emr_ohsp_interface 1.0.1 → 1.2.0

checksums.yaml

@@ -1,7 +1,7 @@
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data/MIT-LICENSE

@@ -1,4 +1,4 @@
-Copyright 2021 petroskayange
+Copyright 2022 petroskayange, dominickasanga
 
 Permission is hereby granted, free of charge, to any person obtaining
 a copy of this software and associated documentation files (the

data/app/controllers/emr_ohsp_interface/emr_ohsp_interface_controller.rb

@@ -18,6 +18,10 @@ class EmrOhspInterface::EmrOhspInterfaceController < ::ApplicationController
     def generate_hmis_15_report
         render json: service.generate_hmis_15_report(params[:start_date],params[:end_date]);
     end
+
+    def generate_hmis_17_report
+        render json: service.generate_hmis_17_report(params[:start_date],params[:end_date]);
+    end
    
     def service
         EmrOhspInterface::EmrOhspInterfaceService

data/app/services/emr_ohsp_interface/emr_ohsp_interface_service.rb

@@ -11,6 +11,10 @@ module EmrOhspInterface
         config = JSON.parse(file)
       end
 
+      def server_config
+        config =YAML.load_file("#{Rails.root}/config/application.yml")
+      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)
@@ -129,11 +133,11 @@ module EmrOhspInterface
 
               #under_five
               under_five = data.select{|record| calculate_age(record["birthdate"]) < 5}.\
-                          collect{|record| record.person_id}
+                          collect{|record| record.person_id}.uniq
               options["<5yrs"] = under_five
               #above 5 years
               over_five = data.select{|record| calculate_age(record["birthdate"]) >=5 }.\
-                          collect{|record| record.person_id}
+                          collect{|record| record.person_id}.uniq
 
               options[">=5yrs"] =  over_five
 
@@ -267,7 +271,10 @@ module EmrOhspInterface
     
         special_indicators = ["Malaria - new cases (under 5)",
           "Malaria - new cases (5 & over)",
-          "HIV confirmed positive (15-49 years) new cases"
+          "HIV confirmed positive (15-49 years) new cases",
+          "Diarrhoea non - bloody -new cases (under5)",
+          "Malnutrition - new case (under 5)",
+          "Acute respiratory infections - new cases (U5)"
         ]
     
         diag_map.each do |key,value|
@@ -317,7 +324,6 @@ module EmrOhspInterface
               options["ids"] = under_five
     
               collection[key] = options
-    
             end
     
             if key.eql?("Malaria - new cases (5 & over)")
@@ -352,11 +358,225 @@ module EmrOhspInterface
     
               collection[key] = options
             end
+
+            if key.eql?("Diarrhoea non - bloody -new cases (under5)")
+              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?("Malnutrition - new case (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?("Acute respiratory infections - new cases (U5)")
+              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
+
         end
         end
          collection
       end
 
+      def disaggregate(disaggregate_key, concept_ids, start_date, end_date, type)
+        options = {"ids"=>nil}
+        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.*')
+
+        if disaggregate_key == "less"
+        options["ids"] = data.select{|record| calculate_age(record["birthdate"]) < 5 }.\
+        collect{|record| record["person_id"]}
+        else 
+          if disaggregate_key == "greater"
+            options["ids"] = data.select{|record| calculate_age(record["birthdate"]) >= 5 }.\
+            collect{|record| record["person_id"]}
+          end
+        end
+
+        options
+      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",
+          "Referal to other institutions",
+          "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"
+        ]
+
+        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
+
+            if key.eql?("OPD total attendance")
+              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
+
+            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" ).to_hash
+              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
+        end
+
+        collection
+
+      end
+
       def generate_notifiable_disease_conditions_report(start_date=nil,end_date=nil)
         diag_map = settings["notifiable_disease_conditions"]
 
@@ -416,7 +636,7 @@ module EmrOhspInterface
       def weeks_generator
 
         weeks = Hash.new
-        first_day = ((Date.today.year.to_s)+"-01-01").to_date
+        first_day = (Date.today - (11).month).at_beginning_of_month
         wk_of_first_day = first_day.cweek
 
         if wk_of_first_day > 1
@@ -455,7 +675,7 @@ module EmrOhspInterface
       def send_data(data,type)
         # method used to post data to the server
         #prepare payload here
-        conn = settings["headers"]
+        conn = server_config['ohsp']
         payload = {
           "dataSet" =>get_data_set_id(type),
           "period"=>(type.eql?("weekly") ? weeks_generator.last[0] : months_generator.first[0]),
@@ -517,18 +737,18 @@ module EmrOhspInterface
                                             headers:{'Content-Type'=> 'application/json'},
                                             payload: payload.to_json,
                                             #headers: {accept: :json},
-                                            user: conn["user"],
-                                            password: conn["pass"])
+                                            user: conn["username"],
+                                            password: conn["password"])
 
         puts send
       end
 
       def send_data_to_sms_portal(data, concept_name_collection)
-        conn2 = settings["sms_server"]
+        conn2 = server_config['idsr_sms']
         data = data.select {|k,v| v.select {|kk,vv| vv.length > 0}.length > 0}
         payload = {
-          "email"=> conn2["user"],
-          "password" => conn2["pass"],
+          "email"=> conn2["username"],
+          "password" => conn2["password"],
           "emr_facility_id" => Location.current_health_center.id,
           "emr_facility_name" => Location.current_health_center.name,
           "payload" => data,

data/config/routes.rb

@@ -6,6 +6,7 @@ EmrOhspInterface::Engine.routes.draw do
     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'
+    get '/generate_hmis_17_report', to: 'emr_ohsp_interface#generate_hmis_17_report'
 
     # for the new crossplatform OPD system
     get 'api/v1/get_lims_user', to: 'emr_lims_interface#get_user_info'
@@ -14,4 +15,5 @@ EmrOhspInterface::Engine.routes.draw do
     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_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 = '1.0.1'
+  VERSION = '1.2.0'
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: emr_ohsp_interface
 version: !ruby/object:Gem::Version
-  version: 1.0.1
+  version: 1.2.0
 platform: ruby
 authors:
-- Justin Manda and Petros Kayange
+- Justin Manda, Petros Kayange, and Dominic Kasanga
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2022-04-11 00:00:00.000000000 Z
+date: 2023-01-15 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rails
@@ -72,9 +72,29 @@ dependencies:
     - - "~>"
       - !ruby/object:Gem::Version
         version: '0'
+- !ruby/object:Gem::Dependency
+  name: sqlite3
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 1.3.6
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.3'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 1.3.6
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.3'
 description: 
 email:
-- justinmandah@gmail.com, kayangepetros@gmail.com
+- justinmandah@gmail.com, kayangepetros@gmail.com, dominickasanga@gmail.com
 executables: []
 extensions: []
 extra_rdoc_files: []
@@ -120,7 +140,8 @@ required_rubygems_version: !ruby/object:Gem::Requirement
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubygems_version: 3.0.9
+rubyforge_project: 
+rubygems_version: 2.7.6
 signing_key: 
 specification_version: 4
 summary: This in a gem that facilitates interfacing of EMR, One Health Surveillance