Class: Inferno::Repositories::IGs

Inherits:
InMemoryRepository show all
Includes:
Utils::IgDownloader
Defined in:
lib/inferno/repositories/igs.rb

Overview

Repository that deals with persistence for the ‘IG` entity.

Constant Summary

Constants included from Utils::IgDownloader

Utils::IgDownloader::FHIR_PACKAGE_NAME_REG_EX, Utils::IgDownloader::FILE_URI_REG_EX, Utils::IgDownloader::HTTP_URI_END_REG_EX, Utils::IgDownloader::HTTP_URI_REG_EX

Instance Method Summary collapse

Methods included from Utils::IgDownloader

#download_file, #ig_file, #ig_http_url, #ig_path, #ig_registry_url, #load_ig

Methods inherited from InMemoryRepository

all, all_by_id, #exists?, #find, #insert, #remove

Instance Method Details

#add_package_to_cache(ig_identifier, temp_tgz) ⇒ Object 



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# File 'lib/inferno/repositories/igs.rb', line 84

def add_package_to_cache(ig_identifier, temp_tgz)
  return temp_tgz if ENV['READ_ONLY_FHIR_PACKAGE_CACHE'].present?

  # In the HL7 FHIR validator, this is handled by the FilesystemPackageCacheManager:
  # https://github.com/hapifhir/org.hl7.fhir.core/blob/3cf2a06e7abda7dc32cdc052d3a356c1201139cf/org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/npm/FilesystemPackageCacheManager.java#L558
  # We try to follow the same approach here

  lockfile_path = File.join(user_package_cache, "#{ig_identifier}.lock")
  lockfile = File.open(lockfile_path, 'w+')
  lockfile.flock(File::LOCK_EX)

  target_cache_dir = File.join(user_package_cache, ig_identifier)

  # Break early 1 - something else already created it while we got the lock
  return target_cache_dir if in_user_package_cache?(ig_identifier)

  # 1. Extract to a temp folder under the cache
  temp_dir = File.join(user_package_cache, SecureRandom.uuid)
  FileUtils.mkdir_p(temp_dir)

  system "tar -xzf #{temp_tgz} --directory #{temp_dir}"

  # Break early 2 - something else already created it
  return target_cache_dir if in_user_package_cache?(ig_identifier)

  # 2. Rename the temp folder to the correct name
  File.rename(temp_dir, target_cache_dir)

  # return the path in cache
  target_cache_dir
rescue StandardError => e
  Application['logger'].error(e.full_message)
  # Don't leave a half extracted package behind
  FileUtils.remove_dir(temp_dir, true)

  # Return the tgz so that processing can continue
  temp_tgz
ensure
  if lockfile.present?
    lockfile.flock(File::LOCK_UN)
    lockfile.close
    File.delete(lockfile)
  end
end

#find_by_path(path) ⇒ Inferno::Entities::IG

Get the instance of the already-loaded IG specified by file path.

Parameters:

  • path (String) —

    file path, eg “./igs/uscore.tgz”

Returns:



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# File 'lib/inferno/repositories/igs.rb', line 30

def find_by_path(path)
  all.find { |ig| ig.source_path == path }
end

#find_local_file(ig_path) ⇒ Object 



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# File 'lib/inferno/repositories/igs.rb', line 57

def find_local_file(ig_path)
  return nil unless ['.tgz', '.tar.gz'].any? { |ext| ig_path.downcase.end_with?(ext) }

  return ig_path if File.exist?(ig_path)

  # IG packages are copied to ./data/igs to be used by the validator,
  # and if referenced by file in the validator block the path given must be "igs/{filename}.tgz"
  data_igs_path = File.join('data', ig_path)
  return data_igs_path if File.exist?(data_igs_path)

  # Last resort, try to find the file under the current working directory,
  # eg, given ig_path: 'igs/package123.tgz'
  # this would find 'lib/my_test_kit/igs/package123.tgz'
  Dir.glob(File.join('**', ig_path))[0]
end

#find_or_load(id_or_path) ⇒ Inferno::Entities::IG

Get the instance of the IG specified by either identifier or file path. An in-memory instance will be returned if already loaded, otherwise the IG will be retrieved from the user package cache (~/.fhir/packages) or from the package server and then loaded into the repository.

Parameters:

  • id_or_path (String) —

    either an identifier, eg “hl7.fhir.us.core#3.1.1” or a file path, eg “./igs/uscore.tgz”

Returns:



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# File 'lib/inferno/repositories/igs.rb', line 18

def find_or_load(id_or_path)
  return find(id_or_path) if exists?(id_or_path)

  ig_by_path = find_by_path(id_or_path) || find_by_path(find_local_file(id_or_path))
  return ig_by_path if ig_by_path

  load(id_or_path)
end

#in_user_package_cache?(ig_identifier) ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/inferno/repositories/igs.rb', line 79

def in_user_package_cache?(ig_identifier)
  File.directory?(File.join(user_package_cache, ig_identifier))
end

#load(ig_path) ⇒ Object 



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# File 'lib/inferno/repositories/igs.rb', line 35

def load(ig_path)
  local_ig_file = find_local_file(ig_path)
  if local_ig_file
    ig = Inferno::Entities::IG.from_file(local_ig_file)
    # To match the HL7 FHIR validator, DO NOT cache igs loaded from file
  elsif in_user_package_cache?(ig_path.sub('@', '#'))
    # NPM syntax for a package identifier is id@version (eg, [email protected])
    # but in the cache the separator is # (hl7.fhir.us.core#3.1.1)
    cache_directory = File.join(user_package_cache, ig_path.sub('@', '#'))
    ig = Inferno::Entities::IG.from_file(cache_directory)
  else
    Tempfile.create(['package', '.tgz']) do |temp_file|
      load_ig(ig_path, nil, temp_file.path)
      cache_directory = add_package_to_cache(ig_path.sub('@', '#'), temp_file.path)
      ig = Inferno::Entities::IG.from_file(cache_directory)
    end
  end
  ig.add_self_to_repository
  ig
end

#user_package_cache ⇒ Object 



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# File 'lib/inferno/repositories/igs.rb', line 74

def user_package_cache
  File.join(Dir.home, '.fhir', 'packages')
end