ruby_astm 0.0.9 → 1.0.0

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: 72ade802a6dc078a0d52242e6e76d6f3a2eb1be6
-  data.tar.gz: 58909cfdb8d0ab54b9bf363030f8025827ae314d
+  metadata.gz: 694ae05d26bb089e9ac086b049a61b334918554c
+  data.tar.gz: 7f64cc2d8ff8e65db4db2344180d09a45aba91c6
 SHA512:
-  metadata.gz: 3e188721bcbe685dbbc312f7d7dff054c571b27993a8f022866464657e1a01e54bc2469ae5e47105491c5a2eaff057713adb159a7951e0edb2ed19030c657588
-  data.tar.gz: 9383ecbdb2f21986b2642881871601ab0fd46848bb338a4e7ffc603b8acdbf15994cb596a710b88ec1792bdf0fac2549bd8047ab9cf4822e7e317364844b792a
+  metadata.gz: 76f380e0fd5b1f15c52f77cc7eed5b094e4970c52f7419a8664b9047e18619fad2e78641cbe718bba92f769c539eb841459be4b5525fa4139a27d58d6bd6301e
+  data.tar.gz: 512ad2242dd67761595af57c02a8d1de61f724029703a105dd63bc1c30536c710b5fca1409385cca56e18e8ffaaf81ef407c7fa050067a710844ee0e845d21fe

data/lib/publisher/google_lab_interface.rb

@@ -17,10 +17,10 @@ class Google_Lab_Interface < Poller
   SCOPES = ["https://www.googleapis.com/auth/documents","https://www.googleapis.com/auth/drive","https://www.googleapis.com/auth/script.projects","https://www.googleapis.com/auth/spreadsheets"]
 
   $service = nil
-  SCRIPT_ID = "M7JDg7zmo0Xldo4RTWFGCsI2yotVzKYhk"
 
   attr_accessor :credentials_path
   attr_accessor :token_path
+  attr_accessor :script_id
   
   ##
   # Ensure valid credentials, either by restoring from the saved credentials
@@ -49,25 +49,26 @@ class Google_Lab_Interface < Poller
   ## @param[String] mpg : path to mappings file. Defaults to nil.
   ## @param[String] credentials_path : the path to look for the credentials.json file, defaults to nil ,and will raise an error unless provided
   ## @param[String] token_path : the path where the oauth token will be stored, also defaults to the path of the gem : eg. ./token.yaml - be careful with write permissions, because token.yaml gets written to this path after the first authorization.
-  def initialize(mpg=nil,credentials_path,token_path)
+  def initialize(mpg=nil,credentials_path,token_path,script_id)
     super(mpg)
     self.credentials_path = credentials_path
     self.token_path = token_path
+    self.script_id = script_id
     raise "Please provide the full path of the google oauth credentials.json file. If you don't have this file, please go to the Apps Script project, which has your google apps script, and Choose Create Credentials -> help me choose -> and use 'Calling Scripts Api from a UI based platform'. Also ensure that your script has permissions set for Drive, Sheets, and more. Lastly in the Apps script project ensure that settings -> google apps script API is ON." if self.credentials_path.nil?
+    raise "Please provide a script id for your google script" if self.script_id.blank?
     AstmServer.log("Initialized Google Lab Interface")
     $service = Google::Apis::ScriptV1::ScriptService.new
     $service.client_options.application_name = APPLICATION_NAME
     $service.authorization = authorize
   end
 
-
+  ## how to decide for what to poll for the requisition.
+  ## this should be tested.
   def poll_LIS_for_requisition
     
-    
-     
     AstmServer.log("polling LIS for new requisitions")
     
-    epoch = (Time.now - 5.days).to_i*1000
+    epoch = get_checkpoint
     
     pp = {
       :input => JSON.generate([epoch])
@@ -79,7 +80,7 @@ class Google_Lab_Interface < Poller
     )
 
     begin 
-      resp = $service.run_script(SCRIPT_ID, request)
+      resp = $service.run_script(self.script_id, request)
       if resp.error
         AstmServer.log("Response Error polling LIS for requisitions: #{resp.error.message}: #{resp.error.code}")
       else
@@ -116,7 +117,7 @@ class Google_Lab_Interface < Poller
     begin
       AstmServer.log("updating following results to LIS")
       AstmServer.log(request.parameters.to_s)
-      resp = $service.run_script(SCRIPT_ID, request)
+      resp = $service.run_script(self.script_id, request)
       if resp.error
         AstmServer.log("Error updating results to LIS, message follows")
         AstmServer.log("error: #{resp.error.message} : code: #{resp.error.code}")

data/lib/publisher/poller.rb

@@ -106,6 +106,8 @@ class Poller
   	end	
 
   	def build_tests_hash(record)
+  		#puts "Record is ---------------------------------------------"
+  		#puts record
 	    tests_hash = {}
 
 	    ## key -> TUBE_NAME : eg: EDTA
@@ -118,38 +120,41 @@ class Poller
 	    ## fluoride -> index 31
 	    ## urine -> index 32
 	    ## esr -> index 33
-	    unless record[28].blank?
-	      tube_ids[EDTA] = record[28].to_s
-	      tests_hash[EDTA + ":" + record[28].to_s] = []
+	    unless record[24].blank?
+	      tube_ids[EDTA] = record[24].to_s
+	      tests_hash[EDTA + ":" + record[24].to_s] = []
 	    end
 
-	    unless record[29].blank?
-	      tube_ids[SERUM] = record[29].to_s
-	      tests_hash[SERUM + ":" + record[29].to_s] = []
+	    unless record[25].blank?
+	      tube_ids[SERUM] = record[25].to_s
+	      tests_hash[SERUM + ":" + record[25].to_s] = []
 	    end
 
-	    unless record[30].blank?
-	      tube_ids[PLASMA] = record[30].to_s
-	      tests_hash[PLASMA + ":" + record[30].to_s] = []
+	    unless record[26].blank?
+	      tube_ids[PLASMA] = record[26].to_s
+	      tests_hash[PLASMA + ":" + record[26].to_s] = []
 	    end
 
-	    unless record[31].blank?
-	      tube_ids[FLUORIDE] = record[31].to_s
-	      tests_hash[FLUORIDE + ":" + record[31].to_s] = []
+	    unless record[27].blank?
+	      tube_ids[FLUORIDE] = record[27].to_s
+	      tests_hash[FLUORIDE + ":" + record[27].to_s] = []
 	    end
 
-	    unless record[32].blank?
-	      tube_ids[URINE] = record[32].to_s
-	      tests_hash[URINE + ":" + record[32].to_s] = []
+	    unless record[28].blank?
+	      tube_ids[URINE] = record[28].to_s
+	      tests_hash[URINE + ":" + record[28].to_s] = []
 	    end
 
-	    unless record[33].blank?
-	      tube_ids[ESR] = record[33].to_s
-	      tests_hash[ESR + ":" + record[33].to_s] = []
+	    unless record[29].blank?
+	      tube_ids[ESR] = record[29].to_s
+	      tests_hash[ESR + ":" + record[29].to_s] = []
 	    end
 
+	    tests = record[7].split(",").compact
 
-	    tests = record[8].split(",")
+	    puts "tests are:"
+	    puts tests.to_s
+	    return tests_hash if tests_hash.empty?
 	    tests.each do |test|
 	      ## use the inverted mappings to 
 	      if machine_code = $inverted_mappings[test]
@@ -159,6 +164,9 @@ class Poller
 	        ## now find the tests_hash which has this tube.
 	        ## and the machine code to its array.
 	        ## so how to find this.
+	        puts "tube is : #{tube}"
+	        puts "tests hash is:"
+	        puts tests_hash.to_s
 	        tube_key = tests_hash.keys.select{|c| c=~/#{tube}/ }[0] 
 	        tests_hash[tube_key] << machine_code   
 	      else
@@ -185,7 +193,19 @@ class Poller
 	      end  
 	    end
 	end
+	
+	def default_checkpoint
+		(Time.now - 5.days).to_i*1000
+	end
 
+	def get_checkpoint
+		latest_two_entries = $redis.zrange Poller::REQUISITIONS_SORTED_SET, -2, -1, {withscores: true}
+		unless latest_two_entries.blank?
+    		latest_two_entries[-1][1].to_i
+    	else
+    		default_checkpoint
+		end
+	end
 
   	## @param[String] json_response : contains the response from the LIS
   	## it should be the jsonified version of a hash that is structured as follows: 

data/lib/ruby_astm/query.rb

@@ -12,20 +12,41 @@ class Query
 		end
 	end
 
+	def get_tests
+		tests = []
+		sample_tests = $redis.hget(Poller::REQUISITIONS_HASH,self.sample_id)
+		unless sample_tests.blank?
+			tests = JSON.parse(sample_tests)
+		end
+		tests
+	end
+
 	## each query will build one patient and one order inside it.
 	## the order can have many tests.
 	def build_response(variables=nil)
+		## so the response is thus incoming.
+=begin		
 		variables ||= {
 			:sequence_number => "0",
 			:patient_id => "abcde",
 			:specimen_id => self.sample_id,
 			:tests => ["TRIG"],
 			:priority => "R"
-		}
+		}	
+=end
+
+		## tests are got from the requisitions hash.
+		tests = get_tests
+
+		## default sequence number is 0 (THIS MAY LEAD TO PROBLEMS.)
+		sequence_number = "0"
+
+		## default patient id:
+		patient_id = "abcde"
 
-		patient = Patient.new({:sequence_number => "0", :patient_id => "abcde"})
+		patient = Patient.new({:sequence_number => sequence_number, :patient_id => patient_id})
 		
-		order = Order.new({:sequence_number => patient.sequence_number, :specimen_id => variables[:specimen_id], :tests => variables[:tests], :priority => variables[:priority]})
+		order = Order.new({:sequence_number => patient.sequence_number, :specimen_id => self.sample_id, :tests => tests, :priority => "R"})
 
 		return patient.build_response + order.build_response
 		

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: ruby_astm
 version: !ruby/object:Gem::Version
-  version: 0.0.9
+  version: 1.0.0
 platform: ruby
 authors:
 - Bhargav Raut