hl7-exporter 0.0.1

checksums.yaml

@@ -0,0 +1,7 @@
+---
+SHA256:
+  metadata.gz: e2b3cd0e7fb20caf79caf410c300a4c809f71c6dc5827848e66d03ed32169813
+  data.tar.gz: b0b4e7378500b1b1928f89618f78dd9a3b403fa1634c9b4460ca7a0dcb175623
+SHA512:
+  metadata.gz: 289ca7eafc4ef48a48565e9d7c90a8ff7ccb736e34bbced39ef2f831ca768d5a568479c2fc0ca08a7778bc0ee96329e0055826a94f1925bb51ed23e0921b3802
+  data.tar.gz: 9d1600d1cc239ac200d7e9668048d9bb28763bea610a4a6a2400a2317c133f5f1fa79e222225e99f9c1c99468ce3157f524783a66de163d54e19caee146a2c54

data/.gitignore

@@ -0,0 +1,17 @@
+*.gem
+*.rbc
+.bundle
+.config
+.yardoc
+Gemfile.lock
+InstalledFiles
+_yardoc
+coverage
+doc/
+lib/bundler/man
+pkg
+rdoc
+spec/reports
+test/tmp
+test/version_tmp
+tmp

data/.rspec

@@ -0,0 +1 @@
+--color

data/.travis.yml

@@ -0,0 +1,16 @@
+branches:
+  only:
+    - master
+language: ruby
+matrix:
+  allow_failures:
+    - rvm: ruby-head
+rvm:
+  - 2.2.0
+  - 2.1.0
+  - 2.0.0
+  - 1.9.3
+  - ruby-head
+  - jruby-19mode # JRuby in 1.9 mode
+  - rbx-2.2
+bundler_args: --without ruby2

data/Gemfile

@@ -0,0 +1,10 @@
+source 'https://rubygems.org'
+
+# Specify your gem's dependencies in hl7-exporter.gemspec
+gemspec
+
+group :ruby2 do
+  gem 'byebug'
+  gem 'pry'
+  gem 'looksee'
+end

data/LICENSE.txt

@@ -0,0 +1,22 @@
+Copyright (c) 2015 Enrique Carlos Mogollan
+
+MIT License
+
+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

@@ -0,0 +1,47 @@
+# HL7::Exporter
+
+A simple library to export 'ruby-hl7' messages into different formats.
+
+## Installation
+
+Add this line to your application's Gemfile:
+
+    gem 'hl7-exporter'
+
+And then execute:
+
+    $ bundle
+
+Or install it yourself as:
+
+    $ gem install hl7-exporter
+
+## Usage
+
+```ruby
+cvs_exporter = HL7::Exporter::Csv
+message = HL7::Message.parse('hl7_file.dat')
+
+# In progress:
+cvs_exporter.export(message) # returns the data
+
+
+# Future implementation:
+cvs_exporter.export(message, template)
+
+# I'm also thinking about this one:
+json_exporter = HL7::Exporter::Json
+json_exporter.export(message)
+
+# Next goal after simple json is
+fhir_exporter = HL7::Exporter::Fhir
+fhir_exporter.export(message)
+```
+
+## Contributing
+
+1. Fork it ( http://github.com/ruby-hl7/hl7-exporter/fork )
+2. Create your feature branch (`git checkout -b my-new-feature`)
+3. Commit your changes (`git commit -am 'Add some feature'`)
+4. Push to the branch (`git push origin my-new-feature`)
+5. Create new Pull Request

data/Rakefile

@@ -0,0 +1,5 @@
+require "bundler/gem_tasks"
+
+require 'rspec/core/rake_task'
+RSpec::Core::RakeTask.new('spec')
+task :default => :spec

data/hl7-exporter.gemspec

@@ -0,0 +1,26 @@
+# coding: utf-8
+lib = File.expand_path('../lib', __FILE__)
+$LOAD_PATH.unshift(lib) unless $LOAD_PATH.include?(lib)
+require 'hl7/exporter/version'
+
+Gem::Specification.new do |spec|
+  spec.name          = "hl7-exporter"
+  spec.version       = HL7::Exporter::VERSION
+  spec.authors       = ["Enrique Carlos Mogollan"]
+  spec.email         = ["emogollan@gmail.com"]
+  spec.summary       = %q{A library to export messages from the ruby-hl7 gem}
+  spec.description   = %q{A simple library to export messages from the ruby-hl7 gem}
+  spec.homepage      = ""
+  spec.license       = "MIT"
+
+  spec.files         = `git ls-files -z`.split("\x0")
+  spec.executables   = spec.files.grep(%r{^bin/}) { |f| File.basename(f) }
+  spec.test_files    = spec.files.grep(%r{^(test|spec|features)/})
+  spec.require_paths = ["lib"]
+
+  spec.add_dependency "ruby-hl7", "~> 1.1.0"
+
+  spec.add_development_dependency "bundler", "~> 1.5"
+  spec.add_development_dependency "rake"
+  spec.add_development_dependency "rspec", "~> 3.5"
+end

data/lib/hl7-exporter.rb

@@ -0,0 +1,2 @@
+require "ruby-hl7"
+require "hl7/exporter"

data/lib/hl7/exporter.rb

@@ -0,0 +1,32 @@
+require_relative "exporter/version"
+require_relative "exporter/csv"
+require_relative "exporter/observation"
+require_relative "exporter/patient"
+
+
+module HL7
+  class Exporter
+    attr_reader :message
+
+    def initialize(message = nil)
+      self.message = message
+    end
+
+    def message=(msg)
+      if hl7? msg
+        @message = msg
+      else
+        @message = HL7::Message.parse msg
+      end
+    end
+
+    private
+    def hl7?(msg)
+      msg.respond_to? :to_hl7
+    end
+
+    def export
+      raise "Not implemented"
+    end
+  end
+end

data/lib/hl7/exporter/csv.rb

@@ -0,0 +1,65 @@
+module HL7
+  class Exporter::Csv < HL7::Exporter
+    attr_accessor :template
+
+    def export
+      template % data
+    end
+
+    def template
+      @template ||= default_template
+    end
+
+    private
+    def default_template
+%[Sending Facility: %{sending_facility}
+Name: %{patient_name}
+DOB: %{patient_dob}
+Nick: %{nick_name}
+Sex: %{sex}
+test, result, flag, units, reference interval
+%{test_results}
+]
+    end
+
+    def obr_row_template(observation)
+      "#{observation.name}, #{observation.result}, #{observation.flags}, " +
+      "#{observation.units}, #{observation.reference_range}"
+    end
+
+    def getDate(date)
+      Date.parse(date).strftime("%Y/%m/%d")
+    end
+
+    def sending_facility
+      return '' unless message[:MSH]
+      message[:MSH].sending_facility || ''
+    end
+
+    def test_results
+      message[:OBR].children.map{ |obr|
+        observation_row(obr)
+      }.join("\n")
+    end
+
+    def observation_row(obr)
+      observation = HL7::Exporter::Observation.new(obr)
+      obr_row_template(observation)
+    end
+
+    def patient
+      @patient ||= HL7::Exporter::Patient.new(message[:PID])
+    end
+
+    def data
+      {
+        sending_facility: sending_facility,
+        patient_name: patient.name,
+        patient_dob:  getDate(patient.dob),
+        nick_name:  patient.nick_name,
+        sex: patient.sex,
+        test_results: test_results,
+      }
+    end
+  end
+end

data/lib/hl7/exporter/observation.rb

@@ -0,0 +1,29 @@
+module HL7
+  class Exporter::Observation
+    attr_accessor :obr
+
+    def initialize(obr)
+      @obr = obr
+    end
+
+    def name
+      obr.observation_id.split('^')[1].sub(",","")
+    end
+
+    def result
+      obr.observation_value
+    end
+
+    def units
+      obr.units
+    end
+
+    def flags
+      obr.abnormal_flags
+    end
+
+    def reference_range
+      obr.references_range
+    end
+  end
+end

data/lib/hl7/exporter/patient.rb

@@ -0,0 +1,29 @@
+module HL7
+  class Exporter::Patient
+    def initialize(pid)
+      @pid_patient_name = pid.patient_name.split("^")
+      @pid_sex = pid.admin_sex
+      @pid_dob = pid.patient_dob
+    end
+
+    def name
+      "#{patient_data[1]} #{patient_data[0]}"
+    end
+
+    def nick_name
+      "#{patient_data[4]}"
+    end
+
+    def sex
+      @pid_sex ? 'Female' : 'Male'
+    end
+
+    def dob
+      @pid_dob
+    end
+
+    def patient_data
+      @patient_name_data ||= @pid_patient_name
+    end
+  end
+end

data/lib/hl7/exporter/version.rb

@@ -0,0 +1,5 @@
+module HL7
+  class Exporter
+    VERSION = "0.0.1"
+  end
+end

data/spec/example/test1.csv

@@ -0,0 +1,9 @@
+Sending Facility: TEST_LAB_INC
+Name: FirstName LastName
+DOB: 1976/02/28
+Nick: NickName
+Sex: Female
+test, result, flag, units, reference interval
+Cholesterol Total, 232, H, mg/dL, 100-199
+Triglycerides, 179, H, mg/dL, 0-149
+HDL Cholesterol, 40, , mg/dL, >39

data/spec/example/test1_custom_template.csv

@@ -0,0 +1,4 @@
+test, result, flag, units, reference interval
+Cholesterol Total, 232, H, mg/dL, 100-199
+Triglycerides, 179, H, mg/dL, 0-149
+HDL Cholesterol, 40, , mg/dL, >39

data/spec/example/test_1.hl7

@@ -0,0 +1,7 @@
+MSH|^~\&|SOURCE|TEST_LAB_INC|HEALTH|382715520|2014100914484648||ORU^R01|0129938170710091448|P|2.3|
+PID|1||333||LastName^FirstName^MiddleInitial^SR^NickName||19760228|F||2106-3^White^HL70005^CAUC^Caucasian^L||||||
+ORC|RE|35748030580^LAB|35748030580^LAB||||||201312240000|||FEDA^^^^^^^L
+OBR|1|35748030580^LAB|35748030580^LAB|221010^Lipid Panel w/ Chol/HDL Ratio^L|||201312230656|||||||201312240329||||||35748030580||201312241108|||F
+OBX|1|NM|001065^Cholesterol, Total^L^2093-3^Cholesterol^LN||232|mg/dL|100-199|H||N|F|20120910||201312241053|01
+OBX|2|NM|001172^Triglycerides^L^2571-8^Triglyceride^LN||179|mg/dL|0-149|H||N|F|20120910||201312241053|01
+OBX|3|NM|011817^HDL Cholesterol^L^2085-9^Cholesterol.in HDL^LN||40|mg/dL|>39|||N|F|20020107||201312241053|01

data/spec/generate_case_base.rb

@@ -0,0 +1,13 @@
+require 'hl7-exporter'
+message = %[MSH|^~\&|SOURCE|TEST_LAB_INC|HEALTH|382715520|2014100914484648||ORU^R01|0129938170710091448|P|2.3|
+\rPID|1||333||LastName^FirstName^MiddleInitial^SR^NickName||19760228|F||2106-3^White^HL70005^CAUC^Caucasian^L||||||
+\rORC|RE|35748030580^LAB|35748030580^LAB||||||201312240000|||FEDA^^^^^^^L
+\rOBR|1|35748030580^LAB|35748030580^LAB|221010^Lipid Panel w/ Chol/HDL Ratio^L|||201312230656|||||||201312240329||||||35748030580||201312241108|||F
+\rOBX|1|NM|001065^Cholesterol, Total^L^2093-3^Cholesterol^LN||232|mg/dL|100-199|H||N|F|20120910||201312241053|01
+\rOBX|2|NM|001172^Triglycerides^L^2571-8^Triglyceride^LN||179|mg/dL|0-149|H||N|F|20120910||201312241053|01
+\rOBX|3|NM|011817^HDL Cholesterol^L^2085-9^Cholesterol.in HDL^LN||40|mg/dL|>39|||N|F|20020107||201312241053|01
+]
+
+hl7_message = HL7::Message.parse(message)
+exporter = HL7::Exporter::Csv.new(hl7_message)
+exporter.export

data/spec/hl7/exporter_spec.rb

@@ -0,0 +1,36 @@
+require 'spec_helper'
+describe HL7::Exporter::Csv do
+  let(:message) {
+%[MSH|^~\&|SOURCE|TEST_LAB_INC|HEALTH|382715520|2014100914484648||ORU^R01|0129938170710091448|P|2.3|
+\rPID|1||333||LastName^FirstName^MiddleInitial^SR^NickName||19760228|F||2106-3^White^HL70005^CAUC^Caucasian^L||||||
+\rORC|RE|35748030580^LAB|35748030580^LAB||||||201312240000|||FEDA^^^^^^^L
+\rOBR|1|35748030580^LAB|35748030580^LAB|221010^Lipid Panel w/ Chol/HDL Ratio^L|||201312230656|||||||201312240329||||||35748030580||201312241108|||F
+\rOBX|1|NM|001065^Cholesterol, Total^L^2093-3^Cholesterol^LN||232|mg/dL|100-199|H||N|F|20120910||201312241053|01
+\rOBX|2|NM|001172^Triglycerides^L^2571-8^Triglyceride^LN||179|mg/dL|0-149|H||N|F|20120910||201312241053|01
+\rOBX|3|NM|011817^HDL Cholesterol^L^2085-9^Cholesterol.in HDL^LN||40|mg/dL|>39|||N|F|20020107||201312241053|01
+]
+  }
+
+  let(:exporter) { HL7::Exporter::Csv.new(hl7_message) }
+  subject(:csv) { exporter.export.split("\n") }
+
+  context "with a full message" do
+    let(:hl7_message) { HL7::Message.parse(message) }
+
+    it { expect(csv[0]).to eq "Sending Facility: TEST_LAB_INC" }
+    it { expect(csv[1]).to eq "Name: FirstName LastName" }
+    it { expect(csv[2]).to eq "DOB: 1976/02/28"  }
+    it { expect(csv[3]).to eq "Nick: NickName"  }
+    it { expect(csv[4]).to eq "Sex: Female"  }
+    it { expect(csv[5]).to eq "test, result, flag, units, reference interval"  }
+    it { expect(csv[6]).to eq "Cholesterol Total, 232, H, mg/dL, 100-199" }
+    it { expect(csv[8]).to include "Cholesterol" }
+  end
+
+  context "with an empty message" do
+    let(:hl7_message) { "" }
+
+    it { expect { exporter.export }.to raise_error(HL7::ParseError)  }
+  end
+
+end

data/spec/spec_helper.rb

@@ -0,0 +1,14 @@
+require 'rspec'
+require 'ruby-hl7'
+
+# Development gems
+# require 'byebug'
+# require 'pry'
+# require 'looksee'
+
+LOCALE_PATH = File.expand_path(File.dirname(__FILE__) + '/../lib/hl7')
+
+require LOCALE_PATH + '/exporter'
+require LOCALE_PATH + '/exporter/csv'
+require LOCALE_PATH + '/exporter/observation'
+require LOCALE_PATH + '/exporter/patient'

metadata

@@ -0,0 +1,126 @@
+--- !ruby/object:Gem::Specification
+name: hl7-exporter
+version: !ruby/object:Gem::Version
+  version: 0.0.1
+platform: ruby
+authors:
+- Enrique Carlos Mogollan
+autorequire: 
+bindir: bin
+cert_chain: []
+date: 2018-07-31 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: ruby-hl7
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 1.1.0
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 1.1.0
+- !ruby/object:Gem::Dependency
+  name: bundler
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.5'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.5'
+- !ruby/object:Gem::Dependency
+  name: rake
+  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'
+- !ruby/object:Gem::Dependency
+  name: rspec
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '3.5'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '3.5'
+description: A simple library to export messages from the ruby-hl7 gem
+email:
+- emogollan@gmail.com
+executables: []
+extensions: []
+extra_rdoc_files: []
+files:
+- ".gitignore"
+- ".rspec"
+- ".travis.yml"
+- Gemfile
+- LICENSE.txt
+- README.md
+- Rakefile
+- hl7-exporter.gemspec
+- lib/hl7-exporter.rb
+- lib/hl7/exporter.rb
+- lib/hl7/exporter/csv.rb
+- lib/hl7/exporter/observation.rb
+- lib/hl7/exporter/patient.rb
+- lib/hl7/exporter/version.rb
+- spec/example/test1.csv
+- spec/example/test1_custom_template.csv
+- spec/example/test_1.hl7
+- spec/generate_case_base.rb
+- spec/hl7/exporter_spec.rb
+- spec/spec_helper.rb
+homepage: ''
+licenses:
+- MIT
+metadata: {}
+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: []
+rubyforge_project: 
+rubygems_version: 2.7.6
+signing_key: 
+specification_version: 4
+summary: A library to export messages from the ruby-hl7 gem
+test_files:
+- spec/example/test1.csv
+- spec/example/test1_custom_template.csv
+- spec/example/test_1.hl7
+- spec/generate_case_base.rb
+- spec/hl7/exporter_spec.rb
+- spec/spec_helper.rb