roqua-healthy 1.0.0

checksums.yaml

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+---
+SHA1:
+  metadata.gz: 55deed92d3c485a1be152d296ee2811252f48947
+  data.tar.gz: 1203252d41c3fb84053d04f0d01a3668fa8ed70f
+SHA512:
+  metadata.gz: 47599a271bec411480ccd2be7d7ec53e4e55e9baa04d82ccd6e40cfcdc40224910ac2a62ab26a690d03d4ac0b6dcc5243c547b70e6f4f583922a1c639d5ba680
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data/.document

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+- 
+ChangeLog.md
+LICENSE.txt

data/.gitignore

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+.idea
+.yardoc
+Gemfile.lock
+doc/
+pkg/
+tmp/
+vendor/cache/*.gem
+tmp/rspec_guard_result

data/.rspec

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+--colour --format progress

data/.rubocop.yml

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+# This configuration was generated by `rubocop --auto-gen-config`.
+# The point is for the user to remove these configuration records
+# one by one as the offences are removed from the code base.
+
+AllCops:
+  Excludes:
+    - vendor/**
+
+Documentation:
+  Enabled: false
+
+LineLength:
+  Enabled: false
+
+Encoding:
+  Enabled: false
+
+StringLiterals:
+  Enabled: false
+
+SpaceInsideHashLiteralBraces:
+  EnforcedStyle: no_space
+
+MethodLength:
+  Max: 20
+
+FinalNewline:
+  Enabled: False
+
+SignalException:
+  Enabled: False

data/.yardopts

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+--markup markdown --title "healthy Documentation" --protected

data/ChangeLog.md

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+### 1.0.0 / 2014-01-22
+
+* Released under the name 'roqua-healthy' to work around name collision on Rubygems.org.
+  This new name also makes it clearer that this gem is probably not very useful to others.
+  Note that everything is now nested under the Roqua::Healthy module instead of Healthy.
+
+### 0.1.0 / 2013-09-24
+
+* Initial release:
+

data/Gemfile

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+source 'https://rubygems.org'
+
+gemspec
+
+# Only add dependencies here if they're only used by CI or other services.
+# Normal development dependencies should go in the gemspec. People shouldn't
+# need to use bundler to develop on our gem.
+gem "codeclimate-test-reporter", group: :test, require: nil

data/Guardfile

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+guard 'rspec', cmd: 'bundle exec rspec -f Fuubar' do
+  watch(%r{^spec/.+_spec\.rb$})
+  watch(%r{^lib/healthy/(.+)\.rb$}) { |m| ["spec/unit/#{m[1]}_spec.rb", "spec/integration"] }
+  watch('spec/spec_helper.rb')  { "spec" }
+  watch(%r{^spec/fixtures/([^_]+)_.*.xml}) { |m| "spec/integration/#{m[1]}_spec.rb" }
+end
+
+guard :rubocop do
+  watch(%r{.+\.rb$})
+  watch(%r{(?:.+/)?\.rubocop\.yml$}) { |m| File.dirname(m[0]) }
+end

data/LICENSE.txt

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+Copyright (c) 2013 Marten Veldthuis
+
+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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+# Healthy [![Code Climate](https://codeclimate.com/repos/524944dd56b10217490074e8/badges/5dd696b69c4614c83c2d/gpa.png)](https://codeclimate.com/repos/524944dd56b10217490074e8/feed) [![CircleCi](https://circleci.com/gh/roqua/healthy.png?circle-token=ece8f36798b00bc8659d5c76f720b22693d6600a)](https://circleci.com/gh/roqua/healthy)
+
+## Patient details aka QRY\^A19
+
+### Usage
+
+```ruby
+Healthy::A19.fetch(patient_identifier)
+```
+
+### Adding integration tests
+
+If you find any A19 response that Healthy currently does not handle correctly, please add a fixture and integration test for it.
+
+* `curl --data "method=A19&application=healthy&patient_id=7767853" "http://10.20.11.100:60401"`
+* Paste the resulting XML into a new file in `spec/fixtures`. Name this after the specific thing that is different, prefixed with the originating EPD. Don't name this after a specific organization, this repository is open-sourced and our customers might not want to be named publicly here.
+* Please run it through an XML pretty printer like `xmllint --format` to get indented output.
+* **<blink>Remove/sanitize/anonymize the XML file where needed.</blink>** We can't do this automatically with a script, because having a script normalize e.g. all names to "Voornaam Achternaam" would defeat the entire point of having multiple fixtures to show the different styles of names we can encounter.
+* Add an integration spec example that uses it and checks all currently returned values.
+
+### Manually trying out parsing of a given record
+
+There are two helpers in `bin`: `get_xml_for_patient` and `parse_local_xml`. The first one takes a patient number and ip+port on the mirth machine, and gets the XML from there. The second parses a chunk of XML from either standard input or a given file.
+
+These two commands are then chained together by `bin/get`:
+
+`bin/get 7767853 10.20.11.100:60201`
+
+## Copyright
+
+Copyright (c) 2013 Marten Veldthuis. Publicly available under an MIT license. See [LICENSE.txt](https://github.com/roqua/healthy/blob/master/LICENSE.txt) for details.

data/Rakefile

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+# encoding: utf-8
+
+require 'rubygems'
+
+begin
+  require 'bundler'
+rescue LoadError => e
+  warn e.message
+  warn "Run `gem install bundler` to install Bundler."
+  exit -1
+end
+
+begin
+  Bundler.setup(:development)
+rescue Bundler::BundlerError => e
+  warn e.message
+  warn "Run `bundle install` to install missing gems."
+  exit e.status_code
+end
+
+require 'rake'
+
+require 'rspec/core/rake_task'
+RSpec::Core::RakeTask.new
+
+task :test    => :spec
+task :default => :spec
+
+require "bundler/gem_tasks"
+
+require 'yard'
+YARD::Rake::YardocTask.new  
+task :doc => :yard

data/bin/get

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+#!/usr/bin/env ruby
+
+unless ARGV[0] && ARGV[1]
+  puts "Usage: get PATIENT_ID IP:PORT"
+  exit 1
+end
+
+exec "bin/get_xml_for_patient #{ARGV[0]} '#{ARGV[1]}' | ruby -Ilib bin/parse_local_xml"

data/bin/get_old_mirth_processing_result

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+#!/bin/bash
+
+COMMAND="curl --data \"method=A19&patient_id=$1\" \"http://$2\""
+XML=$(ssh x3mirth "$COMMAND")
+
+echo $XML | xmllint --format -

data/bin/get_xml_for_patient

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+#!/bin/bash
+
+COMMAND="curl --data \"method=A19&application=healthy&patient_id=$1\" \"http://$2\""
+XML=$(ssh x3mirth "$COMMAND")
+
+echo $XML | xmllint --format -

data/bin/parse_local_xml

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+#!/usr/bin/env ruby
+
+require 'healthy'
+require 'ap'
+
+body    = ARGF.read
+message = Hash.from_xml(body).fetch("HL7Message") { Hash.new }
+
+ap Healthy::A19::Transformer.new(message).to_patient

data/healthy.gemspec

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+# -*- encoding: utf-8 -*-
+
+require File.expand_path('../lib/roqua/healthy/version', __FILE__)
+
+Gem::Specification.new do |gem|
+  gem.name          = "roqua-healthy"
+  gem.version       = Roqua::Healthy::VERSION
+  gem.summary       = %q{Arranges communication between Mirth and RoQua}
+  gem.description   = %q{Receives queries from RoQua, sends them to Mirth, and translates Mirth's responses back into Rubyland.}
+  gem.license       = "MIT"
+  gem.authors       = ["Marten Veldthuis"]
+  gem.email         = "marten@roqua.nl"
+  gem.homepage      = "https://github.com/roqua/healthy"
+
+  gem.files         = `git ls-files`.split($/)
+  gem.executables   = gem.files.grep(%r{^bin/}).map{ |f| File.basename(f) }
+  gem.test_files    = gem.files.grep(%r{^(test|spec|features)/})
+  gem.require_paths = ['lib']
+
+  gem.add_dependency 'activesupport', '~> 3.2'
+  gem.add_dependency 'addressable', '~> 2.3'
+  gem.add_dependency 'roqua-support', '~> 0.1.0'
+
+  gem.add_development_dependency 'bundler', '~> 1.0'
+  gem.add_development_dependency 'rake', '~> 10.0'
+  gem.add_development_dependency 'rspec', '~> 3.0.0.beta1'
+  gem.add_development_dependency 'yard', '~> 0.8'
+
+  # Required for the tests
+  gem.add_development_dependency 'webmock', '~> 1.13'
+
+  # Workflow and tools
+  gem.add_development_dependency 'guard', '~> 2.1'
+  gem.add_development_dependency 'guard-rspec', '~> 4.2.4'
+  gem.add_development_dependency 'listen', '~> 2.1'
+  gem.add_development_dependency 'guard-rubocop', '~> 1.0.1'
+  gem.add_development_dependency 'rubocop', '~> 0.15'
+  gem.add_development_dependency 'fuubar'
+
+  # Documentation generation
+  gem.add_development_dependency 'kramdown', '1.2'
+end

data/lib/roqua/healthy/a19/address_parser.rb

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+module Roqua
+  module Healthy
+    module A19
+      class AddressParser
+        attr_reader :message
+
+        def initialize(message)
+          @message = message
+        end
+
+        def address_type
+          return nil unless record
+          record.fetch('PID.11.7')
+        end
+
+        def street
+          return nil unless record
+          record.fetch('PID.11.1').fetch('PID.11.1.1')
+        end
+
+        def city
+          return nil unless record
+          record.fetch('PID.11.3')
+        end
+
+        def zipcode
+          return nil unless record
+          record.fetch('PID.11.5')
+        end
+
+        def country
+          return nil unless record
+          record.fetch('PID.11.6')
+        end
+
+        def record
+          @record = nil
+          @record ||= message.fetch('PID').fetch('PID.11').find { |record| record.fetch('PID.11.7', :unknown_type_of_address_record) == 'M' }
+          @record ||= message.fetch('PID').fetch('PID.11').find { |record| record.fetch('PID.11.7', :unknown_type_of_address_record) == 'H' }
+          @record ||= message.fetch('PID').fetch('PID.11').find { |record| record.fetch('PID.11.7', :unknown_type_of_address_record) == 'L' }
+          @record
+        end
+      end
+    end
+  end
+end

data/lib/roqua/healthy/a19/cdis_name_parser.rb

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+require 'roqua/healthy/a19/name_parser'
+
+module Roqua
+  module Healthy
+    module A19
+      # The CDIS EPD returns names in a format different from most other EPD vendors.
+      # This parser overrides some methods that are affected by the differences.
+      class CdisNameParser < NameParser
+        def firstname
+          names[:legal].fetch('PID.5.2')
+        end
+
+        def initials
+          names[:legal].fetch('PID.5.3')
+        end
+
+        def lastname
+          names[:legal].fetch('PID.5.1').fetch('PID.5.1.3')
+        end
+      end
+    end
+  end
+end

data/lib/roqua/healthy/a19/correct_patient_check.rb

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+module Roqua
+  module Healthy
+    module A19
+      class CorrectPatientCheck
+        attr_reader :patient_id, :record
+
+        def initialize(patient_id, record)
+          @patient_id = patient_id
+          @record     = record
+        end
+
+        def check
+          record[:identities].any? { |i| i[:ident] == patient_id }
+        end
+      end
+    end
+  end
+end

data/lib/roqua/healthy/a19/fetcher.rb

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+require 'net/http'
+require 'addressable/uri'
+
+require 'roqua/healthy/a19/response_validator'
+require 'roqua/healthy/a19/response_parser'
+
+module Roqua
+  module Healthy
+    module A19
+      class Fetcher
+        attr_reader :patient_id
+
+        def initialize(patient_id)
+          @patient_id = patient_id
+        end
+
+        def fetch
+          response = mirth_response
+          parser   = ResponseParser.new(response)
+
+          if ResponseValidator.new(response.code, parser, patient_id).validate
+            parser.fetch("HL7Message")
+          end
+        end
+
+        def mirth_response
+          Net::HTTP.start(remote_url.host, remote_url.port, use_ssl: use_ssl?) do |http|
+            request = Net::HTTP::Post.new(remote_url.path)
+            request.set_form_data(mirth_params)
+            http.request request
+          end
+        rescue ::Timeout::Error, Errno::ETIMEDOUT => error
+          raise ::Roqua::Healthy::Timeout, error.message
+        rescue Errno::EHOSTUNREACH => error
+          raise ::Roqua::Healthy::HostUnreachable, error.message
+        rescue Errno::ECONNREFUSED => error
+          raise ::Roqua::Healthy::ConnectionRefused, error.message
+        end
+
+        private
+
+        def mirth_params
+          {'method' => 'A19', 'patient_id' => patient_id.to_s, 'application' => "healthy"}
+        end
+
+        def use_ssl?
+          remote_url.port == 443 || remote_url.scheme == 'https'
+        end
+
+        def remote_url
+          return @remote_url if @remote_url
+
+          url = Addressable::URI.parse(Healthy.a19_endpoint)
+          url.path = "/"
+
+          @remote_url = URI.parse(url.to_s)
+        end
+      end
+    end
+  end
+end

data/lib/roqua/healthy/a19/name_parser.rb

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+module Roqua
+  module Healthy
+    module A19
+      class NameParser
+        attr_reader :message
+
+        def initialize(message)
+          @message = message
+        end
+
+        def firstname
+          return unless names[:nick]
+          names[:nick].fetch('PID.5.2')
+        end
+
+        def initials
+          "#{names[:legal].fetch('PID.5.2')} #{names[:legal].fetch('PID.5.3')}".strip
+        end
+
+        def lastname
+          prefix   = names[:legal].fetch('PID.5.1').fetch('PID.5.1.2')
+          lastname = names[:legal].fetch('PID.5.1').fetch('PID.5.1.3')
+          "#{prefix} #{lastname}".strip
+        end
+
+        def display_name
+          return unless names[:display]
+          names[:display].fetch('PID.5.1')
+        end
+
+        private
+
+        def names
+          names = {}
+          message.fetch('PID').fetch('PID.5').each do |record|
+            case record.fetch('PID.5.7', :unknown_type_of_name_record)
+            when 'L'
+              names[:legal] = record
+            when 'D'
+              names[:display] = record
+            when 'N'
+              names[:nick] = record
+            else
+              # ignore record
+            end
+          end
+          names
+        end
+      end
+    end
+  end
+end

data/lib/roqua/healthy/a19/response_parser.rb

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+require 'active_support/core_ext/hash/conversions'
+
+module Roqua
+  module Healthy
+    module A19
+      class ResponseParser
+        attr_reader :response
+
+        def initialize(response)
+          @response = response
+        end
+
+        def fetch(root)
+          parsed_body[root] || {}
+        end
+
+        private
+
+        def parsed_body
+          @parsed_body ||= Hash.from_xml(response.body)
+        rescue REXML::ParseException => e
+          raise IllegalMirthResponse, e.message
+        end
+      end
+    end
+  end
+end

data/lib/roqua/healthy/a19/response_validator.rb

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+require 'roqua/healthy/a19/response_parser'
+
+module Roqua
+  module Healthy
+    module A19
+      class ResponseValidator
+        attr_reader :response_code
+        attr_reader :parser
+        attr_reader :patient_id
+
+        def initialize(response_code, parser, patient_id)
+          @response_code = response_code
+          @parser        = parser
+          @patient_id    = patient_id
+        end
+
+        def validate
+          case response_code
+          when '200'
+            validate_200
+          when '500'
+            validate_500
+          else
+            raise ::Roqua::Healthy::UnknownFailure, "Unexpected HTTP response code #{response_code}."
+          end
+        end
+
+        def validate_200
+          failure = parser.fetch("HL7Message")
+          raise ::Roqua::Healthy::PatientNotFound if failure.key?("ERR") && failure.fetch("ERR").fetch("ERR.1").fetch("ERR.1.4").fetch("ERR.1.4.2") =~ /Patient \(@\) niet gevonden\(.*\)/
+          raise ::Roqua::Healthy::MirthErrors::WrongPatient if failure.key?('QRD') && failure.fetch("QRD").fetch("QRD.8").fetch("QRD.8.1") != patient_id
+          true
+        end
+
+        def validate_500
+          failure = parser.fetch("failure")
+          raise ::Roqua::Healthy::Timeout, failure["error"]           if failure["error"] == "Timeout waiting for ACK"
+          raise ::Roqua::Healthy::Timeout, failure["error"]           if failure["error"] == "Unable to connect to destination\tSocketTimeoutException\tconnect timed out"
+          raise ::Roqua::Healthy::ConnectionRefused, failure["error"] if failure["error"] == "Unable to connect to destination\tConnectException\tConnection refused"
+          raise ::Roqua::Healthy::UnknownFailure, failure["error"]
+        end
+      end
+    end
+  end
+end

data/lib/roqua/healthy/a19/transformer.rb

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+require 'roqua/healthy/a19/name_parser'
+require 'roqua/healthy/a19/cdis_name_parser'
+require 'roqua/healthy/a19/address_parser'
+
+module Roqua
+  module Healthy
+    module A19
+      class Transformer
+        attr_reader :message
+
+        def initialize(message)
+          @message = message
+          @message['PID']['PID.3']  = [@message.fetch('PID').fetch('PID.3')].flatten.compact
+          @message['PID']['PID.5']  = [@message.fetch('PID').fetch('PID.5')].flatten.compact
+          @message['PID']['PID.11'] = [@message.fetch('PID').fetch('PID.11')].flatten.compact
+          @message['PID']['PID.13'] = [@message.fetch('PID').fetch('PID.13')].flatten.compact
+          @message = MessageCleaner.new(@message).message
+        end
+
+        def to_patient
+          {
+            status:       status,
+            source:       source,
+            identities:   identities,
+            firstname:    name.firstname,
+            initials:     name.initials,
+            lastname:     name.lastname,
+            display_name: name.display_name,
+            email:        email,
+            address_type: address.address_type,
+            street:       address.street,
+            city:         address.city,
+            zipcode:      address.zipcode,
+            country:      address.country,
+            birthdate:    birthdate,
+            gender:       gender,
+            phone_cell:   phone_cell
+          }
+        end
+
+        def status
+          'SUCCESS'
+        end
+
+        def source
+          message.fetch('MSH').fetch('MSH.4').fetch('MSH.4.1')
+        end
+
+        def identities
+          message.fetch('PID').fetch('PID.3').map do |identity|
+            next if identity.fetch('PID.3.1').blank?
+            {ident: identity.fetch('PID.3.1'), authority: identity.fetch('PID.3.5')}
+          end.compact
+        end
+
+        def birthdate
+          birthdate_details = message.fetch('PID').fetch('PID.7')
+          birthdate_details.fetch('PID.7.1') if birthdate_details
+        end
+
+        def email
+          email_record = message.fetch('PID').fetch('PID.13').find do |record|
+            record.fetch('PID.13.2', :unknown_type_of_phone_record) == 'NET'
+          end
+          return nil unless email_record
+
+          email_address = email_record.fetch('PID.13.1', "")
+          email_address = email_record.fetch('PID.13.4', "") if email_address.blank?
+          email_address
+        end
+
+        def phone_cell
+          phone_cell_record = message.fetch('PID').fetch('PID.13').find do |record|
+            record.fetch('PID.13.2', :unknown_type_of_phone_record) == 'ORN'
+          end
+          return nil unless phone_cell_record
+
+          phone_cell_record.fetch('PID.13.1', "")
+        end
+
+        def gender
+          message.fetch('PID').fetch('PID.8').fetch('PID.8.1')
+        end
+
+        private
+
+        def name
+          case source
+          when "UMCG", "IMPULSE"
+            CdisNameParser.new(message)
+          else
+            NameParser.new(message)
+          end
+        end
+
+        def address
+          AddressParser.new(message)
+        end
+      end
+    end
+  end
+end

data/lib/roqua/healthy/a19.rb

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+module Roqua
+  module Healthy
+    module A19
+      extend ::Roqua::Logging
+
+      # Fetches a patient record given a `patient_id` and returns a hash containing
+      # the interesting information that was returned from an upstream `ADR^A19`
+      # response.
+      #
+      # @param  patient_id [String] the patient identifier
+      # @return [Hash] the patient details.
+      def self.fetch(patient_id)
+        eventlog.lifecycle('roqua.hl7.a19', patient_id: patient_id) do
+          message = Fetcher.new(patient_id).fetch
+          patient = Transformer.new(message).to_patient
+          patient
+        end
+      end
+    end
+  end
+end
+
+require_relative 'a19/fetcher'
+require_relative 'a19/transformer'
+require_relative 'a19/correct_patient_check'