class Poller
Constants
- COMPLETED
- EDTA
3
require the file that implements the
Adapter
class.- ESR
- FLUORIDE
- LAST_REQUEST_AT
- LAST_REQUEST_STATUS
- PLASMA
- POLL_STATUS_KEY
- REQUISITIONS_HASH
- REQUISITIONS_SORTED_SET
- RUNNING
- SERUM
- URINE
Public Class Methods
# File lib/publisher/poller.rb, line 27 def initialize(mpg=nil,real_time_db=nil) $redis = Redis.new $real_time_db = real_time_db ## this mapping is from MACHINE CODE AS THE KEY $mappings = JSON.parse(IO.read(mpg || AstmServer.default_mappings)) ## INVERTING THE MAPPINGS, GIVES US THE LIS CODE AS THE KEY. $inverted_mappings = Hash[$mappings.values.map{|c| c = c["LIS_CODE"]}.zip($mappings.keys)] end
Public Instance Methods
# File lib/publisher/poller.rb, line 110 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
# File lib/publisher/poller.rb, line 131 def build_tests_hash(record) #puts "Record is ---------------------------------------------" #puts record tests_hash = {} ## key -> TUBE_NAME : eg: EDTA ## value -> its barcode id. tube_ids = {} ## assign. ## lavender -> index 28 ## serum -> index 29 ## plasm -> index 30 ## fluoride -> index 31 ## urine -> index 32 ## esr -> index 33 unless record[24].blank? tube_ids[EDTA] = record[24].to_s tests_hash[EDTA + ":" + record[24].to_s] = [] end unless record[25].blank? tube_ids[SERUM] = record[25].to_s tests_hash[SERUM + ":" + record[25].to_s] = [] end unless record[26].blank? tube_ids[PLASMA] = record[26].to_s tests_hash[PLASMA + ":" + record[26].to_s] = [] end unless record[27].blank? tube_ids[FLUORIDE] = record[27].to_s tests_hash[FLUORIDE + ":" + record[27].to_s] = [] end unless record[28].blank? tube_ids[URINE] = record[28].to_s tests_hash[URINE + ":" + record[28].to_s] = [] end unless record[29].blank? tube_ids[ESR] = record[29].to_s tests_hash[ESR + ":" + record[29].to_s] = [] end tests = record[7].split(",").compact ## these test names are whatever are coming ## from return tests_hash if tests_hash.empty? #puts "inverted mappings are:" #puts $inverted_mappings.keys.to_s #exit(1) #exit(1) tests.each do |test| ## use the inverted mappings to if machine_code = $inverted_mappings[test] puts "machine code is: #{machine_code}" ## now get its tube type ## mappings have to match the tubes defined in this file. if package_components = $mappings[machine_code]["PACKAGE_COMPONENTS"] puts package_components.to_s package_components.each do |component| #puts "doing component: #{component}" ## these are the machine codes. ## so to get the tube, you have to get it from the inverted mappings. ## cant get directly like this. #puts "inverted mappings" #puts $inverted_mappings component_machine_code = $inverted_mappings[component] if component == "UCRE" puts "component machine code: #{component_machine_code}" end ## 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? tube_key = tests_hash.keys.select{|c| c=~/#{tube}/ }[0] tests_hash[tube_key] << machine_code end end else AstmServer.log("ERROR: Test: #{test} does not have an LIS code") end end AstmServer.log("tests hash generated") AstmServer.log(JSON.generate(tests_hash)) tests_hash end
# File lib/publisher/poller.rb, line 273 def default_checkpoint (Time.now - 1.days).to_i*1000 end
first we have to test the packages.
# File lib/publisher/poller.rb, line 120 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
# File lib/publisher/poller.rb, line 277 def get_checkpoint latest_two_entries = $redis.zrange Poller::REQUISITIONS_SORTED_SET, -2, -1, {withscores: true} unless latest_two_entries.blank? last_entry = latest_two_entries[-1][1].to_i #one_year_back = Time.now - 1.year #one_year_back = one_year_back.to_i #time_now = Time.now.to_i #puts "diff is: #{time_now*1000 - one_year_back*1000}" #puts "one year back is " #puts "last entry is: #{last_entry}" #puts "last entry - Time.now is :#{Time.now.to_i*1000 - last_entry}" #puts "default checkpoint is :#{default_checkpoint}" #last_entry #default_checkpoint if (((Time.now.to_i)*1000) - last_entry) >= 86400*1000 puts "diff is too great" default_checkpoint else puts "taking the last entry" last_entry end else default_checkpoint end end
@param epoch : the epoch at which these tests were requested. @param tests : {“EDTA:barcode” => [MCV,MCH,MCHC…]} the test codes here are the lis_codes so we need the inverted mappings for this
# File lib/publisher/poller.rb, line 251 def merge_with_requisitions_hash(epoch,tests) ## so we basically now add this to the epoch ? ## or a sorted set ? ## key -> TUBE:specimen_id ## value -> array of tests as json ## score -> time. $redis.multi do |multi| $redis.zadd REQUISITIONS_SORTED_SET, epoch, JSON.generate(tests) tests.keys.each do |tube_barcode| ## in this hash we want the key to be only the specimen id. ## and not prefixed by the tube type like FLUORIDE etc. ## i don't want the individual tests, ## i want the report name. ## prefixed to it. tube_barcode.scan(/:(?<barcode>.*)$/) { |barcode| $redis.hset REQUISITIONS_HASH, barcode, JSON.generate(tests[tube_barcode]) $real_time_db.assign_test(barcode,tests[tube_barcode],$mappings) unless $real_time_db.blank? } end end end
# File lib/publisher/poller.rb, line 449 def poll pre_poll_LIS poll_LIS_for_requisition update_LIS post_poll_LIS end
this method should be overriden. will poll the lis, and store locally, in a redis sorted set the following: key => specimen_id value => tests designated for that specimen. score => time of requisition of that specimen. name of the sorted set can be defined in the class that inherits from adapter, or will default to “requisitions” when a query is sent from any laboratory equipment to the local ASTMServer, it will query the redis sorted set, for the test information. so this poller basically constantly replicates the cloud based test information to the local server.
# File lib/publisher/poller.rb, line 445 def poll_LIS_for_requisition(to_epoch=nil) end
uses redis CAS to ensure that two requests don't overlap. will update to the requisitions hash the specimen id -> and the now lets test this. how to stub it out ? first we call it direct.
# File lib/publisher/poller.rb, line 82 def post_poll_LIS requisition_status = JSON.parse($redis.get(POLL_STATUS_KEY)) if (requisition_status[LAST_REQUEST_STATUS] == RUNNING) $redis.watch(POLL_STATUS_KEY) do if $redis.get(POLL_STATUS_KEY) == JSON.generate(requisition_status) $redis.multi do |multi| multi.set(POLL_STATUS_KEY,JSON.generate({LAST_REQUEST_STATUS => COMPLETED, LAST_REQUEST_AT => requisition_status[LAST_REQUEST_AT]})) end AstmServer.log("post poll LIS status set to completed") else AstmServer.log("post poll LIS was was interrupted by another client , so exited this thread") $redis.unwatch(POLL_STATUS_KEY) return end end else AstmServer.log("post poll LIS was not in running state") end end
# File lib/publisher/poller.rb, line 47 def pre_poll_LIS previous_requisition_request_status = nil if previous_requisition_request_status = $redis.get(POLL_STATUS_KEY) last_request_at = previous_requisition_request_status[LAST_REQUEST_AT] last_request_status = previous_requisition_request_status[LAST_REQUEST_STATUS] end running_time = Time.now.to_i $redis.watch(POLL_STATUS_KEY) do if $redis.get(POLL_STATUS_KEY) == previous_requisition_request_status if ((last_request_status != RUNNING) || ((Time.now.to_i - last_request_at) > 600)) $redis.multi do |multi| multi.set(POLL_STATUS_KEY, JSON.generate({LAST_REQUEST_STATUS => RUNNING, LAST_REQUEST_AT => running_time})) end AstmServer.log("pre poll lis status set to running") end else AstmServer.log("pre poll lis status check interrupted by another client, so exiting here") $redis.unwatch return end end end
# File lib/publisher/poller.rb, line 41 def prepare_redis if ($redis.exists "processing") == 0 $redis.lpush("processing",JSON.generate([])) end end
## @param json_response : contains the response from the LIS ## it should be the jsonified version of a hash that is structured as follows:
{ "epoch" => [ [index_8 : list_of_LIS_TEST_CODES_seperated_by_commas, index 28 => lavender, index 29 => serum, index 30 => plasma, index 31 => fluoride, index 32 => urine, index 33 => esr] }
## @return
# File lib/publisher/poller.rb, line 312 def process_LIS_response(json_response) lab_results = JSON.parse(json_response) AstmServer.log("requisitions downloaded from LIS") AstmServer.log(JSON.generate(lab_results)) lab_results.keys.each do |epoch| merge_with_requisitions_hash(epoch,build_tests_hash(lab_results[epoch][0])) end end
# File lib/publisher/poller.rb, line 36 def root_path File.dirname __dir__ end
override to define how the data is updated. expected to return Boolean value, depending on whether the update was successfull or not.
# File lib/publisher/poller.rb, line 323 def update(data) true end
##@param data : array of objects. ##@return true/false : depending on whether it was successfully updated or not. ## recommended structure for data.
data = [ { :id => "ARUBA", :results => [ { :name => "TLCparam", :value => 10 }, { :name => "Nparam", :value => 23 }, { :name => "ANCparam", :value => 25 }, { :name => "Lparam", :value => 10 }, { :name => "ALCparam", :value => 44 }, { :name => "Mparam", :value => 55 }, { :name => "AMCparam", :value => 22 }, { :name => "Eparam", :value => 222 }, { :name => "AECparam", :value => 21 }, { :name => "BASOparam", :value => 222 }, { :name => "ABCparam", :value => 300 }, { :name => "RBCparam", :value => 2.22 }, { :name => "HBparam", :value => 19 }, { :name => "HCTparam", :value => 22 }, { :name => "MCVparam", :value => 222 }, { :name => "MCHparam", :value => 21 }, { :name => "MCHCparam", :value => 10 }, { :name => "MCVparam", :value => 222 }, { :name => "RDWCVparam", :value => 12 }, { :name => "PCparam", :value => 1.22322 } ] } ]
## pretty simple, if the value is not already there it will be updated, otherwise it won't be.
# File lib/publisher/poller.rb, line 420 def update_LIS prepare_redis patients_to_process = $redis.llen("patients") > 0 while patients_to_process == true if patient_results = $redis.rpoplpush("patients","processing") patient_results = JSON.parse(patient_results) ## do this before the update, so that we don't go into an endless loop if the current update fails. patients_to_process = $redis.llen("patients") > 0 unless update(patient_results) $redis.lpush("patients",JSON.generate(patient_results)) end else patients_to_process = false end end end