emr_ohsp_interface 0.1.0

checksums.yaml

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data/MIT-LICENSE

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+Copyright 2021 petroskayange
+
+Permission is hereby granted, free of charge, to any person obtaining
+a copy of this software and associated documentation files (the
+"Software"), to deal in the Software without restriction, including
+without limitation the rights to use, copy, modify, merge, publish,
+distribute, sublicense, and/or sell copies of the Software, and to
+permit persons to whom the Software is furnished to do so, subject to
+the following conditions:
+
+The above copyright notice and this permission notice shall be
+included in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
+LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
+OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
+WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

data/README.md

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+# EmrOhspInterface
+Short description and motivation.
+
+## Usage
+How to use my plugin.
+
+## Installation
+Add this line to your application's Gemfile:
+
+```ruby
+gem 'emr_ohsp_interface'
+```
+
+And then execute:
+```bash
+$ bundle
+```
+
+Or install it yourself as:
+```bash
+$ gem install emr_ohsp_interface
+```
+
+## Contributing
+Contribution directions go here.
+
+## License
+The gem is available as open source under the terms of the [MIT License](https://opensource.org/licenses/MIT).

data/Rakefile

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+begin
+  require 'bundler/setup'
+rescue LoadError
+  puts 'You must `gem install bundler` and `bundle install` to run rake tasks'
+end
+
+require 'rdoc/task'
+
+RDoc::Task.new(:rdoc) do |rdoc|
+  rdoc.rdoc_dir = 'rdoc'
+  rdoc.title    = 'EmrOhspInterface'
+  rdoc.options << '--line-numbers'
+  rdoc.rdoc_files.include('README.md')
+  rdoc.rdoc_files.include('lib/**/*.rb')
+end
+
+APP_RAKEFILE = File.expand_path("test/dummy/Rakefile", __dir__)
+load 'rails/tasks/engine.rake'
+
+load 'rails/tasks/statistics.rake'
+
+require 'bundler/gem_tasks'
+
+require 'rake/testtask'
+
+Rake::TestTask.new(:test) do |t|
+  t.libs << 'test'
+  t.pattern = 'test/**/*_test.rb'
+  t.verbose = false
+end
+
+task default: :test

data/app/assets/config/emr_ohsp_interface_manifest.js

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+//= link_directory ../javascripts/emr_ohsp_interface .js
+//= link_directory ../stylesheets/emr_ohsp_interface .css

data/app/assets/javascripts/emr_ohsp_interface/application.js

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+// This is a manifest file that'll be compiled into application.js, which will include all the files
+// listed below.
+//
+// Any JavaScript/Coffee file within this directory, lib/assets/javascripts, vendor/assets/javascripts,
+// or any plugin's vendor/assets/javascripts directory can be referenced here using a relative path.
+//
+// It's not advisable to add code directly here, but if you do, it'll appear at the bottom of the
+// compiled file. JavaScript code in this file should be added after the last require_* statement.
+//
+// Read Sprockets README (https://github.com/rails/sprockets#sprockets-directives) for details
+// about supported directives.
+//
+//= require rails-ujs
+//= require activestorage
+//= require_tree .

data/app/assets/stylesheets/emr_ohsp_interface/application.css

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+/*
+ * This is a manifest file that'll be compiled into application.css, which will include all the files
+ * listed below.
+ *
+ * Any CSS and SCSS file within this directory, lib/assets/stylesheets, vendor/assets/stylesheets,
+ * or any plugin's vendor/assets/stylesheets directory can be referenced here using a relative path.
+ *
+ * You're free to add application-wide styles to this file and they'll appear at the bottom of the
+ * compiled file so the styles you add here take precedence over styles defined in any other CSS/SCSS
+ * files in this directory. Styles in this file should be added after the last require_* statement.
+ * It is generally better to create a new file per style scope.
+ *
+ *= require_tree .
+ *= require_self
+ */

data/app/controllers/emr_ohsp_interface/application_controller.rb

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+module EmrOhspInterface
+  class ApplicationController < ActionController::Base
+    protect_from_forgery with: :exception
+  end
+end

data/app/controllers/emr_ohsp_interface/emr_OHSP_interface_controller.rb

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+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/helpers/emr_ohsp_interface/application_helper.rb

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+module EmrOhspInterface
+  module ApplicationHelper
+  end
+end

data/app/jobs/emr_ohsp_interface/application_job.rb

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+module EmrOhspInterface
+  class ApplicationJob < ActiveJob::Base
+  end
+end

data/app/mailers/emr_ohsp_interface/application_mailer.rb

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+module EmrOhspInterface
+  class ApplicationMailer < ActionMailer::Base
+    default from: 'from@example.com'
+    layout 'mailer'
+  end
+end

data/app/models/emr_ohsp_interface/application_record.rb

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+module EmrOhspInterface
+  class ApplicationRecord < ActiveRecord::Base
+    self.abstract_class = true
+  end
+end

data/app/services/emr_ohsp_interface/emr_OHSP_interface_service.rb

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+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

data/app/views/layouts/emr_ohsp_interface/application.html.erb

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+<!DOCTYPE html>
+<html>
+<head>
+  <title>Emr ohsp interface</title>
+  <%= csrf_meta_tags %>
+  <%= csp_meta_tag %>
+
+  <%= stylesheet_link_tag    "emr_ohsp_interface/application", media: "all" %>
+  <%= javascript_include_tag "emr_ohsp_interface/application" %>
+</head>
+<body>
+
+<%= yield %>
+
+</body>
+</html>

data/config/routes.rb

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+EmrOhspInterface::Engine.routes.draw do
+    resources :radiology, path: 'api/v1/emr_ohsp_interface'      
+    get '/get_weeks', to: 'emr_ohsp_interface#weeks_generator'
+    get '/get_months', to: 'emr_ohsp_interface#months_generator'
+end

data/lib/emr_ohsp_interface/engine.rb

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+module EmrOhspInterface
+  class Engine < ::Rails::Engine
+    isolate_namespace EmrOhspInterface
+  end
+end

data/lib/emr_ohsp_interface/version.rb

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+module EmrOhspInterface
+  VERSION = '0.1.0'
+end

data/lib/emr_ohsp_interface.rb

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+require "emr_ohsp_interface/engine"
+
+module EmrOhspInterface
+  # Your code goes here...
+end

data/lib/tasks/emr_ohsp_interface_tasks.rake

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+# desc "Explaining what the task does"
+# task :emr_ohsp_interface do
+#   # Task goes here
+# end

metadata

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+--- !ruby/object:Gem::Specification
+name: emr_ohsp_interface
+version: !ruby/object:Gem::Version
+  version: 0.1.0
+platform: ruby
+authors:
+- Justin Manda
+autorequire: 
+bindir: bin
+cert_chain: []
+date: 2021-09-14 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: rails
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 5.2.4
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 5.2.4.3
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 5.2.4
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 5.2.4.3
+- !ruby/object:Gem::Dependency
+  name: rspec
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '3.0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '3.0'
+- !ruby/object:Gem::Dependency
+  name: rest-client
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1'
+- !ruby/object:Gem::Dependency
+  name: mysql2
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0'
+description: 
+email:
+- justinmandah@gmail.com
+executables: []
+extensions: []
+extra_rdoc_files: []
+files:
+- MIT-LICENSE
+- README.md
+- Rakefile
+- app/assets/config/emr_ohsp_interface_manifest.js
+- 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/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/views/layouts/emr_ohsp_interface/application.html.erb
+- config/routes.rb
+- lib/emr_ohsp_interface.rb
+- lib/emr_ohsp_interface/engine.rb
+- lib/emr_ohsp_interface/version.rb
+- lib/tasks/emr_ohsp_interface_tasks.rake
+homepage: https://github.com/LUKEINTERNATIONAL/emr_OHSP_interface
+licenses:
+- MIT
+metadata:
+  homepage_uri: https://github.com/LUKEINTERNATIONAL/emr_OHSP_interface
+post_install_message: 
+rdoc_options: []
+require_paths:
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: '0'
+required_rubygems_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: '0'
+requirements: []
+rubygems_version: 3.0.8
+signing_key: 
+specification_version: 4
+summary: This in a gem that facilitates interfacing of EMR and One Health Surveillance
+  Platform
+test_files: []