emr_ohsp_interface 2.2.3 → 2.2.5

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: 6ca9634e36555a67204142daadaef5e7c15c390654d5481ee41c753c8b040e33
-  data.tar.gz: f12fa09bf6867abff6f52e31902989b6d16cb5938644fc2095417186c48074d3
+  metadata.gz: c1e2f8f301b8057aed4f7ddb6e62eefd3c8108171cd949d5c329134ccae53c66
+  data.tar.gz: aa4515b396f441535ba766eb68ea0c71ea481f42f285dd457b7f1520fecb9bc8
 SHA512:
-  metadata.gz: bb7b7599d5c501e5784b5ee039df5eb04f4c8b417aaf9049648436e2d67d1b435d6b9cfd4c63e4b007c6db410f1f712e5387e4731a512daed54f820b1f5a3d83
-  data.tar.gz: 076bee885a2a2c8634ac7a81676be77dd32f2b7d8acf459b10163e3de435ada2de4885492d00f2c43cb9de8bde517021a26b22f57105b4fcd5202d9982666cd7
+  metadata.gz: a5e32307d05ce57d5badf73902fe312b1944ac66be0caa055da6dc05123c9219e63e6c9288fe85edd03069ace7c4c750557454a1cee16542a407e87ee00185c8
+  data.tar.gz: 9faf563358135620f679014461235bcfb05df09e7337e343746da1117bdaf3ea475133ae05b1282359d3f6f03fd791919af4b74fa713ba513fec113f26450482

data/app/controllers/emr_ohsp_interface/emr_ohsp_interface_controller.rb

@@ -5,7 +5,15 @@ class EmrOhspInterface::EmrOhspInterfaceController < ::ApplicationController
 
     def months_generator
         render json: service.months_generator();
-    end  
+    end
+
+    def quarters_generator
+        render json: service.quarters_generator
+    end
+
+    def generate_quarterly_idsr_report
+        render json: service.generate_quarterly_idsr_report(params[:request],params[:start_date],params[:end_date]);
+    end
 
     def generate_weekly_idsr_report
         render json: service.generate_weekly_idsr_report(params[:request],params[:start_date],params[:end_date]);

data/app/services/emr_ohsp_interface/emr_ohsp_interface_service.rb

@@ -6,6 +6,8 @@ module EmrOhspInterface
       require 'csv'
       require 'rest-client'
       require 'json'
+      include EmrOhspInterface::Utils
+
       def settings
         file = File.read(Rails.root.join("db","idsr_metadata","idsr_ohsp_settings.json"))
         config = JSON.parse(file)
@@ -102,6 +104,106 @@ module EmrOhspInterface
         return collection
       end
 
+      def generate_quarterly_idsr_report(request=nil,start_date=nil,end_date=nil)
+        epi_month = quarters_generator.first.first.strip
+        start_date = quarters_generator.first.last[1].split("to").first.strip if start_date.nil?
+        end_date =  quarters_generator.first.last[1].split("to").last.strip if end_date.nil?
+        indicators = [
+          'Diabetes Mellitus',
+          'Cervical Cancer',
+          'Hypertension',
+          'Onchocerciasis',
+          'Trachoma',
+          'Lymphatic Filariasis',
+          'Tuberculosis',
+          'Trypanosomiasis',
+          'Epilepsy',
+          'Depression',
+          'Suicide',
+          'Psychosis'
+        ]
+
+        diagnosis_concepts = ['Primary Diagnosis','Secondary Diagnosis']
+        encounters = ['OUTPATIENT DIAGNOSIS','ADMISSION DIAGNOSIS']
+
+        report_struct = indicators.each_with_object({}) do |indicator, report|
+          report[indicator.downcase] = ['<5 yrs','>=5 yrs'].each_with_object({}) do |group, sub_report|
+            sub_report[group] = {
+              outpatient_cases: [],
+              inpatient_cases: [],
+              inpatient_cases_death: [],
+              tested_malaria: [],
+              tested_positive_malaria: []
+            }
+          end
+        end
+
+        diagonised = ActiveRecord::Base.connection.select_all <<~SQL
+          SELECT
+            e.patient_id,
+            p.birthdate,
+            d.name diagnosis,
+            et.name visit_type
+          FROM
+            encounter e
+          INNER JOIN
+            obs ON obs.encounter_id = e.encounter_id
+          INNER JOIN
+            person p ON p.person_id = e.patient_id
+          INNER JOIN concept_name d ON d.concept_id = obs.value_coded
+          INNER JOIN 
+            encounter_type et ON et.encounter_type_id = e.encounter_type
+          WHERE
+            e.encounter_type IN (#{EncounterType.where(name: encounters).pluck(:encounter_type_id).join(',')})
+            AND DATE(e.encounter_datetime) > '#{start_date}'
+            AND DATE(e.encounter_datetime) < '#{end_date}'
+            AND obs.concept_id IN (#{ConceptName.where(name: diagnosis_concepts).pluck(:concept_id).join(',')})
+            AND obs.value_coded IN (#{ConceptName.where(name: indicators).pluck(:concept_id).join(',')})
+          GROUP BY
+            p.person_id, obs.concept_id
+        SQL
+
+        malaria_tests = lab_results(test_types: ['Malaria Screening'], start_date: start_date, end_date: end_date)
+
+        tested_patient_ids = malaria_tests.map{|patient| patient['patient_id']}
+
+        diagonised.each do |patient|
+          diagnosis = patient['diagnosis']&.downcase
+          visit_type = patient['visit_type']
+          patient_id = patient['patient_id']
+          birthdate = patient['birthdate']
+
+          five_plus = '>=5 yrs'
+          less_than_5 = '<5 yrs'
+
+          age_group = birthdate > 5.years.ago ? less_than_5 : five_plus
+          
+          report_struct[diagnosis][age_group][:outpatient_cases] << patient_id if visit_type == 'OUTPATIENT DIAGNOSIS'
+          report_struct[diagnosis][age_group][:inpatient_cases] << patient_id if visit_type == 'ADMISSION DIAGNOSIS'
+          report_struct[diagnosis][age_group][:tested_malaria] << patient_id if tested_patient_ids.include?(patient_id)
+          report_struct[diagnosis][age_group][:tested_positive_malaria] << patient_id if tested_positive(tested_patient_ids, patient)
+          report_struct[diagnosis][age_group][:inpatient_cases_death] << patient_id if admitted_patient_died(patient)
+        end
+        
+        report_struct
+          
+      end
+
+      def tested_positive(ids, patient)
+        patient_id = patient['patient_id']
+        return false unless ids.include?(patient_id)
+
+        results = malaria_tests.find{|test| test['patient_id'] == patient_id}['results']
+        ['positive', 'parasites seen'].include?(results)
+      end
+
+      def admitted_patient_died(patient)
+        visit_type = patient['visit_type']
+        dead = patient['dead']
+
+        visit_type == 'ADMISSION DIAGNOSIS' && dead
+      end
+
       #idsr monthly report
       def generate_monthly_idsr_report(request=nil,start_date=nil,end_date=nil)
         diag_map = settings["monthly_idsr_map"]
@@ -443,8 +545,13 @@ module EmrOhspInterface
       end
 
       def generate_hmis_17_report(start_date=nil,end_date=nil)
+
         diag_map = settings["hmis_17_map"]
+    
+        #pull the data
+        type = EncounterType.find_by_name 'Outpatient diagnosis'
         collection = {}
+    
         special_indicators = [
           "Referals from other institutions",
           "OPD total attendance",
@@ -452,68 +559,124 @@ module EmrOhspInterface
           "Malaria 5 years and older - new",
           "HIV/AIDS - new"
         ]
+
         special_under_five_indicators = [
           "Measles under five years - new",
           "Pneumonia under 5 years- new",
           "Dysentery under 5 years - new",
           "Diarrhoea non - bloody -new cases (under5)",
-          "Malaria under 5 years - new",
-          "Acute respiratory infections U5 - new"
+          "Malaria under 5 years - new"
         ]
 
-        
-        reg_data = registration_report(start_date,end_date)
-       
-        data =Observation.where(Arel.sql("obs_datetime BETWEEN '#{start_date.to_date.strftime('%Y-%m-%d 00:00:00')}' AND '#{end_date.to_date.strftime('%Y-%m-%d 23:59:59')}' AND c.voided = 0 AND obs.concept_id IN (6543, 6542) "))\
-                          .joins(Arel.sql('INNER JOIN concept_name c ON c.concept_id = obs.value_coded
-          INNER JOIN person p ON p.person_id = obs.person_id'))\
-                          .pluck(Arel.sql("c.name, CASE WHEN  (SELECT timestampdiff(year, birthdate, '#{end_date.to_date.strftime('%Y-%m-%d')}')) >= 5 THEN 'more_than_5'
-          ELSE 'less_than_5' END AS age_group,p.person_id")).group_by(&:shift)
+        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) && !special_under_five_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.*')
+    
+            all = data.collect{|record| record.person_id}
+    
+    
+            options["ids"] = all
+    
+            collection[key] = options
+          else
+            if key.eql?("Referals from other institutions") 
+              _type = EncounterType.find_by_name 'PATIENT REGISTRATION'
+              visit_type = ConceptName.find_by_name 'Type of visit'
+      
+              data = Encounter.where('encounter_datetime BETWEEN ? AND ?
+              AND encounter_type = ? AND value_coded IS NOT NULL
+              AND obs.concept_id = ?', start_date.to_date.strftime('%Y-%m-%d 00:00:00'),
+              end_date.to_date.strftime('%Y-%m-%d 23:59:59'),_type.id, visit_type.concept_id).\
+              joins('INNER JOIN obs ON obs.encounter_id = encounter.encounter_id
+              INNER JOIN person p ON p.person_id = encounter.patient_id
+              INNER JOIN concept_name c ON c.concept_id = 6541').\
+              select('encounter.encounter_type, obs.value_coded, obs.obs_datetime, p.*, c.name visit_type').\
+              group('p.person_id, encounter.encounter_id')
 
+              all = data.collect{|record| record.person_id}
+    
+              options["ids"] = all
+      
+              collection[key] = options
+            end
 
-          diag_map.each do |key, value|
-            collection[key] = { "ids" => [] }
             if key.eql?("OPD total attendance")
-              collection[key]["ids"] = reg_data.map { |item| item[1] }
-            else
-              if key.eql?("Referals from other institutions")
-                reg_data = reg_data.rows.group_by(&:shift)
-                collection[key]["ids"]= reg_data['Referral'] ? reg_data['Referral'].flatten : []
-              end
+              programID = Program.find_by_name 'OPD Program'
+              data = Encounter.find_by_sql(
+                "SELECT patient_id, DATE_FORMAT(encounter_datetime,'%Y-%m-%d') enc_date
+                FROM encounter e
+                LEFT OUTER JOIN person p ON p.person_id = e.patient_id
+                WHERE e.voided = 0 AND encounter_datetime BETWEEN '" + start_date.to_date.strftime('%Y-%m-%d 00:00:00') +"'
+                  AND '" + end_date.to_date.strftime('%Y-%m-%d 23:59:59') + "'
+                  AND program_id ='" + programID.program_id.to_s + "'
+                GROUP BY enc_date"
+              ).map{|e| e. patient_id}
+        
+              options["ids"] = data
+              collection[key] = options
             end
-            data.each do |phrase, counts|
-              next unless value.include?(phrase)
-            
-              counts.each do |label, count|
-                if !key.eql?("Malaria 5 years and older - new") && !special_under_five_indicators.include?(key)
-                  collection[key]["ids"] << count
-                else
-                  if ((special_under_five_indicators.include?(key) && label.eql?("less_than_5")) ||
-                      (key.eql?("Malaria 5 years and older - new") && label.eql?("more_than_5")))
-                    collection[key]["ids"] << count
-                  end
-                end
-              end
+
+            if key.eql?("Referal to other institutions")
+              data = Observation.where("obs_datetime BETWEEN ? AND ?
+              AND concept_id = ?",start_date.to_date.strftime('%Y-%m-%d 00:00:00'),
+              end_date.to_date.strftime('%Y-%m-%d 23:59:59'),'7414').\
+              joins('LEFT JOIN location l ON l.location_id = obs.value_text').\
+              select('obs.person_id').order('obs_datetime DESC')
+              all = data.collect{|record| record.person_id}
+              options["ids"] = all
+              collection[key] = options
+            end
+
+            if key.eql?("HIV/AIDS - new")
+              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" )
+              all = data.collect{|record| record["patient_id"]}
+              options["ids"] = all
+              collection[key] = options
+            end
+
+            if key.eql?("Measles under five years - new")
+              collection[key] = disaggregate('less',concept_ids, start_date, end_date, type)
+            end
+
+            if key.eql?("Pneumonia under 5 years- new")
+              collection[key] = disaggregate('less', concept_ids, start_date, end_date, type)
+            end
+
+            if key.eql?("Malaria under 5 years - new")
+              collection[key] = disaggregate('less', concept_ids, start_date, end_date, type)
+            end
+
+            if key.eql?("Malaria 5 years and older - new")
+              collection[key] = disaggregate('greater',concept_ids, start_date, end_date, type)
+            end
+
+            if key.eql?("Dysentery under 5 years - new")
+              collection[key] = disaggregate('less', concept_ids, start_date, end_date, type)
+            end
+
+            if key.eql?("Diarrhoea non - bloody -new cases (under5)")
+              collection[key] = disaggregate('less', concept_ids, start_date, end_date, type)
             end
+
           end
-          collection
-      end
+        end
+
+        collection
 
-      def registration_report(start_date=nil,end_date=nil)
-        ActiveRecord::Base.connection.select_all <<~SQL
-        SELECT
-        MIN(IFNULL(c.name, 'Unidentified')) AS visit_type,
-          obs.person_id
-          FROM `encounter`
-          LEFT JOIN obs ON obs.encounter_id = encounter.encounter_id AND obs.voided = 0
-          LEFT JOIN concept_name c ON c.concept_id = obs.value_coded 
-          AND c.name IN ('New patient','Revisiting','Referral') AND c.voided = 0
-          WHERE
-              encounter.voided = 0
-              AND  DATE(encounter_datetime) BETWEEN '#{start_date}' AND '#{end_date}'
-              AND encounter.program_id = 14 -- OPD program
-          GROUP BY encounter.patient_id, DATE(encounter_datetime);
-        SQL
       end
 
       def generate_notifiable_disease_conditions_report(start_date=nil,end_date=nil)
@@ -571,6 +734,25 @@ module EmrOhspInterface
           return months.to_a
       end
 
+      def quarters_generator
+        quarters = Hash.new
+
+        to_quarter = Proc.new do |date|
+          ((date.month - 1) / 3) + 1
+        end
+
+        init_quarter = Date.today.beginning_of_year - 2.years
+
+        while init_quarter <= Date.today do
+          quarter = init_quarter.strftime("%Y")+" Q"+to_quarter.call(init_quarter).to_s
+          dates = "#{(init_quarter.beginning_of_quarter).to_s} to #{(init_quarter.end_of_quarter).to_s}"
+          quarters[quarter] = dates
+          init_quarter = init_quarter + 3.months
+        end
+
+        return quarters.to_a
+      end
+
       # helper menthod
       def weeks_generator
 
@@ -719,4 +901,4 @@ module EmrOhspInterface
     end
   end
 
-end
+end

data/app/services/emr_ohsp_interface/utils.rb

@@ -0,0 +1,31 @@
+module EmrOhspInterface
+    module Utils
+        def lab_results(test_types:, start_date:, end_date:)
+            test_type_ids = ConceptName.where(name: test_types).pluck(:concept_id)
+
+            ActiveRecord::Base.connection.select_all <<~SQL
+                SELECT lab.patient_id,
+                   tt.name,
+                   COALESCE(result.value_numeric, result.value_text,
+                           result.value_coded) AS results
+                FROM orders
+                        INNER JOIN encounter lab ON lab.patient_id = orders.patient_id
+                    AND lab.encounter_datetime >= '#{start_date}'
+                    AND lab.encounter_datetime <= '#{end_date}'
+                    AND lab.program_id = #{Program.find_by_name('OPD Program').program_id}
+                    AND lab.voided = 0
+                    AND orders.voided = 0
+                        INNER JOIN obs test_type ON test_type.encounter_id = lab.encounter_id
+                    AND test_type.concept_id = #{ConceptName.find_by_name('Test type').concept_id}
+                    AND test_type.value_coded IN (#{test_type_ids.join(', ')})
+                        INNER JOIN concept_name tt ON tt.concept_id = test_type.value_coded
+                        INNER JOIN obs tr ON tr.order_id = orders.order_id
+                    AND tr.voided = 0
+                    AND tr.concept_id = #{ConceptName.find_by_name('Lab test result').concept_id}
+                    AND tr.obs_group_id = test_type.obs_id
+                        INNER JOIN obs result ON result.obs_group_id = tr.obs_id
+                GROUP BY lab.patient_id
+              SQL
+        end
+    end
+end

data/config/routes.rb

@@ -4,6 +4,7 @@ EmrOhspInterface::Engine.routes.draw do
     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_quarterly_idsr_report', to: 'emr_ohsp_interface#generate_quarterly_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'
     get '/generate_hmis_17_report', to: 'emr_ohsp_interface#generate_hmis_17_report'
@@ -12,8 +13,10 @@ EmrOhspInterface::Engine.routes.draw do
     get 'api/v1/get_lims_user', to: 'emr_lims_interface#get_user_info'
     get 'api/v1/get_weeks', to: 'emr_ohsp_interface#weeks_generator'
     get 'api/v1/get_months', to: 'emr_ohsp_interface#months_generator'
+    get 'api/v1/get_quarters', to: 'emr_ohsp_interface#quarters_generator'
     get 'api/v1/generate_weekly_idsr_report', to: 'emr_ohsp_interface#generate_weekly_idsr_report'
     get 'api/v1/generate_monthly_idsr_report', to: 'emr_ohsp_interface#generate_monthly_idsr_report'
+    get 'api/v1/generate_quarterly_idsr_report', to: 'emr_ohsp_interface#generate_quarterly_idsr_report'
     get 'api/v1/generate_hmis_15_report', to: 'emr_ohsp_interface#generate_hmis_15_report'
     get 'api/v1/generate_hmis_17_report', to: 'emr_ohsp_interface#generate_hmis_17_report'
 end

data/lib/emr_ohsp_interface/version.rb

@@ -1,3 +1,3 @@
 module EmrOhspInterface
-  VERSION = '2.2.3'
+  VERSION = '2.2.5'
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: emr_ohsp_interface
 version: !ruby/object:Gem::Version
-  version: 2.2.3
+  version: 2.2.5
 platform: ruby
 authors:
 - Justin Manda, Petros Kayange, Dominic Kasanga
-autorequire: 
+autorequire:
 bindir: bin
 cert_chain: []
-date: 2024-05-11 00:00:00.000000000 Z
+date: 2025-01-20 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rails
@@ -86,7 +86,7 @@ dependencies:
     - - "~>"
       - !ruby/object:Gem::Version
         version: '1.3'
-description: 
+description:
 email:
 - justinmandah@gmail.com, kayangepetros@gmail.com, dominickasanga@gmail.com
 executables: []
@@ -108,6 +108,7 @@ files:
 - 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/services/emr_ohsp_interface/utils.rb
 - app/views/layouts/emr_ohsp_interface/application.html.erb
 - config/routes.rb
 - lib/emr_ohsp_interface.rb
@@ -119,7 +120,7 @@ licenses:
 - MIT
 metadata:
   homepage_uri: https://github.com/LUKEINTERNATIONAL/emr_OHSP_interface
-post_install_message: 
+post_install_message:
 rdoc_options: []
 require_paths:
 - lib
@@ -135,7 +136,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
       version: '0'
 requirements: []
 rubygems_version: 3.4.1
-signing_key: 
+signing_key:
 specification_version: 4
 summary: This in a gem that facilitates interfacing of EMR, One Health Surveillance
   Platform and Lims