cqm-models 0.7.2

data/lib/cqm/models.rb

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+require_relative '../../app/models/models'

data/lib/generate_models.rb

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+#! /usr/bin/env ruby
+
+require 'nokogiri'
+require 'active_support/all'
+require 'rails/generators'
+require 'erb'
+require 'json'
+
+###############################################################################
+# Helpers
+###############################################################################
+
+# Lookups for modelinfo 'element types' to Ruby+Mongoid types.
+TYPE_LOOKUP_RB = {
+  'System.DateTime': 'DateTime',
+  'System.Integer': 'Integer',
+  'System.Quantity': 'Quantity',
+  'System.Code': 'Code',
+  'System.Any': 'Any',
+  'interval<System.DateTime>': 'Interval',
+  'interval<System.Quantity>': 'Interval',
+  'list<QDM.Component>': 'Array',
+  'System.String': 'String',
+  'list<QDM.Id>': 'Array',
+  'list<QDM.ResultComponent>': 'Array',
+  'list<QDM.FacilityLocation>': 'Array',
+  'list<System.Code>': 'Array',
+  'QDM.Id': 'String',
+  'System.Decimal': 'Float',
+  'System.Time': 'Time',
+  'System.Concept': 'Any'
+}.stringify_keys!
+
+# Lookups for modelinfo 'element types' to JavaScript+Mongoose types.
+TYPE_LOOKUP_JS = {
+  'System.DateTime': 'DateTime',
+  'System.Integer': 'Number',
+  'System.Quantity': 'Quantity',
+  'System.Code': 'Code',
+  'System.Any': '{}',
+  'interval<System.DateTime>': 'Interval',
+  'interval<System.Quantity>': 'Interval',
+  'list<QDM.Component>': '[]',
+  'System.String': 'String',
+  'list<QDM.Id>': '[String]',
+  'list<QDM.ResultComponent>': '[]',
+  'list<QDM.FacilityLocation>': '[]',
+  'list<System.Code>': '[Code]',
+  'QDM.Id': 'String',
+  'System.Decimal': 'Number',
+  'System.Time': 'DateTime',
+  'System.Concept': '{}'
+}.stringify_keys!
+
+###############################################################################
+# Start of modelinfo file parsing
+###############################################################################
+
+puts 'Parsing modelinfo file...'
+
+Dir.chdir ENV['TRAVIS_BUILD_DIR'] if ENV['CI']
+puts Dir.pwd
+puts Dir.entries('.')
+
+# Open specified modelinfo file
+modelinfo_file = ARGV[0]
+raise 'Please provide a valid modelinfo file path and name.' if modelinfo_file.blank? || !File.file?(modelinfo_file)
+modelinfo = File.open(modelinfo_file) { |f| Nokogiri::XML(f) }
+
+# Open specified HQMF oid file
+oids_file = ARGV[1]
+raise 'Please provide a valid HQMF oid file path and name.' if oids_file.blank? || !File.file?(oids_file)
+oids = JSON.parse(File.read(oids_file))
+
+# If this script was run with a third parameter of 'TEST', then generate the models in a
+# not standard location. This helps with testing.
+IS_TEST = (ARGV[2] == 'TEST')
+
+# Grab QDM version as defined in the modelinfo file
+qdm_version = modelinfo.xpath('//ns4:modelInfo').first.attributes['version'].value
+
+# Datatypes (keys are the datatype name, values are the datatype attributes)
+datatypes = {}
+
+# Loop through each typeInfo node (each of these is a QDM datatype)
+modelinfo.xpath('//ns4:typeInfo').each do |type|
+  # Grab the name of this QDM datatype
+  datatype_name = type.attributes['name'].value.split('.').last
+
+  # Grab the QDM attributes for this datatype
+  attributes = []
+  type.xpath('./ns4:element').each do |attribute|
+    # Grab the name of this QDM datatype attribute
+    attribute_name = attribute.attributes['name'].value
+
+    # Grab the type of this QDM datatype attribute
+    attribute_type = if attribute.attributes['type']
+                       attribute.attributes['type'].value
+                     else
+                       'System.Any'
+                     end
+
+    next if attribute_name.blank? || attribute_type.blank?
+
+    # Store name and type
+    attributes << { name: attribute_name, type: attribute_type }
+  end
+
+  # Store datatype and its attributes (reject irrelevant datatypes)
+  next if datatype_name.include?('Negative') || datatype_name.include?('Positive') || datatype_name.include?('QDMBaseType')
+  datatypes[datatype_name] = attributes
+end
+
+###############################################################################
+# Start of model generation
+###############################################################################
+
+puts 'Generating Ruby models...'
+
+# Do a quick sanity check on attribute types
+datatypes.each do |datatype, attributes|
+  attributes.each do |attribute|
+    raise 'Unsupported type from modelinfo file for Ruby types: ' + attribute[:type] + 'from: ' + datatype if TYPE_LOOKUP_RB[attribute[:type]].blank?
+    raise 'Unsupported type from modelinfo file for JavaScript types: ' + attribute[:type] + 'from: ' + datatype if TYPE_LOOKUP_JS[attribute[:type]].blank?
+  end
+end
+
+# Create Ruby models
+extra_fields_rb = [
+  'hqmfOid:String',
+  'qrdaOid:String',
+  'category:String',
+  'qdmStatus:String',
+  'qdmVersion:String'
+]
+base_module = 'QDM::'
+base_module = 'Test::QDM::' if IS_TEST
+datatypes.each do |datatype, attributes|
+  Rails::Generators.invoke('mongoid:model', [base_module + datatype] + attributes.collect { |attribute| attribute[:name] + ':' + TYPE_LOOKUP_RB[attribute[:type]] } + extra_fields_rb)
+end
+
+# Create require file (if not in test mode)
+unless IS_TEST
+  model_template = File.read('templates/models_template.rb.erb')
+  renderer = ERB.new(model_template, nil, '-')
+  file_path = 'app/models/models.rb'
+  File.open(file_path, 'w') { |file| file.puts renderer.result(binding) }
+end
+
+puts 'Generating JavaScript models...'
+
+# Create JavaScript models
+template = File.read('templates/mongoose_template.js.erb')
+renderer = ERB.new(template, nil, '-')
+file_path = 'app/assets/javascripts/'
+file_path = 'tmp/' if IS_TEST
+extra_fields_js = [
+  { name: 'hqmfOid', type: 'System.String' },
+  { name: 'qrdaOid', type: 'System.String' },
+  { name: 'category', type: 'System.String' },
+  { name: 'qdmStatus', type: 'System.String' },
+  { name: 'qdmVersion', type: 'System.String' },
+  { name: '_type', type: 'System.String' }
+]
+datatypes.each do |datatype, attributes|
+  if datatype == 'Patient'
+    # Handle Patient as its own special case, with its own template.
+    patient_template = File.read('templates/patient_template.js.erb')
+    patient_renderer = ERB.new(patient_template, nil, '-')
+    attrs_with_extras = attributes + extra_fields_js
+    puts '  ' + file_path + datatype + '.js'
+    File.open(file_path + datatype + '.js', 'w') { |file| file.puts patient_renderer.result(binding) }
+  else
+    attrs_with_extras = attributes + extra_fields_js
+    puts '  ' + file_path + datatype + '.js'
+    File.open(file_path + datatype + '.js', 'w') { |file| file.puts renderer.result(binding) }
+  end
+end
+
+# Create require file (if not in test mode)
+unless IS_TEST
+  indtemplate = File.read('templates/index_template.js.erb')
+  renderer = ERB.new(indtemplate, nil, '-')
+  file_path = 'app/assets/javascripts/index.js'
+  File.open(file_path, 'w') { |file| file.puts renderer.result(binding) }
+
+  alltemplate = File.read('templates/all_data_elements_template.js.erb')
+  renderer = ERB.new(alltemplate, nil, '-')
+  file_path = 'app/assets/javascripts/AllDataElements.js'
+  File.open(file_path, 'w') { |file| file.puts renderer.result(binding) }
+end
+
+###############################################################################
+# Model post processing
+###############################################################################
+
+puts 'Post processing...'
+
+# Ruby post processing
+ruby_models_path = 'app/models/qdm/'
+ruby_models_path = 'app/models/test/qdm/' if IS_TEST
+Dir.glob(ruby_models_path + '*.rb').each do |file_name|
+  contents = File.read(file_name)
+
+  # Cut out the 'Any' type placeholder (these attributes could point to anything).
+  contents.gsub!(/, type: Any/, '')
+
+  # Add QDM version
+  contents.gsub!(/field :qdmVersion, type: String/, "field :qdmVersion, type: String, default: '#{qdm_version}'")
+
+  # Add HQMF oid (if it exists in the given HQMF oid mapping file)
+  dc_name = File.basename(file_name, '.*')
+  if oids[dc_name].present? && oids[dc_name]['hqmf_oid'].present?
+    contents.gsub!(/  field :hqmfOid, type: String\n/, "  field :hqmfOid, type: String, default: '#{oids[dc_name]['hqmf_oid']}'\n")
+  else
+    contents.gsub!(/  field :hqmfOid, type: String\n/, '') # Don't include this field
+  end
+
+  # Add QRDA oid (if it exists in the given QRDA oid mapping file)
+  if oids[dc_name].present? && oids[dc_name]['qrda_oid'].present?
+    contents.gsub!(/  field :qrdaOid, type: String\n/, "  field :qrdaOid, type: String, default: '#{oids[dc_name]['qrda_oid']}'\n")
+  else
+    contents.gsub!(/  field :qrdaOid, type: String\n/, '') # Don't include this field
+  end
+
+  # Add category
+  if oids[dc_name].present? && oids[dc_name]['category'].present?
+    contents.gsub!(/  field :category, type: String\n/, "  field :category, type: String, default: '#{oids[dc_name]['category']}'\n")
+  else
+    contents.gsub!(/  field :category, type: String\n/, '') # Don't include this field
+  end
+
+  # Add status
+  if oids[dc_name].present? && oids[dc_name]['status'].present?
+    contents.gsub!(/  field :qdmStatus, type: String\n/, "  field :qdmStatus, type: String, default: '#{oids[dc_name]['status']}'\n")
+  else
+    contents.gsub!(/  field :qdmStatus, type: String\n/, '') # Don't include this field
+  end
+
+  File.open(file_name, 'w') { |file| file.puts contents }
+end
+
+# JavaScript post processing
+js_models_path = 'app/assets/javascripts/'
+js_models_path = 'tmp/' if IS_TEST
+files = Dir.glob(js_models_path + '*.js').each do |file_name|
+  contents = File.read(file_name)
+
+  # Replace 'Any' type placeholder (these attributes could point to anything).
+  contents.gsub!(/: Any/, ': {}')
+
+  # Add QDM version
+  contents.gsub!(/qdmVersion: String/, "qdmVersion: { type: String, default: '#{qdm_version}' }")
+
+  # Add HQMF oid (if it exists in the given HQMF oid mapping file)
+  dc_name = File.basename(file_name.underscore, '.*')
+  if oids[dc_name].present? && oids[dc_name]['hqmf_oid'].present?
+    contents.gsub!(/  hqmfOid: String,\n/, "  hqmfOid: { type: String, default: '#{oids[dc_name]['hqmf_oid']}' },\n")
+  else
+    contents.gsub!(/  hqmfOid: String,\n/, '') # Don't include this field
+  end
+
+  # Add QRDA oid (if it exists in the given QRDA oid mapping file)
+  if oids[dc_name].present? && oids[dc_name]['qrda_oid'].present?
+    contents.gsub!(/  qrdaOid: String,\n/, "  qrdaOid: { type: String, default: '#{oids[dc_name]['qrda_oid']}' },\n")
+  else
+    contents.gsub!(/  qrdaOid: String,\n/, '') # Don't include this field
+  end
+
+  # Add category
+  if oids[dc_name].present? && oids[dc_name]['category'].present?
+    contents.gsub!(/  category: String,\n/, "  category: { type: String, default: '#{oids[dc_name]['category']}' },\n")
+  else
+    contents.gsub!(/  category: String,\n/, '') # Don't include this field
+  end
+
+  # Add status
+  if oids[dc_name].present? && oids[dc_name]['status'].present?
+    contents.gsub!(/  qdmStatus: String,\n/, "  qdmStatus: { type: String, default: '#{oids[dc_name]['status']}' },\n")
+  else
+    contents.gsub!(/  qdmStatus: String,\n/, '') # Don't include this field
+  end
+
+  # Add class
+  contents.gsub!(/  _type: String,\n/, "  _type: { type: String, default: '#{dc_name.camelize}' },\n")
+
+  File.open(file_name, 'w') { |file| file.puts contents }
+end
+
+# Inject Ruby Patient model extensions
+template = File.read('templates/patient_extension.rb.erb')
+renderer = ERB.new(template, nil, '-')
+rb_patient = File.read(ruby_models_path + 'patient.rb')
+rb_patient.gsub!(/end/, renderer.result(binding))
+File.open(ruby_models_path + 'patient.rb', 'w') { |file| file.write(rb_patient) }
+
+# Make sure Ruby models are in the correct module
+ruby_models_path = 'app/models/qdm/'
+ruby_models_path = 'app/models/test/qdm/' if IS_TEST
+Dir.glob(ruby_models_path + '*.rb').each do |file_name|
+  contents = File.read(file_name)
+  contents.gsub!('Qdm', 'QDM')
+  contents.gsub!('Code', 'QDM::Code')
+  contents.gsub!('Interval', 'QDM::Interval')
+  contents.gsub!('Quantity', 'QDM::Quantity')
+  File.open(file_name, 'w') { |file| file.puts contents }
+end
+
+# Set embedded in for datatypes
+Dir.glob(ruby_models_path + '*.rb').each do |file_name|
+  contents = File.read(file_name)
+  next if File.basename(file_name) == 'patient.rb'
+  contents.gsub!(/  include Mongoid::Document\n/, "  include Mongoid::Document\n  embedded_in :patient\n")
+  File.open(file_name, 'w') { |file| file.puts contents }
+end
+
+# Make sure Ruby datatypes models have the correct inheritance
+Dir.glob(ruby_models_path + '*.rb').each do |file_name|
+  contents = ''
+  File.open(file_name).each_line.with_index do |line, index|
+    line.gsub!("\n", " < DataElement\n") if index.zero? && !file_name.include?('/patient.rb')
+    contents += "module QDM\n  # #{file_name}\n  #{line.gsub('QDM::', '')}" if index.zero?
+    contents += '  ' unless index.zero? || line.blank?
+    contents += line unless index.zero?
+  end
+  contents += 'end'
+  File.open(file_name, 'w') { |file| file.puts contents }
+end
+
+puts 'Done.'