fhir_scorecard 1.0

checksums.yaml

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+---
+SHA1:
+  metadata.gz: f2da74ec899e9c534a4a76c9aaca39fd1299dcaf
+  data.tar.gz: 874605dc5bf4f111daacb081c5acecb58b6e2844
+SHA512:
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data/.gitignore

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+terminology/*
+logs/*.log*
+**/.DS_Store
+
+### Following content generated by Github ###
+
+*.gem
+*.rbc
+/.config
+/coverage/
+/InstalledFiles
+/pkg/
+/spec/reports/
+/spec/examples.txt
+/test/tmp/
+/test/version_tmp/
+/tmp/
+
+# Used by dotenv library to load environment variables.
+# .env
+
+## Specific to RubyMotion:
+.dat*
+.repl_history
+build/
+*.bridgesupport
+build-iPhoneOS/
+build-iPhoneSimulator/
+
+## Specific to RubyMotion (use of CocoaPods):
+#
+# We recommend against adding the Pods directory to your .gitignore. However
+# you should judge for yourself, the pros and cons are mentioned at:
+# https://guides.cocoapods.org/using/using-cocoapods.html#should-i-check-the-pods-directory-into-source-control
+#
+# vendor/Pods/
+
+## Documentation cache and generated files:
+/.yardoc/
+/_yardoc/
+/doc/
+/rdoc/
+
+## Environment normalization:
+/.bundle/
+/vendor/bundle
+/lib/bundler/man/
+
+# for a library or gem, you might want to ignore these files since the code is
+# intended to run in multiple environments; otherwise, check them in:
+# Gemfile.lock
+# .ruby-version
+# .ruby-gemset
+
+# unless supporting rvm < 1.11.0 or doing something fancy, ignore this:
+.rvmrc

data/.simplecov

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+SimpleCov.command_name 'Unit Tests'
+SimpleCov.start do
+  add_filter "test/"
+  add_group "Library", "lib"
+end
+
+class SimpleCov::Formatter::QualityFormatter
+  def format(result)
+    SimpleCov::Formatter::HTMLFormatter.new.format(result)
+    File.open("coverage/covered_percent", "w") do |f|
+      f.puts result.source_files.covered_percent.to_f
+    end
+  end
+end
+
+SimpleCov.formatter = SimpleCov::Formatter::QualityFormatter

data/.travis.yml

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+language: ruby
+rvm:
+  - "2.0.0"
+script:
+  - bundle exec rake test

data/Gemfile

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+source "https://rubygems.org"
+gemspec
+
+gem 'rake'
+gem 'pry'
+gem 'fhir_models', '~> 1.6'
+
+group :test do
+  gem 'simplecov', :require => false
+  gem 'minitest', '~> 5.3'
+  gem 'minitest-reporters'
+  gem 'awesome_print', :require => 'ap'
+end

data/Gemfile.lock

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+PATH
+  remote: .
+  specs:
+    fhir_scorecard (0.1.0)
+      fhir_models
+
+GEM
+  remote: https://rubygems.org/
+  specs:
+    ansi (1.5.0)
+    awesome_print (1.7.0)
+    bcp47 (0.3.3)
+      i18n
+    builder (3.2.2)
+    coderay (1.1.1)
+    date_time_precision (0.8.1)
+    docile (1.1.5)
+    fhir_models (1.6.8)
+      bcp47 (>= 0.3)
+      date_time_precision (>= 0.8)
+      mime-types (>= 1.16, < 3)
+      nokogiri (>= 1.6)
+    i18n (0.7.0)
+    json (2.0.2)
+    method_source (0.8.2)
+    mime-types (2.99.3)
+    mini_portile2 (2.1.0)
+    minitest (5.9.0)
+    minitest-reporters (1.1.11)
+      ansi
+      builder
+      minitest (>= 5.0)
+      ruby-progressbar
+    nokogiri (1.6.8.1)
+      mini_portile2 (~> 2.1.0)
+    pry (0.10.4)
+      coderay (~> 1.1.0)
+      method_source (~> 0.8.1)
+      slop (~> 3.4)
+    rake (11.3.0)
+    ruby-progressbar (1.8.1)
+    simplecov (0.12.0)
+      docile (~> 1.1.0)
+      json (>= 1.8, < 3)
+      simplecov-html (~> 0.10.0)
+    simplecov-html (0.10.0)
+    slop (3.6.0)
+
+PLATFORMS
+  ruby
+
+DEPENDENCIES
+  awesome_print
+  fhir_models (~> 1.6)
+  fhir_scorecard!
+  minitest (~> 5.3)
+  minitest-reporters
+  pry
+  rake
+  simplecov
+
+BUNDLED WITH
+   1.13.6

data/LICENSE

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data/README.md

@@ -0,0 +1,94 @@
+# fhir_scorecard [![Build Status](https://travis-ci.org/fhir-crucible/fhir_scorecard.svg?branch=master)](https://travis-ci.org/fhir-crucible/fhir_scorecard)
+
+`fhir_scorecard` provides a scorecard for a FHIR Patient Record (as Bundle). Achieving interoperability
+of a Patient Healthcare Record within FHIR will require agreement on "best practices" beyond the base specification.
+Those agreements could be in the form of an Implementation Guide, with associated Profiles, but `fhir_scorecard`
+provides them in the form of testable rubrics.
+
+This project borrows inspiration and rubrics from [ccdaScorecard](https://github.com/chb/ccdaScorecard),
+a scorecard for C-CDA documents.
+
+## Scorecard on the Command Line
+
+```
+$ bundle exec rake fhir:score[fhir_bundle.json]
+
+  POINTS            CATEGORY   MESSAGE
+  ------            --------   -------
+    10                bundle   Patient Record is a FHIR Bundle.
+    10               patient   Patient Record contains one FHIR Patient.
+     2           codes_exist   21% (282/1323) of codes, Codings, and CodeableConcepts had values. Maximum of 10 points.
+     4            codes_umls   42% (145/344) of SNOMED, LOINC, RxNorm, ICD9, and ICD10 validated against UMLS. Maximum of 10 points.
+     0          descriptions   7% (26/344) of SNOMED, LOINC, RxNorm, ICD9, and ICD10 codes use preferred descriptions. Maximum of 10 points.
+    17          completeness   85% of REQUIRED Resources and 9% of EXPECTED Resources were present. Maximum of 20 points.
+    10     cvx_immunizations   100% (6/6) of Immunization vaccine codes use CVX. Maximum of 10 points.
+     0       cvx_medications   0% (0/4) of Medication[x] Resource codes use CVX. Maximum of 10 point penalty.
+     3         iso8601_dates   30% (149/494) of date/time/dateTime/instant fields were populated with reasonable iso8601 values. Maximum of 10 points.
+     6            loinc_labs   68% (75/110) of Observations and DiagnosticReports validated against the LOINC Top 2000. Maximum of 10 points.
+     8       ucum_quantities   83% (80/96) of physical quantities used or declared UCUM. Maximum of 10 points.
+     4    references_resolve   43% (326/750) of all possible References resolved locally within the Bundle. Maximum of 10 points.
+    10           rxnorm_meds   100% (4/4) of Medication[x] Resource codes use RxNorm. Maximum of 10 points.
+     0        smoking_status   The Patient Record should include Smoking Status (DAF-core-smokingstatus profile on Observation).
+     2           snomed_core   29% (5/17) of Condition Resource codes use the SNOMED Core Subset. Maximum of 10 points.
+     2           vital_signs   22% (2/9) of Vital Signs had at least one recorded Observation. Maximum of 10 points.
+  ------
+    88                 TOTAL
+
+
+```
+
+## Scorecard in Ruby
+
+```ruby
+bundle_json = "{\"entry\":[{\"resource\":{\"resourceType\":\"Patient\"}}],\"resourceType\":\"Bundle\"}"
+scorecard = FHIR::Scorecard.new
+report = scorecard.score(bundle_json)
+=> {:bundle=>{:points=>10, :message=>"Patient Record is a FHIR Bundle."},
+    :patient=>{:points=>10, :message=>"Patient Record contains one FHIR Patient."},
+    :points=>20}
+```
+
+## Optional Terminology Support
+
+The scorecard requires some terminology files to operate several rubrics related
+to codes. Download the files (requires accounts) and place them in `./terminology`
+
+- https://www.nlm.nih.gov/research/umls/licensedcontent/umlsknowledgesources.html
+ - When installing the metathesaurus, include the following sources:
+  `CVX|CVX;
+   ICD10CM|ICD10CM;
+   ICD10PCS|ICD10PCS;
+   ICD9CM|ICD9CM;
+   LNC|LNC;
+   MTHICD9|ICD9CM;
+   RXNORM|RXNORM;
+   SNOMEDCT_US|SNOMEDCT`
+
+- https://www.nlm.nih.gov/research/umls/Snomed/core_subset.html
+- http://loinc.org/usage/obs/loinc-top-2000-plus-loinc-lab-observations-us.csv
+- http://download.hl7.de/documents/ucum/concepts.tsv
+
+After downloading the files, run these rake tasks to post-process each terminology file:
+
+```
+> bundle exec rake fhir:process_umls
+> bundle exec rake fhir:process_snomed
+> bundle exec rake fhir:process_loinc
+> bundle exec rake fhir:process_ucum
+```
+
+# License
+
+Copyright 2016 The MITRE Corporation
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+    http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.

data/Rakefile

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+require 'rake'
+require 'rake/testtask'
+require 'fileutils'
+require 'pry'
+
+require_relative 'lib/fhir_scorecard'
+
+# Pull in any rake task defined in lib/tasks
+Dir['lib/tasks/**/*.rake'].sort.each do |ext|
+  load ext
+end
+
+desc "Run basic tests"
+Rake::TestTask.new(:test_unit) do |t|
+  t.libs << "test"
+  t.test_files = FileList['test/**/*_test.rb']
+  t.verbose = true
+  t.warning = false
+end
+
+task :test => [:test_unit] do
+  system("open coverage/index.html")
+end
+
+task :default => [:test]

data/fhir_scorecard.gemspec

@@ -0,0 +1,15 @@
+# -*- encoding: utf-8 -*-
+
+Gem::Specification.new do |s|
+  s.name = "fhir_scorecard"
+  s.summary = "Scorecard for a FHIR Patient Record (as Bundle)"
+  s.description = "A Gem for scoring FHIR Patient Records (as Bundles)"
+  s.email = "jwalonoski@mitre.org"
+  s.homepage = "https://github.com/fhir-crucible/fhir_scorecard"
+  s.authors = ["Jason Walonoski"]
+  s.version = '1.0'
+
+  s.files = s.files = `git ls-files`.split("\n")
+
+  s.add_runtime_dependency 'fhir_models'
+end

data/lib/fhir_scorecard.rb

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+# Top level include file that brings in all the necessary code
+require 'bundler/setup'
+require 'fhir_models'
+
+root = File.expand_path '..', File.dirname(File.absolute_path(__FILE__))
+
+FHIR.logger = Logger.new(File.join(root,'logs','fhir_models.log'),1,1024000)
+
+require File.join(root,'lib','scorecard.rb')
+require File.join(root,'lib','terminology.rb')
+require File.join(root,'lib','rubrics.rb')
+
+Dir.glob(File.join(root, 'lib','rubrics','**','*.rb')).each do |file|
+  require file
+end

data/lib/rubrics/codes_exist.rb

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+module FHIR
+  class CodesExist < FHIR::Rubrics
+
+    # Codes are present for all codes, Codings, and CodeableConcepts
+    rubric :codes_exist do |record|
+      results = {
+        :codeable_fields => 0,
+        :coded_fields => 0
+      }
+      resources = record.entry.map{|e|e.resource}
+      resources.each do |resource|
+        results.merge!(check_metadata(resource)){|k,a,b|a+b}
+      end
+
+      percentage = results[:coded_fields].to_f / results[:codeable_fields].to_f
+      percentage = 0.0 if percentage.nan?
+      points = 10.0 * percentage
+      message = "#{(100 * percentage).to_i}% (#{results[:coded_fields]}/#{results[:codeable_fields]}) of codes, Codings, and CodeableConcepts had values. Maximum of 10 points."
+      response(points.to_i,message)
+    end
+
+    def self.check_metadata(fhir_model)
+      results = {
+        :codeable_fields => 0,
+        :coded_fields => 0
+      }
+      # check for metadata
+      # count all codeable fields
+      fhir_model.class::METADATA.each do |key, meta|
+        field_name = meta['local_name'] || key
+        if ['code','Coding','CodeableConcept'].include?(meta['type'])
+          results[:codeable_fields] += 1
+          value = fhir_model.instance_variable_get("@#{field_name}")
+          # check that the field is actually the correct type
+          if !value.nil?
+            if value.is_a?(Array)
+              if !value.empty? # the Array has at least one value
+                results[:coded_fields] += 1 if value.any?{|x|type_okay(meta['type'],x)}
+              end
+            else # not an Array
+              results[:coded_fields] += 1 if type_okay(meta['type'],value)
+            end
+          end
+        else
+          value = fhir_model.instance_variable_get("@#{field_name}")
+          if !value.nil?
+            if value.is_a?(Array)
+              value.each{|v| results.merge!(check_metadata(v)){|k,a,b|a+b} if v.is_a?(FHIR::Model)}
+            else # not an Array
+              results.merge!(check_metadata(value)){|k,a,b|a+b} if value.is_a?(FHIR::Model)
+            end
+          end            
+        end
+      end
+      results
+    end
+
+    def self.type_okay(type,item)
+      case type
+      when 'code'
+        item.is_a?(String)
+      when 'Coding'
+        item.is_a?(FHIR::Coding) && !item.code.nil? && !item.system.nil?
+      when 'CodeableConcept'
+        item.is_a?(FHIR::CodeableConcept) && item.coding.any?{|c| c.is_a?(FHIR::Coding) && !c.code.nil? && !c.system.nil?}
+      else
+        false
+      end
+    end
+
+  end
+end