ruby_astm 1.4.4 → 1.4.6

checksums.yaml

@@ -1,7 +1,7 @@
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-  data.tar.gz: c0da0a6d63ec31c478b083ecbf11c5772f709ab9
+  metadata.gz: cd2c1d542ca88df2907a1ced3c504be478562cc1
+  data.tar.gz: 9498ee9636238cf9320c2d7da27ac3dd117eca40
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data/lib/mappings.json

@@ -529,6 +529,23 @@
 		"REPORT_NAME" : "kidney_function_tests",
 		"PACKAGE_COMPONENTS" : ["CRE", "UREA", "BUN"],
         "TYPE" : "BIOCHEM"	
+	},
+	"SPT" : {
+		"LIS_CODE" : "SPT",
+		"TUBE" : "SERUM",
+		"REPORT_NAME" : "PTAPTT",
+        "TYPE" : "BIOCHEM-EXL"	
+	},
+	"SAPTT" : {
+		"LIS_CODE" : "SAPTT",
+		"TUBE" : "SERUM",
+		"REPORT_NAME" : "PTAPTT",
+        "TYPE" : "BIOCHEM-EXL"	
+	},
+	"SINR" : {
+		"LIS_CODE" : "SINR",
+		"TUBE" : "SERUM",
+		"REPORT_NAME" : "PTAPTT",
+        "TYPE" : "BIOCHEM-EXL"	
 	}
-
 }

data/lib/publisher/poller.rb

@@ -235,8 +235,12 @@ class Poller
 	      tests.keys.each do |tube_barcode|
 	      	## in this hash we want the key to be only the specimen id.
 	      	## and not prefixed by the tube type like FLUORIDE etc.
+	      	## i don't want the individual tests,
+	      	## i want the report name.
+	      	## prefixed to it.
 	      	tube_barcode.scan(/:(?<barcode>.*)$/) { |barcode|  
 	      		$redis.hset REQUISITIONS_HASH, barcode, JSON.generate(tests[tube_barcode])
+	      		$real_time_db.assign_test(barcode,tests[tube_barcode],$mappings) unless $real_time_db.blank?
 	      	}
 	      end  
 	    end

data/lib/publisher/real_time_db.rb

@@ -1,11 +1,27 @@
 require 'rest-firebase'
 require "resolv-replace"
+require "jwt"
+require "net/http"
+
+RestFirebase.class_eval do 
+	def query
+    	{:access_token => auth}
+  	end
+end
+
 class RealTimeDb
 
 	SITE_URL = ENV["FIREBASE_SITE"]
 	SECRET = ENV["FIREBASE_SECRET"]
+	ENDPOINT = "pathofast"
+	ACCESSION_DONE = "ACCESSION_DONE"
+	PROCESSING = "PROCESSING"
+	
+
 	attr_accessor :connection
 	attr_accessor :work_allotment_hash
+	attr_accessor :private_key_hash
+
 	WORK_TYPES = {
 		"IMMUNO" => "",
 		"BIOCHEM" => "",
@@ -16,15 +32,50 @@ class RealTimeDb
 		"OUTSOURCE" => ""
 	}
 
-	## first i email myself the site and secret
-	## then we proceed.
+
+	def get_jwt
+		puts Base64.encode64(JSON.generate(self.private_key_hash))
+		# Get your service account's email address and private key from the JSON key file
+		$service_account_email = self.private_key_hash["client_email"]
+		$private_key = OpenSSL::PKey::RSA.new self.private_key_hash["private_key"]
+		  now_seconds = Time.now.to_i
+		  payload = {:iss => $service_account_email,
+		             :sub => $service_account_email,
+		             :aud => self.private_key_hash["token_uri"],
+		             :iat => now_seconds,
+		             :exp => now_seconds+(60*60), # Maximum expiration time is one hour
+		             :scope => 'https://www.googleapis.com/auth/userinfo.email https://www.googleapis.com/auth/firebase.database'
+
+		         }
+		  JWT.encode payload, $private_key, "RS256"
+		
+	end
+
+	def generate_access_token
+	  uri = URI.parse(self.private_key_hash["token_uri"])
+	  https = Net::HTTP.new(uri.host, uri.port)
+	  https.use_ssl = true
+	  req = Net::HTTP::Post.new(uri.path)
+	  req['Cache-Control'] = "no-store"
+	  req.set_form_data({
+	    grant_type: "urn:ietf:params:oauth:grant-type:jwt-bearer",
+	    assertion: get_jwt
+	  })
+
+	  resp = JSON.parse(https.request(req).body)
+	  puts "response is:"
+	  puts resp.to_s
+	  resp["access_token"]
+	end
 
 	## @param[Hash] work_allotment_hash :
 	## key => one of the work types
 	## value => name of a worker
-	def initialize(work_allotment_hash)
+	def initialize(work_allotment_hash,private_key_hash)
+		self.private_key_hash = private_key_hash
+		raise "please provide the private key hash, from firebase service account -> create private key " if private_key_hash.blank?
 		self.connection = RestFirebase.new :site => SITE_URL,
-                     :secret => SECRET
+                     :secret => SECRET, :auth =>generate_access_token
         puts "initialized"
         self.work_allotment_hash = work_allotment_hash || WORK_TYPES
 	end
@@ -46,31 +97,63 @@ class RealTimeDb
 		self.connection.wait
 	end
 
+	## if the barcode exists,
+	## otherwise create it.
+	def barcode_exists?(barcode)
+		begin
+			self.connection.get(ENDPOINT, :orderBy => 'barcode', :equalTo => barcode)
+		rescue
+			## reestablish the connection
+			self.connection = RestFirebase.new :site => SITE_URL,
+                     :secret => SECRET, :auth =>generate_access_token
+			true
+		end
+	end
 
-
+	## idea is simple
+	## send the image -> to one collection, as a post
+	## take it -> analyze it -> update the result
+	## to another collection
+	## show it in the UI.
+	## knock off the earlier one.
 
 	## we pass the real_time_data instance into the 
-
 	def assign_test(barcode,tests,mappings)
 		## so do we get the name of the worker.
-		inverted_mappings = {}
-		mappings.keys.each do |machine_code|
-			lis_code = mappings[machine_code][LIS_CODE]
-			inverted_mappings[lis_code] = mappings[machine_code]
-		end
-		worker_hash = {}
-		tests.each do |lis_code|
-			worker_name = "NO_ONE"
-			unless inverted_mappings[lis_code].blank?
-				test_type = inverted_mappings[lis_code]["TYPE"]
-				worker_name = self.work_allotment_hash[test_type]
+		if barcode_exists?(barcode[0]).blank?
+
+			worker_hash = {}
+			tests.each do |machine_code|
+				worker_name = "NO_ONE"
+				
+				unless mappings[machine_code].blank?
+					test_type = mappings[machine_code]["TYPE"]
+					worker_name = self.work_allotment_hash[test_type]
+
+					worker_hash[worker_name] ||= []
+
+					#puts "worker name: #{worker_name}"
+					#puts "lis code: #{machine_code}"
+					#puts mappings[machine_code].to_s
+					worker_hash[worker_name] << mappings[machine_code]["REPORT_NAME"]
+				else
+					worker_hash[worker_name] ||= []
+					worker_hash[worker_name] << machine_code
+				end
+				
+				
 			end
-			worker_hash[worker_name] ||= []
-			worker_hash[worker_name] << lis_code
-		end
-		worker_hash.keys.each do |worker_name|
-			#self.connection.post("lab/work/#{worker_name}", :tests => worker_hash[worker_name], :barcode => barcode, :timestamp => Time.now.to_i)
+
+			#puts "this is the workers hash"
+			#puts worker_hash.to_s
+			worker_hash.keys.each do |worker_name|
+				k = self.connection.post(ENDPOINT, :tests => worker_hash[worker_name].uniq, :barcode => barcode[0], :timestamp => Time.now.strftime("%b %-d %Y %I:%M %P"), :worker_name => worker_name, :status => ACCESSION_DONE, :next_step =>  PROCESSING, :combi_key => worker_name + "_pending")
+				#puts k.to_s
+			end
+		else
+			puts "this barcode: #{barcode[0]} already exists."
 		end
+
 	end
 	
 end

data/lib/ruby_astm/custom/siemens_abg_electrolyte_module.rb

@@ -124,6 +124,7 @@ module SiemensAbgElectrolyteModule
 	    		p.patient_id = patient_id
 	    		p.orders ||= []
 	    		o = Order.new
+	    		o.id = patient_id
 	    		o.results ||= {}
 	    		if sodium = get_na
 	    			r = Result.new
@@ -158,7 +159,7 @@ module SiemensAbgElectrolyteModule
 	    		if ph = get_ph
 	    			r = Result.new
 	    			r.name = "pH"
-	    			r.report_name = "Serum Electrolytes"
+	    			r.report_name = "ABG"
 	    			r.value = ph
 	    			r.units = "mmol/L"
 	    			r.timestamp = Time.now.to_i
@@ -168,7 +169,7 @@ module SiemensAbgElectrolyteModule
 	    		if po2 = get_po2
 	    			r = Result.new
 	    			r.name = "po2"
-	    			r.report_name = "Serum Electrolytes"
+	    			r.report_name = "ABG"
 	    			r.value = po2
 	    			r.units = "mmHg"
 	    			r.timestamp = Time.now.to_i
@@ -178,7 +179,7 @@ module SiemensAbgElectrolyteModule
 	    		if pco2 = get_pco2
 	    			r = Result.new
 	    			r.name = "pco2"
-	    			r.report_name = "Serum Electrolytes"
+	    			r.report_name = "ABG"
 	    			r.value = pco2
 	    			r.units = "mmHg"
 	    			r.timestamp = Time.now.to_i
@@ -190,6 +191,12 @@ module SiemensAbgElectrolyteModule
 	    	end
 	    end
 
+	    if self.headers.size > 0
+            self.headers[-1].commit
+            clear
+            #send_data(self.headers[-1].generate_ack_success_response)
+        end
+
 	end
 
 	def process_text_file(full_file_path)
@@ -197,6 +204,12 @@ module SiemensAbgElectrolyteModule
 		process_electrolytes(k.bytes)
 	end
 
+	def clear
+		self.data_buffer = ''
+		self.test_data_bytes = []
+		self.data_bytes = []
+	end
+
 
 	def receive_data(data)
       

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: ruby_astm
 version: !ruby/object:Gem::Version
-  version: 1.4.4
+  version: 1.4.6
 platform: ruby
 authors:
 - Bhargav Raut
@@ -136,6 +136,20 @@ dependencies:
     - - ">="
       - !ruby/object:Gem::Version
         version: '0'
+- !ruby/object:Gem::Dependency
+  name: jwt
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
 description: This gem provides a server that can handle communication from medical
   instruments that send/receive information on the ASTM protocol.
 email: bhargav.r.raut@gmail.com