emr_ohsp_interface 0.1.0 → 0.5.0

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

@@ -0,0 +1,21 @@
+class EmrOhspInterface::EmrOhspInterfaceController < ::ApplicationController
+    def weeks_generator
+        render json: service.weeks_generator();
+    end   
+
+    def months_generator
+        render json: service.months_generator();
+    end  
+
+    def generate_weekly_idsr_report
+        render json: service.generate_weekly_idsr_report(params[:request],params[:start_date],params[:end_date]);
+    end 
+    
+    def generate_monthly_idsr_report
+        render json: service.generate_monthly_idsr_report(params[:request],params[:start_date],params[:end_date]);
+    end
+   
+    def service
+        EmrOhspInterface::EmrOhspInterfaceService
+    end
+end

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

@@ -0,0 +1,312 @@
+require "emr_ohsp_interface/version"
+
+module EmrOhspInterface
+  module EmrOhspInterfaceService
+    class << self
+      require 'csv'
+      require 'rest-client'
+      def settings
+        file = File.read(Rails.root.join("db","idsr_metadata","idsr_ohsp_settings.json"))
+        config = JSON.parse(file)
+      end
+
+      def get_ohsp_facility_id
+        file = File.open(Rails.root.join("db","idsr_metadata","emr_ohsp_facility_map.csv"))
+        data = CSV.parse(file,headers: true)
+        emr_facility_id = Location.current_health_center.id
+        facility = data.select{|row| row["EMR_Facility_ID"].to_i == emr_facility_id}
+        ohsp_id = facility[0]["OrgUnit ID"]
+      end
+
+      def get_ohsp_de_ids(de,type)
+        #this method returns an array ohsp report line ids
+        result = []
+        #["waoQ016uOz1", "r1AT49VBKqg", "FPN4D0s6K3m", "zE8k2BtValu"]
+        #  ds,              de_id     ,  <5yrs       ,  >=5yrs
+        puts de
+        if type == "weekly"
+        file = File.open(Rails.root.join("db","idsr_metadata","idsr_weekly_ohsp_ids.csv"))
+        else
+        file = File.open(Rails.root.join("db","idsr_metadata","idsr_monthly_ohsp_ids.csv"))
+        end
+        data = CSV.parse(file,headers: true)
+        row = data.select{|row| row["Data Element Name"].strip.downcase.eql?(de.downcase.strip)}
+        ohsp_ds_id = row[0]["Data Set ID"]
+        result << ohsp_ds_id
+        ohsp_de_id = row[0]["UID"]
+        result << ohsp_de_id
+        option1 = row[0]["<5Yrs"]
+        result << option1
+        option2 = row[0][">=5Yrs"]
+        result << option2
+
+        return result
+      end
+
+      def get_data_set_id(type)
+        if type == "weekly"
+          file = File.open(Rails.root.join("db","idsr_metadata","idsr_weekly_ohsp_ids.csv"))
+        else
+          file = File.open(Rails.root.join("db","idsr_metadata","idsr_monthly_ohsp_ids.csv"))
+        end
+        data = CSV.parse(file,headers: true)
+        data_set_id = data.first["Data Set ID"]
+      end
+
+      def generate_weekly_idsr_report(request=nil,start_date=nil,end_date=nil)
+
+        diag_map = settings["weekly_idsr_map"]
+
+        epi_week = weeks_generator.last.first.strip
+        start_date = weeks_generator.last.last.split("to")[0].strip if start_date.nil?
+        end_date = weeks_generator.last.last.split("to")[1].strip if end_date.nil?
+
+        #pull the data
+        type = EncounterType.find_by_name 'Outpatient diagnosis'
+        collection = {}
+
+        diag_map.each do |key,value|
+          options = {"<5yrs"=>nil,">=5yrs"=>nil}
+          concept_ids = ConceptName.where(name: value).collect{|cn| cn.concept_id}
+
+          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
+
+          collection[key] = options
+        end
+          if request == nil
+           response = send_data(collection,"weekly")
+          end
+        return collection
+      end
+      #idsr monthly report
+
+      def generate_monthly_idsr_report(request=nil,start_date=nil,end_date=nil)
+        diag_map = settings["monthly_idsr_map"]
+        epi_month = months_generator.first.first.strip
+        start_date = months_generator.first.last[1].split("to").first.strip if start_date.nil?
+        end_date =  months_generator.first.last[1].split("to").last.strip if end_date.nil?
+        type = EncounterType.find_by_name 'Outpatient diagnosis'
+        collection = {}
+
+        special_indicators = ["Malaria in Pregnancy","HIV New Initiated on ART"]
+
+        diag_map.each do |key,value|
+          options = {"<5yrs"=>nil,">=5yrs"=>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
+
+              collection[key] = options
+          else
+            if key.eql?("Malaria in Pregnancy")
+              mal_patient_id = 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.*')
+
+              mal_patient_id=   mal_patient_id.collect{|record| record.person_id}
+              #find those that are pregnant
+              preg = Observation.where(["concept_id = 6131 AND obs_datetime
+                                         BETWEEN ? AND ? AND person_id IN(?)
+                                          AND value_coded =1065",
+                                          start_date.to_date.strftime('%Y-%m-%d 00:00:00'),
+                                          end_date.to_date.strftime('%Y-%m-%d 23:59:59'),mal_patient_id ])
+
+               options[">=5yrs"] =   preg.collect{|record| record.person_id} rescue 0
+               collection[key] = options
+            end
+
+            if key.eql?("HIV New Initiated on ART")
+             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
+
+              under_five = data.select{|record| calculate_age(record["birthdate"]) < 5 }.\
+                             collect{|record| record["patient_id"]}
+
+              over_five = data.select{|record| calculate_age(record["birthdate"]) >=5 }.\
+                             collect{|record| record["patient_id"]}
+
+              options["<5yrs"] = under_five
+              options[">=5yrs"] =  over_five
+
+              collection[key] = options
+            end
+          end
+        end
+          if request == nil
+           response = send_data(collection,"monthly")
+          end
+        return collection
+      end
+
+      # helper menthod
+      def months_generator
+          months = Hash.new
+          count = 1
+          curr_date = Date.today
+          while count < 13 do
+              curr_date = curr_date - 1.month
+              months[curr_date.strftime("%Y%m")] = [curr_date.strftime("%B-%Y"),\
+                                        (curr_date.beginning_of_month.to_s+" to " + curr_date.end_of_month.to_s)]
+              count +=  1
+          end
+          return months.to_a
+      end
+
+      # helper menthod
+      def weeks_generator
+
+        weeks = Hash.new
+        first_day = ((Date.today.year.to_s)+"-01-01").to_date
+        wk_of_first_day = first_day.cweek
+
+        if wk_of_first_day > 1
+          wk = first_day.prev_year.year.to_s+"W"+wk_of_first_day.to_s
+          dates = "#{(first_day-first_day.wday+1).to_s} to #{((first_day-first_day.wday+1)+6).to_s}"
+          weeks[wk] = dates
+        end
+
+        #get the firt monday of the year
+        while !first_day.monday? do
+          first_day = first_day+1
+        end
+        first_monday = first_day
+        #generate week numbers and date ranges
+
+        while first_monday <= Date.today do
+            wk = (first_monday.year).to_s+"W"+(first_monday.cweek).to_s
+            dates =  "#{first_monday.to_s} to #{(first_monday+6).to_s}"
+            #add to the hash
+            weeks[wk] = dates
+            #step by week
+            first_monday += 7
+        end
+      #remove the last week
+      this_wk = (Date.today.year).to_s+"W"+(Date.today.cweek).to_s
+      weeks = weeks.delete_if{|key,value| key==this_wk}
+
+      return weeks.to_a
+      end
+
+      #Age calculator
+      def calculate_age(dob)
+        age = ((Date.today-dob.to_date).to_i)/365 rescue 0
+      end
+
+      def send_data(data,type)
+        # method used to post data to the server
+        #prepare payload here
+        conn = settings["headers"]
+        payload = {
+          "dataSet" =>get_data_set_id(type),
+          "period"=>(type.eql?("weekly") ? weeks_generator.last[0] : months_generator.first[0]),
+          "orgUnit"=> get_ohsp_facility_id,
+          "dataValues"=> []
+        }
+         special = ["Severe Pneumonia in under 5 cases","Malaria in Pregnancy",
+                   "Underweight Newborns < 2500g in Under 5 Cases","Diarrhoea In Under 5"]
+
+        data.each do |key,value|
+          if !special.include?(key)
+              option1 =  {"dataElement"=>get_ohsp_de_ids(key,type)[1],
+                          "categoryOptionCombo"=> get_ohsp_de_ids(key,type)[2],
+                          "value"=>value["<5yrs"].size }
+
+              option2 = {"dataElement"=>get_ohsp_de_ids(key,type)[1],
+                          "categoryOptionCombo"=> get_ohsp_de_ids(key,type)[3],
+                          "value"=>value[">=5yrs"].size}
+
+            #fill data values array
+              payload["dataValues"] << option1
+              payload["dataValues"] << option2
+          else
+              case key
+                when special[0]
+                  option1 =  {"dataElement"=>get_ohsp_de_ids(key,type)[1],
+                              "categoryOptionCombo"=> get_ohsp_de_ids(key,type)[2],
+                              "value"=>value["<5yrs"].size }
+
+                  payload["dataValues"] << option1
+                when special[1]
+                  option2 = {"dataElement"=>get_ohsp_de_ids(key,type)[1],
+                              "categoryOptionCombo"=> get_ohsp_de_ids(key,type)[3],
+                              "value"=>value[">=5yrs"].size }
+
+                  payload["dataValues"] << option2
+                when special[2]
+                  option1 =  {"dataElement"=>get_ohsp_de_ids(key,type)[1],
+                              "categoryOptionCombo"=> get_ohsp_de_ids(key,type)[2],
+                              "value"=>value["<5yrs"].size }
+
+                  payload["dataValues"] << option1
+                when special[3]
+                  option1 =  {"dataElement"=>get_ohsp_de_ids(key,type)[1],
+                              "categoryOptionCombo"=> get_ohsp_de_ids(key,type)[2],
+                              "value"=>value["<5yrs"].size}
+
+                  payload["dataValues"] << option1
+              end
+          end
+        end
+
+        puts "now sending these values: #{payload.to_json}"
+        url = "#{conn["url"]}/api/dataValueSets"
+        puts url
+        puts "pushing #{type} IDSR Reports"
+        send = RestClient::Request.execute(method: :post,
+                                            url: url,
+                                            headers:{'Content-Type'=> 'application/json'},
+                                            payload: payload.to_json,
+                                            #headers: {accept: :json},
+                                            user: conn["user"],
+                                            password: conn["pass"])
+
+        puts send
+      end
+
+    end
+  end
+
+
+end

data/config/routes.rb

@@ -1,5 +1,8 @@
 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'
 end

data/lib/emr_ohsp_interface/version.rb

@@ -1,3 +1,3 @@
 module EmrOhspInterface
-  VERSION = '0.1.0'
+  VERSION = '0.5.0'
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: emr_ohsp_interface
 version: !ruby/object:Gem::Version
-  version: 0.1.0
+  version: 0.5.0
 platform: ruby
 authors:
-- Justin Manda
+- Justin Manda and Petros Kayange
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2021-09-14 00:00:00.000000000 Z
+date: 2021-12-02 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: []
@@ -86,12 +86,14 @@ 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_OHSP_interface_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_OHSP_interface_service.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
 - lib/emr_ohsp_interface.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: []

data/app/controllers/emr_ohsp_interface/emr_OHSP_interface_controller.rb

@@ -1,12 +0,0 @@
-class EmrOHSPInterface::EmrOHSPInterfaceController < ::ApplicationController
-    def weeks_generator
-        render json: service.weeks_generator();
-    end   
-    def months_generator
-        render json: service.months_generator();
-    end
-   
-    def service
-        EmrOHSPInterface::EmrOHSPInterfaceService
-    end
-end

data/app/services/emr_ohsp_interface/emr_OHSP_interface_service.rb

@@ -1,196 +0,0 @@
-require "emr_OHSP_interface/version"
-
-module EmrOHSPInterface
-  module EmrOHSPInterfaceService
-    class << self
-      require 'csv'
-      require 'rest-client'
-      def settings
-        file = File.read(Rails.root.join("db","idsr_metadata","idsr_ohsp_settings.json"))
-        config = JSON.parse(file)
-      end
-
-      def get_ohsp_facility_id
-        file = File.open(Rails.root.join("db","idsr_metadata","emr_ohsp_facility_map.csv"))
-        data = CSV.parse(file,headers: true)
-        emr_facility_id = Location.current_health_center.id
-        facility = data.select{|row| row["EMR_Facility_ID"].to_i == emr_facility_id}
-        ohsp_id = facility[0]["OrgUnit ID"]
-      end
-
-      def get_ohsp_de_ids(de,type)
-        #this method returns an array ohsp report line ids
-        result = []
-        #["waoQ016uOz1", "r1AT49VBKqg", "FPN4D0s6K3m", "zE8k2BtValu"]
-        #  ds,              de_id     ,  <5yrs       ,  >=5yrs
-        if type == "weekly"
-        file = File.open(Rails.root.join("db","idsr_metadata","idsr_weekly_ohsp_ids.csv"))
-        else
-        file = File.open(Rails.root.join("db","idsr_metadata","idsr_monthly_ohsp_ids.csv"))
-        end
-        data = CSV.parse(file,headers: true)
-        row = data.select{|row| row["Data Element Name"].strip.downcase.eql?(de.downcase)}
-        ohsp_ds_id = row[0]["Data Set ID"]
-        result << ohsp_ds_id
-        ohsp_de_id = row[0]["UID"]
-        result << ohsp_de_id
-        option1 = row[0]["<5Yrs"]
-        result << option1
-        option2 = row[0][">=5Yrs"]
-        result << option2
-
-        return result
-      end
-
-      def get_data_set_id(type)
-        if type == "weekly"
-          file = File.open(Rails.root.join("db","idsr_metadata","idsr_weekly_ohsp_ids.csv"))
-        else
-          file = File.open(Rails.root.join("db","idsr_metadata","idsr_monthly_ohsp_ids.csv"))
-        end
-        data = CSV.parse(file,headers: true)
-        data_set_id = data.first["Data Set ID"]
-      end
-
-      def generate_weekly_idsr_report()
-
-        diag_map = settings["weekly_idsr_map"]
-
-        epi_week = weeks_generator.last.first.strip
-        start_date = weeks_generator.last.last.split("to")[0].strip
-        end_date = weeks_generator.last.last.split("to")[1].strip
-
-        #pull the data
-        type = EncounterType.find_by_name 'Outpatient diagnosis'
-        collection = {}
-
-        diag_map.each do |key,value|
-          options = {"<5yrs"=>nil,">=5yrs"=>nil}
-          concept_ids = ConceptName.where(name: value).collect{|cn| cn.concept_id}
-
-          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
-
-          collection[key] = options
-        end
-
-        response = send_data(collection,"weekly")
-      end
-
-      def generate_monthly_idsr_report()
-      end
-
-      # helper menthod
-      def months_generator
-          months = Hash.new
-          count = 1
-          curr_date = Date.today
-          while count < 13 do
-              curr_date = curr_date - 1.month
-              months[curr_date.strftime("%Y%m")] = [curr_date.strftime("%B-%Y"),\
-                                        (curr_date.beginning_of_month.to_s+" to " + curr_date.end_of_month.to_s)]
-              count +=  1
-          end
-          return months.to_a
-      end
-
-      # helper menthod
-      def weeks_generator
-
-        weeks = Hash.new
-        first_day = ((Date.today.year.to_s)+"-01-01").to_date
-        wk_of_first_day = first_day.cweek
-
-        if wk_of_first_day > 1
-          wk = first_day.prev_year.year.to_s+"W"+wk_of_first_day.to_s
-          dates = "#{(first_day-first_day.wday+1).to_s} to #{((first_day-first_day.wday+1)+6).to_s}"
-          weeks[wk] = dates
-        end
-
-        #get the firt monday of the year
-        while !first_day.monday? do
-          first_day = first_day+1
-        end
-        first_monday = first_day
-        #generate week numbers and date ranges
-
-        while first_monday <= Date.today do
-            wk = (first_monday.year).to_s+"W"+(first_monday.cweek).to_s
-            dates =  "#{first_monday.to_s} to #{(first_monday+6).to_s}"
-            #add to the hash
-            weeks[wk] = dates
-            #step by week
-            first_monday += 7
-        end
-      #remove the last week
-      this_wk = (Date.today.year).to_s+"W"+(Date.today.cweek).to_s
-      weeks = weeks.delete_if{|key,value| key==this_wk}
-
-      return weeks.to_a
-      end
-
-      #Age calculator
-      def calculate_age(dob)
-        age = ((Date.today-dob.to_date).to_i)/365 rescue 0
-      end
-
-      def send_data(data,type)
-        # method used to post data to the server
-        #prepare payload here
-        conn = settings["headers"]
-        payload = {
-          "dataSet" =>get_data_set_id(type),
-          "period"=>(type.eql?("weekly") ? weeks_generator.last[0] : months_generator.first[0]),
-          "orgUnit"=> get_ohsp_facility_id,
-          "dataValues"=> []
-        }
-
-        data.each do |key,value|
-            option1 =  {"dataElement"=>get_ohsp_de_ids(key,type)[1],
-                        "categoryOptionCombo"=> get_ohsp_de_ids(key,type)[2],
-                        "value"=>value["<5yrs"].size }
-
-            option2 = {"dataElement"=>get_ohsp_de_ids(key,type)[1],
-                        "categoryOptionCombo"=> get_ohsp_de_ids(key,type)[3],
-                        "value"=>value[">=5yrs"].size}
-
-        #fill data values array
-          payload["dataValues"] << option1
-          payload["dataValues"] << option2
-        end
-
-        puts "now sending these values: #{payload.to_s}"
-        url = "#{conn["url"]}/api/dataValueSets"
-        puts url
-        send = RestClient::Request.execute(method: :post,
-                                            url: url,
-                                            headers:{'Content-Type'=> 'application/json'},
-                                            payload: payload.to_json,
-                                            #headers: {accept: :json},
-                                            user: conn["user"],
-                                            password: conn["pass"])
-
-        puts send
-      end
-
-    end
-  end
-
-
-end