there is another problem that we have to deal with here. When going bidirectional, in some machines like Roche Cobas e411, the test codes come in as numbers, and not letters, so the keys here in this file are numbers, for those tests. Because Roche is a bitch basically.",
 	"A1c" : {
         "LIS_CODE" : "HBA1C",
+        "TUBE" : "EDTA",
         "REPORT_NAME" : "Glycosylated Hemoglobin",
         "TYPE" : "HEMAT"
     },
@@ -195,7 +196,10 @@
 		"LIS_CODE" : "ALB",
 		"TUBE" : "SERUM",
 		"REPORT_NAME" : "Albumin",
-        "TYPE" : "BIOCHEM"
+        "TYPE" : "BIOCHEM",
+        "MACHINE_SPECIFIC_LIS_CODES" : {
+        	"CLINITEK" : "UALB"
+        }
 	},
 	"GGTP" : {
 		"LIS_CODE" : "GGT",
@@ -479,6 +483,18 @@
 		"REPORT_NAME" : "Urine Routine",
         "TYPE" : "URINE"
 	},
+	"CRE" : {
+		"LIS_CODE" : "UCRE",
+		"TUBE" : "URINE_CONTAINER",
+		"REPORT_NAME" : "Urine Routine",
+        "TYPE" : "URINE"
+	},
+	"UALB" : {
+		"LIS_CODE" : "UALB",
+		"TUBE" : "URINE_CONTAINER",
+		"REPORT_NAME" : "Urine Routine",
+        "TYPE" : "URINE"
+	},
 	"UA" : {
 		"LIS_CODE" : "SURIC",
 		"TUBE" : "SERUM",
@@ -501,13 +517,13 @@
 		"LIS_CODE" : "full_body_package",
 		"TUBE" : "",
 		"REPORT_NAME" : "full body package",
-		"PACKAGE_COMPONENTS" : ["HBA1C", "TLCparam", "RBCparam", "HBparam", "HCTparam", "MCVparam", "MCHparam", "MCHCparam", "PCparam", "Nparam", "Lparam", "Mparam", "Eparam", "BASOparam", "ANCparam", "ALCparam", "AMCparam", "AECparam", "ABCparam", "RDWCVparam", "GLUR", "GLUPP", "GLUF", "CHOL", "TRIG", "HDLC", "LDL", "VLDLC", "CRE", "UREA", "BUN", "ALB", "GGT", "BID", "CA", "BIT", "BII", "ALPU", "GOTHL", "GPTHL", "HOMCY", "SIRON", "SUIBC", "STIBC", "SURIC", "SPHOS", "SMAG", "SNATRIUM", "SPOTASSIUM", "SCHLORIDE", "SIGE", "SPSA", "SFER", "TSH", "T4", "T3", "VITD", "HCV", "B12", "ESR", "GLU", "BIL", "KET", "SG", "BLO", "pH", "PRO", "URO", "NIT", "LEU", "COL", "CLA"]
+		"PACKAGE_COMPONENTS" : ["HBA1C", "TLCparam", "RBCparam", "HBparam", "HCTparam", "MCVparam", "MCHparam", "MCHCparam", "PCparam", "Nparam", "Lparam", "Mparam", "Eparam", "BASOparam", "ANCparam", "ALCparam", "AMCparam", "AECparam", "ABCparam", "RDWCVparam", "GLUR", "GLUPP", "GLUF", "CHOL", "TRIG", "HDLC", "LDL", "VLDLC", "CRE", "UREA", "BUN", "ALB", "GGT", "BID", "CA", "BIT", "BII", "ALPU", "GOTHL", "GPTHL", "HOMCY", "SIRON", "SUIBC", "STIBC", "SURIC", "SPHOS", "SMAG", "SNATRIUM", "SPOTASSIUM", "SCHLORIDE", "SIGE", "SPSA", "SFER", "TSH", "T4", "T3", "VITD", "HCV", "B12", "ESR", "GLU", "BIL", "KET", "SG", "BLO", "pH", "PRO", "URO", "NIT", "LEU", "COL", "CLA","UCRE","UALB"]
 	},
 	"PRE_OP_PACKAGE" : {
 		"LIS_CODE" : "pre_op_package",
 		"TUBE" : "",
 		"REPORT_NAME" : "pre_op_package",
-		"PACKAGE_COMPONENTS" : ["TLCparam", "RBCparam", "HBparam", "HCTparam", "MCVparam", "MCHparam", "MCHCparam", "PCparam", "Nparam", "Lparam", "Mparam", "Eparam", "BASOparam", "ANCparam", "ALCparam", "AMCparam", "AECparam", "ABCparam", "RDWCVparam", "GLUR","ESR", "GLU", "BIL", "KET", "SG", "BLO", "pH", "PRO", "URO", "NIT", "LEU", "COL", "CLA", "HIV", "HBS"]
+		"PACKAGE_COMPONENTS" : ["TLCparam", "RBCparam", "HBparam", "HCTparam", "MCVparam", "MCHparam", "MCHCparam", "PCparam", "Nparam", "Lparam", "Mparam", "Eparam", "BASOparam", "ANCparam", "ALCparam", "AMCparam", "AECparam", "ABCparam", "RDWCVparam", "GLUR","ESR", "GLU", "BIL", "KET", "SG", "BLO", "pH", "PRO", "URO", "NIT", "LEU", "COL", "CLA", "HIV", "HBS","UCRE","UALB"]
 	},
 	"LIPID_PROFILE" : {
 		"LIS_CODE" : "lipid_profile",

data/lib/publisher/google_lab_interface.rb

@@ -2,11 +2,10 @@ require 'google/apis/script_v1'
 require 'googleauth'
 require 'googleauth/stores/file_token_store'
 require 'fileutils'
-require 'publisher/poller'
+require_relative "poller"
 
 class Google_Lab_Interface < Poller
 
-
   OOB_URI = 'urn:ietf:wg:oauth:2.0:oob'.freeze
   APPLICATION_NAME = 'Google Apps Script API Ruby Quickstart'.freeze
   ## these two cannot be hardcoded.

data/lib/publisher/poller.rb

@@ -107,8 +107,27 @@ class Poller
 
   	end	
 
+  	def assign_tube(component_machine_code,tests_hash,tube_type)
+  		tube_key = nil
+        unless tests_hash.keys.select{|c| c=~/#{tube_type}/ }.blank?
+        	tube_key = tests_hash.keys.select{|c| c=~/#{tube_type}/ }[0] 
+        	tests_hash[tube_key] << component_machine_code 
+        end
+  	end
+
   	## first we have to test the packages.
 
+  	def determine_tube(component_machine_code,tests_hash)
+  		res = $mappings[component_machine_code]["TUBE"]
+        if res.is_a? Array
+        	res.each do |tube|
+        		assign_tube(component_machine_code,tests_hash,tube)
+        	end
+        elsif res.is_a? String
+       		assign_tube(component_machine_code,tests_hash,res)	
+        end
+  	end
+
   	def build_tests_hash(record)
   		#puts "Record is ---------------------------------------------"
   		#puts record
@@ -190,17 +209,21 @@ class Poller
 	        		## for eg plasma tube can do all the tests
 	        		## so can serum
 	        		## but we use the plasma tube only for some.
-
+=begin
 	        		tube = $mappings[component_machine_code]["TUBE"]
 			        tube_key = nil
 			        unless tests_hash.keys.select{|c| c=~/#{tube}/ }.blank?
 			        	tube_key = tests_hash.keys.select{|c| c=~/#{tube}/ }[0] 
 			        	tests_hash[tube_key] << component_machine_code 
 			        end   
+=end
+					determine_tube(component_machine_code,tests_hash)
+
 	        	end
 
 	        else
 	        	## here also it is the same problem.
+	        	## this can be sorted out by using the array of the tube.
 	        	tube = $mappings[machine_code]["TUBE"]
 		        tube_key = nil
 		        unless tests_hash.keys.select{|c| c=~/#{tube}/ }.blank?

data/lib/ruby_astm/custom/siemens_abg_electrolyte_module.rb

@@ -93,6 +93,7 @@ module SiemensAbgElectrolyteModule
 	## @param[String] barcode : the barcode
 	## @param[Result] result  : result_object
 	def add_result?(barcode,result)
+		puts "Came to add result"
 		return true if $redis.hget(SIEMENS_ELEC_ABG_RESULTS_HASH,barcode).blank?
 		existing_results = JSON.parse($redis.hget(SIEMENS_ELEC_ABG_RESULTS_HASH,barcode))
 		if existing_results[result.name].blank?
@@ -103,6 +104,8 @@ module SiemensAbgElectrolyteModule
 		false
 	end
 
+	
+
 	## we override the lab interface methods
 	## and we don't pollute the lab interface itself.
 	## as this is a custom analyzer.
@@ -203,6 +206,7 @@ module SiemensAbgElectrolyteModule
 	    		
 	    		unless o.results.blank?
 	    			p.orders << o
+	    			$redis.hset(SIEMENS_ELEC_ABG_RESULTS_HASH,patient_id,JSON.generate(o.results_values_hash))
 	    			self.headers[-1].patients << p
 	    		end
 

data/lib/ruby_astm/lab_interface.rb

@@ -266,10 +266,10 @@ module LabInterface
       if data.bytes.to_a[-1] == 4
         puts "GOT EOT --- PROCESSING BUFFER, AND CLEARING."
         process_text(self.data_buffer)
-        #root_path = File.dirname __dir__
-        #puts "root path #{root_path}"
-        #IO.write((File.join root_path,'../test','resources','stago.txt'),self.test_data_bytes.to_s)
-        puts self.test_data_bytes.flatten.to_s
+        root_path = File.dirname __dir__
+        puts "root path #{root_path}"
+        IO.write((File.join root_path,'../test','resources','d10_error.txt'),self.test_data_bytes.to_s)
+        #puts self.test_data_bytes.flatten.to_s
         self.data_buffer = ''
         unless self.headers.blank?
           if self.headers[-1].queries.blank?
@@ -381,7 +381,7 @@ module LabInterface
         self.headers[-1].patients << hl7_patient
       when "Hl7_Order"
         unless self.headers[-1].patients.blank?
-          hl7_order = Hl7Order.new({:line => line, :patient_id => self.headers[-1].patients[-1].patient_id})
+          hl7_order = Hl7Order.new({:line => line, :patient_id => self.headers[-1].patients[-1].patient_id}, :machine_name => self.headers[-1].machine_name)
           self.headers[-1].patients[-1].orders << hl7_order
         end
       when "Header"

data/lib/ruby_astm/order.rb

@@ -146,4 +146,12 @@ class Order
 
 	end	
 
+	def results_values_hash
+		values_hash = {}
+		self.results.keys.each do |k|
+			values_hash[k] = self.results[k].value
+		end
+		values_hash
+	end
+
 end

data/lib/ruby_astm/result.rb

@@ -8,6 +8,9 @@ class Result
 	attr_accessor :reference_ranges
 	attr_accessor :dilution
 
+	## sometimes we customize the lis code based on the machine which is sending it, so we need this.
+	attr_accessor :machine_name
+
 	def set_name(args)
 		puts "came to set name"
 		if line = args[:line]
@@ -109,6 +112,10 @@ class Result
 		end
 	end
 
+	def set_machine_name(args)
+		self.machine_name = args[:machine_name]
+	end
+
 	
 
 	## here will call mappings and check the result correlation
@@ -121,6 +128,7 @@ class Result
 		set_dilution(args)
 		set_units(args)
 
+
 =begin
 		if args[:line]
 			line = args[:line]
@@ -148,7 +156,23 @@ class Result
 
 	## @return[String] the name defined in the mappings.json file, or the name that wqs passed in.
 	def lookup_mapping(name)
-		$mappings[name] ? $mappings[name]["LIS_CODE"] : name 
+		unless $mappings[name].blank?
+			unless self.machine_name.blank?
+				unless $mappings[name]["MACHINE_SPECIFIC_LIS_CODES"].blank?
+					unless $mappings[name]["MACHINE_SPECIFIC_LIS_CODES"][self.machine_name].blank?
+						redirect = $mappings[name]["MACHINE_SPECIFIC_LIS_CODES"][self.machine_name]
+						unless $mappings[redirect].blank?
+							$mappings[redirect]["LIS_CODE"]
+						end
+					end
+				end		
+			else
+				$mappings[name]["LIS_CODE"]
+			end
+		else
+			name
+		end
+		#$mappings[name] ? $mappings[name]["LIS_CODE"] : name 
 	end
 
 	def lookup_transform(name)

data/lib/ruby_astm/usb_module.rb

@@ -5,6 +5,9 @@ module UsbModule
 	mattr_accessor :usb_response_bytes
 
 	ESR_RESULTS_HASH = "ESR_RESULTS_HASH"
+	ESR_SORTED_SET = "ESR_SORTED_SET"
+	## a particular barcode will be allowed to have 3 different results, after which the next time it won't be uploaded.
+	MAX_REPEAT_RESULT_COUNT = 3
 
 	def begin_patient_results
 		">00A00013"
@@ -32,6 +35,21 @@ module UsbModule
 		self.usb_response_bytes[-3] == 13
 	end	
 
+	def add_result_by_count?(barcode,result)
+		begin
+
+			
+		rescue => e
+			puts e.to_s
+			return true
+		end
+	end
+	## total times repeated, we can have that as max 3 times.
+	## so after that it wont add.
+	## so we keep a sorted set with the barcode and the count
+	## like key -> value, score
+	## key(barcode) -> value(time) -> score(count)
+	## so we can zincrby, each time.
 	def add_result?(barcode,result)
 		begin
 			Integer(result)
@@ -40,12 +58,17 @@ module UsbModule
 			#puts "the result is not zero"
 			existing_result = $redis.hget(ESR_RESULTS_HASH,barcode)
 			#puts "existing result is: #{existing_result}"
-			if ((existing_result.blank?) || (existing_result != result))
-				return true
+			if (existing_result.blank?)
+				true
+			else
+				if existing_result != result
+				current_count = $redis.zincrby(ESR_SORTED_SET,1,barcode)
+				current_count <= MAX_REPEAT_RESULT_COUNT
+			end
 			end 
 		rescue => e
 			puts e.to_s
-			return false
+			false
 		end
 		
 	end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: ruby_astm
 version: !ruby/object:Gem::Version
-  version: 1.5.0
+  version: 1.5.2
 platform: ruby
 authors:
 - Bhargav Raut
@@ -214,7 +214,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 2.7.8
+rubygems_version: 2.6.14.4
 signing_key: 
 specification_version: 4
 summary: A Ruby gem to interface with Medical instruments that work on the ASTM protocol