Class: HealthDataStandards::Import::Bundle::Importer

Inherits:
Object
  • Object
show all
Defined in:
lib/health-data-standards/import/bundle/importer.rb

Constant Summary collapse

SOURCE_ROOTS = 
{bundle: 'bundle.json', 
libraries: File.join('library_functions','*.js'), 
measures: 'measures', results: 'results', 
valuesets: File.join('value_sets','json','*.json'), 
patients: 'patients'}
COLLECTION_NAMES = 
["bundles", "records", "measures", "selected_measures", "patient_cache", "query_cache", "system.js"]
CLEAR_ONLY_COLLECTIONS = 
["system.js"]
DEFAULTS = 
{type: nil,
  delete_existing: false,
  update_measures: true,
  clear_collections: COLLECTION_NAMES
}

Class Method Summary collapse

Class Method Details

.entry_key(original, extension) ⇒ Object

A utility function for finding files in a bundle. Strip a file path of it’s extension and just give the filename.

Parameters:

  • original (String) —

    A file path.

  • extension (String) —

    A file extension.

Returns:

  • The filename at the end of the original String path with the extension removed. e.g. “/boo/urns.html” -> “urns”



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# File 'lib/health-data-standards/import/bundle/importer.rb', line 88

def self.entry_key(original, extension)
  original.split('/').last.gsub(".#{extension}", '')
end

.import(zip, options = {}) ⇒ Object

Import a quality bundle into the database. This includes metadata, measures, test patients, supporting JS libraries, and expected results.

Parameters:

  • zip (File) —

    The bundle zip file.

  • Type (String) —

    of measures to import, either ‘ep’, ‘eh’ or nil for all

  • keep_existing (Boolean) —

    If true, delete all current collections related to patients and measures.



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# File 'lib/health-data-standards/import/bundle/importer.rb', line 26

def self.import(zip,  options={})
  options = DEFAULTS.merge(options)

  bundle = nil
  Zip::ZipFile.open(zip.path) do |zip_file|

    bundle = unpack_bundle(zip_file)

    bundle_versions = Hash[* HealthDataStandards::CQM::Bundle.where({}).collect{|b| [b._id, b.version]}.flatten]
    if bundle_versions.invert[bundle.version] && !(options[:delete_existing])
      raise "A bundle with version #{bundle.version} already exists in the database. "
    end

    HealthDataStandards::CQM::Bundle.where({:version => bundle.version}).each do |b| 
      puts "deleting existing bundle version: #{b.version}"
      b.delete
    end if options[:delete_existing]

    #find the highest bundle version and see if one is installed that is greater than the one
    # we are currently installing.  Do not load the libs other wise 
    vers = bundle_versions.values.sort.reverse[0]
    if (vers.nil? || vers <= bundle.version || options["force_js_install"])
      unpack_and_store_system_js(zip_file) 
    else
      puts "javascript libraries will not being updated as a more recent bundle version is already installed"
    end  
    # Store the bundle metadata.
    unless bundle.save
      raise bundle.errors.full_messages.join(",")
    end
    puts "bundle metadata unpacked..."

    measure_ids = unpack_and_store_measures(zip_file, options[:type], bundle, options[:update_measures])
    unpack_and_store_patients(zip_file, options[:type], bundle)
    unpack_and_store_valuesets(zip_file, bundle)
    unpack_and_store_results(zip_file, options[:type], measure_ids, bundle)

  end

  bundle
end

.report_progress(label, percent) ⇒ Object 



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# File 'lib/health-data-standards/import/bundle/importer.rb', line 178

def self.report_progress(label, percent)
  print "\rLoading: #{label} #{percent}% complete"
  STDOUT.flush
end

.save_system_js_fn(name, fn) ⇒ Object

Save a javascript function into Mongo’s system.js collection for measure execution.

Parameters:

  • name (String) —

    The name by which the function will be referred.

  • fn (String) —

    The body of the function being saved.



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# File 'lib/health-data-standards/import/bundle/importer.rb', line 73

def self.save_system_js_fn(name, fn)
  fn = "function () {\n #{fn} \n }"
  Mongoid.default_session['system.js'].find('_id' => name).upsert(
    {
      "_id" => name,
      "value" => Moped::BSON::Code.new(fn)
    }
  )
end

.unpack_and_store_measures(zip, type, bundle, update_measures) ⇒ Object 



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# File 'lib/health-data-standards/import/bundle/importer.rb', line 104

def self.unpack_and_store_measures(zip, type, bundle, update_measures)
  measure_ids = []
  entries = zip.glob(File.join(SOURCE_ROOTS[:measures],type || '**','*.json'))
  entries.each_with_index do |entry, index|
    source_measure = unpack_json(entry)
    # we clone so that we have a source without a bundle id
    measure = source_measure.clone
    measure_ids << measure['id']
    measure['bundle_id'] = bundle.id
    Mongoid.default_session["measures"].insert(measure)

    if update_measures
      Mongoid.default_session["measures"].where({hqmf_id: measure["hqmf_id"], sub_id: measure["sub_id"]}).each do |m|
        b = HealthDataStandards::CQM::Bundle.find(m["bundle_id"])
        if b.version < bundle.version
          m.merge!(source_measure)
          Mongoid.default_session["measures"].where({"_id" => m["_id"]}).update(m)
        end
      end
    end
    report_progress('measures', (index*100/entries.length)) if index%10 == 0
  end
  puts "\rLoading: Measures Complete          "
  measure_ids
end

.unpack_and_store_patients(zip, type, bundle) ⇒ Object 



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# File 'lib/health-data-standards/import/bundle/importer.rb', line 130

def self.unpack_and_store_patients(zip, type, bundle)
  entries = zip.glob(File.join(SOURCE_ROOTS[:patients],type || '**','json','*.json'))
  entries.each_with_index do |entry, index|
    patient = Record.new(unpack_json(entry))
    patient['bundle_id'] = bundle.id
    patient.save
    report_progress('patients', (index*100/entries.length)) if index%10 == 0
  end
  puts "\rLoading: Patients Complete          "
end

.unpack_and_store_results(zip, type, measure_ids, bundle) ⇒ Object 



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# File 'lib/health-data-standards/import/bundle/importer.rb', line 154

def self.unpack_and_store_results(zip, type, measure_ids, bundle)
  zip.glob(File.join(SOURCE_ROOTS[:results],'*.json')).each do |entry|
    name = Pathname.new(entry.name).basename('.json').to_s
    collection = (name == "by_patient") ? "patient_cache" : "query_cache"

    contents = unpack_json(entry)

    if (type)
      contents.select! {|entry| measure_ids.include? entry['measure_id']} if collection == 'query_cache'
      contents.select! {|entry| measure_ids.include? entry['value']['measure_id']} if collection == 'patient_cache'
    end

    contents.each do |document| 
      document['bundle_id'] = bundle.id
      Mongoid.default_session[collection].insert(document)
    end
  end
  puts "\rLoading: Results Complete          "
end

.unpack_and_store_system_js(zip) ⇒ Object 



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# File 'lib/health-data-standards/import/bundle/importer.rb', line 96

def self.unpack_and_store_system_js(zip)
  zip.glob(SOURCE_ROOTS[:libraries]).each do |entry|
    name = Pathname.new(entry.name).basename('.js').to_s
    contents = entry.get_input_stream.read
    save_system_js_fn(name, contents)
  end
end

.unpack_and_store_valuesets(zip, bundle) ⇒ Object 



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# File 'lib/health-data-standards/import/bundle/importer.rb', line 141

def self.unpack_and_store_valuesets(zip, bundle)
  entries = zip.glob(SOURCE_ROOTS[:valuesets])
  bulk = []
  entries.each_with_index do |entry, index|
    vs = HealthDataStandards::SVS::ValueSet.new(unpack_json(entry))
    vs['bundle_id'] = bundle.id
    bulk << vs
    report_progress('Value Sets', (index*100/entries.length)) if index%10 == 0
  end
  HealthDataStandards::SVS::ValueSet.collection.insert(bulk.map {|vs| vs.as_document})
  puts "\rLoading: Value Sets Complete          "
end

.unpack_bundle(zip) ⇒ Object 



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# File 'lib/health-data-standards/import/bundle/importer.rb', line 92

def self.unpack_bundle(zip)
  HealthDataStandards::CQM::Bundle.new(JSON.parse(zip.read(SOURCE_ROOTS[:bundle]),max_nesting: 100))
end

.unpack_json(entry) ⇒ Object 



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# File 'lib/health-data-standards/import/bundle/importer.rb', line 174

def self.unpack_json(entry)
  JSON.parse(entry.get_input_stream.read,:max_nesting => 100)
end