emr_ohsp_interface 0.3.0 → 0.5.2

checksums.yaml

@@ -1,7 +1,7 @@
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data/app/controllers/emr_ohsp_interface/emr_lims_interface_controller.rb

@@ -0,0 +1,24 @@
+# frozen_string_literal: true
+
+class EmrOhspInterface::EmrLimsInterfaceController < ::ApplicationController
+  def create
+    # lab_details = params.require %i[lab_details]
+    # render json: "#{lab_details[0]['firstname']}"
+    # render json:
+    order_params_list, clinician_id = params.require %i[lab_details clinician_id]
+
+    render json: service.create_lab_order(order_params_list, clinician_id)
+  end
+
+  def index
+    render json: service.get_lims_test_results(params[:id],params[:patient_id])
+  end
+
+  def get_user_info()
+    render json: service.get_user_details(params[:id])
+  end
+
+  def service
+    EmrOhspInterface::EmrLimsInterfaceService
+  end
+end

data/app/controllers/emr_ohsp_interface/emr_ohsp_interface_controller.rb

@@ -14,6 +14,10 @@ class EmrOhspInterface::EmrOhspInterfaceController < ::ApplicationController
     def generate_monthly_idsr_report
         render json: service.generate_monthly_idsr_report(params[:request],params[:start_date],params[:end_date]);
     end
+
+    def generate_hmis_15_report
+        render json: service.generate_hmis_15_report(params[:start_date],params[:end_date]);
+    end
    
     def service
         EmrOhspInterface::EmrOhspInterfaceService

data/app/services/emr_ohsp_interface/emr_lims_interface_service.rb

@@ -0,0 +1,410 @@
+# frozen_string_literal: true
+
+require 'emr_ohsp_interface/version'
+module EmrOhspInterface
+  module EmrLimsInterfaceService
+    class << self
+      require 'csv'
+      require 'rest-client'
+
+      def initialize
+        @mysql_connection_pool = {}
+      end
+      ######################################### start creation of lab test in lims  #####################################################
+      def settings
+        file = File.read(Rails.root.join('db', 'lims_metadata', 'lims_map.json'))
+        JSON.parse(file)
+      end
+
+      def get_patient_number
+        get_patient_id = query "SELECT id FROM iblis.patients order by id desc limit 1;"
+
+        get_patient_id.each do |x|
+         return patient_number = x['id']
+        end
+        
+
+
+      end
+
+      def check_patient_number(patient_id)
+          get_patient_id = query "SELECT patient_number FROM patients WHERE `external_patient_number` ='#{patient_id}'; "
+
+          get_patient_id.each do |x|
+            return patient_number = x['patient_number']
+          end
+
+      end
+
+      def filterpatient_number(data)
+        patient_number = 0
+        data.each do |x|
+          patient_number = x['patient_identify']
+        end
+        patient_number
+      end
+
+      def get_patient_dentifier(patient_id)
+        patient_dentifier =PatientIdentifier.where('patient_id= ? AND identifier_type = ?', patient_id,3)[0]
+        patient_dentifier[:identifier]
+      end
+      def create_lab_order(lab_details, clinician_id)
+        external_patient_number = get_patient_dentifier(lab_details[0][:patient_id])
+        patient_number = check_patient_number(external_patient_number)
+        time = Time.new
+        date = time.strftime('%Y-%m-%d %H:%M:%S')
+        lab_details.map do |order_params|
+          if patient_number.blank?
+            patient_number = get_patient_number() + 1
+
+            person_data = Person.where('person_id= ?', order_params[:patient_id])[0]
+            address_data = PersonAddress.where('person_id= ?', order_params[:patient_id])[0]
+            name_data = PersonName.where('person_id= ?', order_params[:patient_id])[0]
+
+            gender = person_data[:gender].match(/f/i) ? 1 : (person_data[:gender].match(/m/i) ? 0 : 2)
+            create_patient(
+              name_data[:given_name],
+              name_data[:family_name],
+              clinician_id[0][:requesting_clinician_id],
+              address_data[:address1],
+              gender,
+              person_data[:birthdate],
+              person_data[:birthdate_estimated],
+              external_patient_number,
+              patient_number,
+              date
+            )
+          end
+          create_visit(patient_number, date)
+          create_specimens(
+            clinician_id[0][:requesting_clinician_id],
+            order_params[:specimen][:name],
+            order_params[:accession_number]
+          )
+          specimen_id = get_specimen_id
+          create_unsync_orders(date, specimen_id)
+
+          create_test(specimen_id, order_params[:requesting_clinician], order_params[:tests][0][:name])
+        end
+      end
+
+      def create_patient(
+        firstname, surname,
+        user_id, address,
+        gender, dob,
+        dob_estimated, external_patient_number,
+        patient_number, date
+      )
+        query(
+          "INSERT INTO `patients` (`name`, `first_name_code`, `last_name_code`, `created_by`, `address`, `gender`, `patient_number`, `dob`, `dob_estimated`, `external_patient_number`, `created_at`, `updated_at`)
+          VALUES ('#{firstname} #{surname}', SOUNDEX('#{firstname}'), SOUNDEX('#{surname}'), #{user_id}, '#{address}',#{gender},'#{patient_number}', '#{dob}', '#{dob_estimated}', '#{external_patient_number}', '#{date}', '#{date}')"
+        )
+      end
+
+      def create_visit(patient_number, date)
+        query "INSERT INTO `visits` (`patient_id`, `visit_type`, `ward_or_location`, `created_at`, `updated_at`)
+                VALUES ('#{patient_number}', 'Out Patient', 'EM OPD', '#{date}', '#{date}')"
+      end
+
+      def create_specimens(user_id, specimen_type, tracking_number)
+        specimen_type_id = settings['lims_specimen_map'][specimen_type.to_s]
+        accession_number = new_accession_number
+        # prepare_next_tracking_number()
+        # tracking_number = create_local_tracking_number()
+        query(" INSERT INTO `specimens` (`specimen_type_id`, `accepted_by`, `priority`, `accession_number`, `tracking_number`)
+        VALUES ('#{specimen_type_id}', '#{user_id}', 'Stat', '#{accession_number}', '#{tracking_number}')")
+      end
+
+      def create_unsync_orders(date, specimen_id)
+        query(" INSERT INTO `unsync_orders` (`specimen_id`, `data_not_synced`, `data_level`, `sync_status`, `updated_by_name`, `updated_by_id`, `created_at`, `updated_at`)
+        VALUES ('#{specimen_id}', 'new order', 'specimen', 'not-synced', 'kBLIS Administrator', '1', '#{date}', '#{date}')")
+      end
+
+      def create_test(specimen_id, requested_by, test_type)
+        visit_id = get_visit_id
+        test_type_id = settings['lims_test_type_map'][test_type.to_s]
+        query("INSERT INTO `tests` (`visit_id`, `test_type_id`, `specimen_id`, `test_status_id`, `not_done_reasons`, `person_talked_to_for_not_done`, `created_by`, `requested_by`)
+         VALUES ('#{visit_id}', '#{test_type_id}', '#{specimen_id}', '2', '0', '0', 1, '#{requested_by}')")
+      end
+
+      def new_accession_number
+        # Generate the next accession number for specimen registration
+        @mutex = Mutex.new if @mutex.blank?
+        @mutex.lock
+        max_acc_num = 0
+        return_value = nil
+        sentinel = 99_999_999
+
+        settings = YAML.load_file("#{Rails.root}/config/application.yml")[Rails.env]
+        code = settings['facility_code']
+        year = Date.today.year.to_s[2..3]
+
+        record = get_last_accession_number
+
+        unless record.blank?
+          max_acc_num = record[5..20].match(/\d+/)[0].to_i # first 5 chars are for facility code and 2 digit year
+        end
+
+        if max_acc_num < sentinel
+          max_acc_num += 1
+        else
+          max_acc_num = 1
+        end
+
+        max_acc_num = max_acc_num.to_s.rjust(8, '0')
+        return_value = "#{code}#{year}#{max_acc_num}"
+        @mutex.unlock
+
+        return_value
+      end
+
+      def get_last_accession_number
+        data = query('SELECT * FROM specimens WHERE accession_number IS NOT NULL ORDER BY id DESC LIMIT 1')
+        data.each do |x|
+          return last_accession_number = x['accession_number']
+        end
+      end
+
+      def get_specimen_id
+        data = query('SELECT * FROM specimens WHERE accession_number IS NOT NULL ORDER BY id DESC LIMIT 1')
+        data.each do |x|
+          return specimen_id = x['id']
+        end
+      end
+
+      def get_visit_id
+        data = query('SELECT * FROM visits WHERE id IS NOT NULL ORDER BY id DESC LIMIT 1')
+        data.each do |x|
+          return specimen_id = x['id']
+        end
+      end
+
+      def prepare_next_tracking_number
+        file = JSON.parse(File.read("#{Rails.root}/public/tracker.json"))
+        todate = Time.now.strftime('%Y%m%d')
+
+        counter = file[todate]
+        counter = counter.to_i + 1
+        fi = {}
+        fi[todate] = counter
+        File.open("#{Rails.root}/public/tracker.json", 'w') do |f|
+          f.write(fi.to_json)
+        end
+      end
+
+      ###### lims tracking number ###############
+      def create_local_tracking_number
+        configs = YAML.load_file "#{Rails.root}/config/application.yml"
+        site_code = configs['facility_code']
+        file = JSON.parse(File.read("#{Rails.root}/public/tracker.json"))
+        todate = Time.now.strftime('%Y%m%d')
+        year = Time.now.strftime('%Y%m%d').to_s.slice(2..3)
+        month = Time.now.strftime('%m')
+        day = Time.now.strftime('%d')
+
+        key = file.keys
+
+        if todate > key[0]
+
+          fi = {}
+          fi[todate] = 1
+          File.open("#{Rails.root}/public/tracker.json", 'w') do |f|
+            f.write(fi.to_json)
+          end
+
+          value = '001'
+          tracking_number = "X#{site_code}#{year}#{get_month(month)}#{get_day(day)}#{value}"
+
+        else
+          counter = file[todate]
+
+          value = if counter.to_s.length == 1
+                    '00' + counter.to_s
+                  elsif counter.to_s.length == 2
+                    '0' + counter.to_s
+                  else
+                    begin
+                        counter.to_s
+                    rescue StandardError
+                      '001'
+                      end
+                  end
+
+          tracking_number = "X#{site_code}#{year}#{get_month(month)}#{get_day(day)}#{value}"
+
+        end
+        tracking_number
+      end
+
+      def get_month(month)
+        case month
+
+        when '01'
+          '1'
+        when '02'
+          '2'
+        when '03'
+          '3'
+        when '04'
+          '4'
+        when '05'
+          '5'
+        when '06'
+          '6'
+        when '07'
+          '7'
+        when '08'
+          '8'
+        when '09'
+          '9'
+        when '10'
+          'A'
+        when '11'
+          'B'
+        when '12'
+          'C'
+          end
+      end
+
+      def get_day(day)
+        case day
+
+        when '01'
+          '1'
+        when '02'
+          '2'
+        when '03'
+          '3'
+        when '04'
+          '4'
+        when '05'
+          '5'
+        when '06'
+          '6'
+        when '07'
+          '7'
+        when '08'
+          '8'
+        when '09'
+          '9'
+        when '10'
+          'A'
+        when '11'
+          'B'
+        when '12'
+          'C'
+        when '13'
+          'E'
+        when '14'
+          'F'
+        when '15'
+          'G'
+        when '16'
+          'H'
+        when '17'
+          'Y'
+        when '18'
+          'J'
+        when '19'
+          'K'
+        when '20'
+          'Z'
+        when '21'
+          'M'
+        when '22'
+          'N'
+        when '23'
+          'O'
+        when '24'
+          'P'
+        when '25'
+          'Q'
+        when '26'
+          'R'
+        when '27'
+          'S'
+        when '28'
+          'T'
+        when '29'
+          'V'
+        when '30'
+          'W'
+        when '31'
+          'X'
+          end
+      end
+############################################# end creation of lab test in lims  #####################################################
+
+############## get results from lims ###############
+
+def get_lims_test_results(tracking_number,patient_id)
+  external_patient_number = get_patient_dentifier(patient_id)
+  data = query("
+    SELECT
+    visits.ward_or_location, specimens.accession_number,
+    tests.created_by, tests.verified_by,
+    tests.time_completed,tests.requested_by,tests.interpretation,
+    tests.time_created         as         tests_time_created,       
+    test_types.name            as    test_types_name,          
+    test_categories.name       as   test_categories_name,     
+    tests.time_verified        as    tests_time_verified,      
+    users.name                 as  users_name,               
+    specimen_types.name        as        specimen_types_name,      
+    specimen_statuses.name     as              specimen_statuses_name,   
+    test_results.result        as          test_results_result,      
+    test_results.device_name   as              test_results_device_name, 
+    measures.name              as  measures_name,            
+    measures.unit             as  measures_unit,            
+    measure_ranges.range_lower as measure_ranges_range_lower,
+    measure_ranges.range_upper   as  measure_ranges_range_upper                                      
+    FROM iblis.patients 
+    inner join iblis.visits on `visits`.`patient_id` = `patients`.`patient_number` 
+    inner join iblis.tests on `tests`.`visit_id` = `visits`.`id` 
+    inner join iblis.test_types on `test_types`.`id` = `tests`.`test_type_id`
+    inner join iblis.test_categories on `test_categories`.`id` = `test_types`.`test_category_id`
+    inner join iblis.users on `users`.`id` = `tests`.`tested_by`
+    inner join iblis.specimens on `specimens`.`id` = `tests`.`specimen_id`
+    inner join iblis.specimen_types on `specimen_types`.`id` = `specimens`.`specimen_type_id`
+    inner join iblis.specimen_statuses on `specimen_statuses`.`id` = `specimens`.`specimen_status_id`
+    right join iblis.test_results on `test_results`.`test_id` = `tests`.`id`
+    right join iblis.measures on `measures`.`id` = `test_results`.`measure_id`
+    right join iblis.measure_ranges on `measure_ranges`.`measure_id` = `measures`.`id`
+    where `patients`.`deleted_at` is null and `specimens`.`tracking_number` = '#{tracking_number}' and  `patients`.`external_patient_number` = '#{external_patient_number}' and `measure_ranges`.`deleted_at` 
+    is null group by(`measure_ranges`.`measure_id`) order by time_completed asc ;
+    ")
+    data
+end
+def get_user_details(user_id)
+  data = query("SELECT * FROM iblis.users where id = #{user_id};")
+  data
+end
+############################################# start connection to lims database  ######################################################
+      def query(sql)
+        Rails.logger.debug(sql.to_s)
+        result = mysql.query(sql)
+     end
+
+      def mysql
+        # self.initialize
+        return mysql_connection if mysql_connection
+
+        connection = Mysql2::Client.new(host: settings['headers']['host'],
+                                        username: settings['headers']['username'],
+                                        password: settings['headers']['password'],
+                                        port: settings['headers']['port'],
+                                        database: settings['headers']['database'],
+                                        reconnect: true)
+        self.mysql_connection = connection
+      end
+
+      def mysql_connection=(connection)
+        @mysql_connection_pool = connection
+      end
+
+      def mysql_connection
+        @mysql_connection_pool
+      end
+############################################# end connection to lims database  ######################################################
+    end
+  end
+end

data/app/services/emr_ohsp_interface/emr_ohsp_interface_service.rb

@@ -180,6 +180,106 @@ module EmrOhspInterface
         return collection
       end
 
+      def generate_hmis_15_report(start_date=nil,end_date=nil)
+
+        diag_map = settings["hmis_15_map"]
+    
+        #pull the data
+        type = EncounterType.find_by_name 'Outpatient diagnosis'
+        collection = {}
+    
+        special_indicators = ["Malaria - new cases (under 5)",
+          "Malaria - new cases (5 & over)",
+          "HIV confirmed positive (15-49 years) new cases"
+        ]
+    
+        diag_map.each do |key,value|
+          options = {"ids"=>nil}
+          concept_ids = ConceptName.where(name: value).collect{|cn| cn.concept_id}
+    
+          if !special_indicators.include?(key)
+            data = Encounter.where('encounter_datetime BETWEEN ? AND ?
+            AND encounter_type = ? AND value_coded IN (?)
+            AND concept_id IN(6543, 6542)',
+            start_date.to_date.strftime('%Y-%m-%d 00:00:00'),
+            end_date.to_date.strftime('%Y-%m-%d 23:59:59'),type.id,concept_ids).\
+            joins('INNER JOIN obs ON obs.encounter_id = encounter.encounter_id
+            INNER JOIN person p ON p.person_id = encounter.patient_id').\
+            select('encounter.encounter_type, obs.value_coded, p.*')
+    
+            # #under_five
+            # under_five = data.select{|record| calculate_age(record["birthdate"]) < 5}.\
+            #             collect{|record| record.person_id}
+            # options["<5yrs"] = under_five
+            # #above 5 years
+            # over_five = data.select{|record| calculate_age(record["birthdate"]) >=5 }.\
+            #             collect{|record| record.person_id}
+    
+            # options[">=5yrs"] =  over_five
+    
+            all = data.collect{|record| record.person_id}
+    
+    
+            options["ids"] = all
+    
+            collection[key] = options
+          else
+            if key.eql?("Malaria - new cases (under 5)")
+              data = Encounter.where('encounter_datetime BETWEEN ? AND ?
+              AND encounter_type = ? AND value_coded IN (?)
+              AND concept_id IN(6543, 6542)',
+              start_date.to_date.strftime('%Y-%m-%d 00:00:00'),
+              end_date.to_date.strftime('%Y-%m-%d 23:59:59'),type.id,concept_ids).\
+              joins('INNER JOIN obs ON obs.encounter_id = encounter.encounter_id
+              INNER JOIN person p ON p.person_id = encounter.patient_id').\
+              select('encounter.encounter_type, obs.value_coded, p.*')
+    
+              under_five = data.select{|record| calculate_age(record["birthdate"]) < 5 }.\
+                            collect{|record| record["person_id"]}
+    
+              options["ids"] = under_five
+    
+              collection[key] = options
+    
+            end
+    
+            if key.eql?("Malaria - new cases (5 & over)")
+              data = Encounter.where('encounter_datetime BETWEEN ? AND ?
+              AND encounter_type = ? AND value_coded IN (?)
+              AND concept_id IN(6543, 6542)',
+              start_date.to_date.strftime('%Y-%m-%d 00:00:00'),
+              end_date.to_date.strftime('%Y-%m-%d 23:59:59'),type.id,concept_ids).\
+              joins('INNER JOIN obs ON obs.encounter_id = encounter.encounter_id
+              INNER JOIN person p ON p.person_id = encounter.patient_id').\
+              select('encounter.encounter_type, obs.value_coded, p.*')
+    
+              over_and_five = data.select{|record| calculate_age(record["birthdate"])  >= 5 }.\
+                            collect{|record| record["person_id"]}
+    
+              options["ids"] = over_and_five
+    
+              collection[key] = options
+            end
+    
+            if key.eql?("HIV confirmed positive (15-49 years) new cases")
+              data =  ActiveRecord::Base.connection.select_all(
+                "SELECT * FROM temp_earliest_start_date
+                  WHERE date_enrolled BETWEEN '#{start_date}' AND '#{end_date}'
+                  AND date_enrolled = earliest_start_date
+                  GROUP BY patient_id" ).to_hash
+    
+              over_and_15_49 = data.select{|record| calculate_age(record["birthdate"])  >= 15 && calculate_age(record["birthdate"]) <=49 }.\
+                     collect{|record| record["patient_id"]}
+    
+              options["ids"] = over_and_15_49
+    
+              collection[key] = options
+            end
+        end
+        end
+         collection
+      end
+
       # helper menthod
       def months_generator
           months = Hash.new

data/config/routes.rb

@@ -1,7 +1,9 @@
 EmrOhspInterface::Engine.routes.draw do
-    resources :radiology, path: 'api/v1/emr_ohsp_interface'      
+    resources :emr_lims_interface, path: 'api/v1/emr_lims_interface'
+    get '/get_lims_user', to: 'emr_lims_interface#get_user_info'
     get '/get_weeks', to: 'emr_ohsp_interface#weeks_generator'
     get '/get_months', to: 'emr_ohsp_interface#months_generator'
     get '/generate_weekly_idsr_report', to: 'emr_ohsp_interface#generate_weekly_idsr_report'
     get '/generate_monthly_idsr_report', to: 'emr_ohsp_interface#generate_monthly_idsr_report'
+    get '/generate_hmis_15_report', to: 'emr_ohsp_interface#generate_hmis_15_report'
 end

data/lib/emr_ohsp_interface/version.rb

@@ -1,3 +1,3 @@
 module EmrOhspInterface
-  VERSION = '0.3.0'
+  VERSION = '0.5.2'
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: emr_ohsp_interface
 version: !ruby/object:Gem::Version
-  version: 0.3.0
+  version: 0.5.2
 platform: ruby
 authors:
-- Justin Manda
+- Justin Manda and Petros Kayange
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2021-09-19 00:00:00.000000000 Z
+date: 2022-01-06 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rails
@@ -74,7 +74,7 @@ dependencies:
         version: '0'
 description: 
 email:
-- justinmandah@gmail.com
+- justinmandah@gmail.com, kayangepetros@gmail.com
 executables: []
 extensions: []
 extra_rdoc_files: []
@@ -86,11 +86,13 @@ files:
 - app/assets/javascripts/emr_ohsp_interface/application.js
 - app/assets/stylesheets/emr_ohsp_interface/application.css
 - app/controllers/emr_ohsp_interface/application_controller.rb
+- app/controllers/emr_ohsp_interface/emr_lims_interface_controller.rb
 - app/controllers/emr_ohsp_interface/emr_ohsp_interface_controller.rb
 - app/helpers/emr_ohsp_interface/application_helper.rb
 - app/jobs/emr_ohsp_interface/application_job.rb
 - app/mailers/emr_ohsp_interface/application_mailer.rb
 - app/models/emr_ohsp_interface/application_record.rb
+- app/services/emr_ohsp_interface/emr_lims_interface_service.rb
 - app/services/emr_ohsp_interface/emr_ohsp_interface_service.rb
 - app/views/layouts/emr_ohsp_interface/application.html.erb
 - config/routes.rb
@@ -118,9 +120,9 @@ required_rubygems_version: !ruby/object:Gem::Requirement
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubygems_version: 3.0.8
+rubygems_version: 3.2.32
 signing_key: 
 specification_version: 4
-summary: This in a gem that facilitates interfacing of EMR and One Health Surveillance
-  Platform
+summary: This in a gem that facilitates interfacing of EMR, One Health Surveillance
+  Platform and Lims
 test_files: []