Class: HealthDataStandards::Import::Bundle::Importer
- Inherits:
-
Object
- Object
- HealthDataStandards::Import::Bundle::Importer
- 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
-
.entry_key(original, extension) ⇒ Object
A utility function for finding files in a bundle.
-
.import(zip, options = {}) ⇒ Object
Import a quality bundle into the database.
- .report_progress(label, percent) ⇒ Object
-
.save_system_js_fn(name, fn) ⇒ Object
Save a javascript function into Mongo’s system.js collection for measure execution.
- .unpack_and_store_measures(zip, type, bundle, update_measures) ⇒ Object
- .unpack_and_store_patients(zip, type, bundle) ⇒ Object
- .unpack_and_store_results(zip, type, measure_ids, bundle) ⇒ Object
- .unpack_and_store_system_js(zip) ⇒ Object
- .unpack_and_store_valuesets(zip, bundle) ⇒ Object
- .unpack_bundle(zip) ⇒ Object
- .unpack_json(entry) ⇒ Object
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.
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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.
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# File 'lib/health-data-standards/import/bundle/importer.rb', line 26 def self.import(zip, ={}) = DEFAULTS.merge() 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] && !([: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 [: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 || ["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..join(",") end puts "bundle metadata unpacked..." measure_ids = unpack_and_store_measures(zip_file, [:type], bundle, [:update_measures]) unpack_and_store_patients(zip_file, [:type], bundle) unless [:exclude_results] unpack_and_store_valuesets(zip_file, bundle) unpack_and_store_results(zip_file, [:type], measure_ids, bundle) unless [:exclude_results] end bundle end |
.report_progress(label, percent) ⇒ Object
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# File 'lib/health-data-standards/import/bundle/importer.rb', line 186 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.
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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| if name == "by_patient" # Set the patient_id to the actual _id of # newly created patient record medical_record_id = document['value']['medical_record_id'] if patient = Record.by_patient_id(medical_record_id).first document['value']['patient_id'] = patient.id end end 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 182 def self.unpack_json(entry) JSON.parse(entry.get_input_stream.read,:max_nesting => 100) end |