moab-versioning 4.2.1 → 4.4.2

checksums.yaml

@@ -1,7 +1,7 @@
 ---
-SHA1:
-  metadata.gz: 8226ecfe5e815a81aa72bc564fc1abc341b4f570
-  data.tar.gz: 9d085cad25bc601caec626edb5cf4f778a979fc3
+SHA256:
+  metadata.gz: 4b576c73187205ae4548c6460bac2b68cedab5dc7c3b94a66a5d8ec13729c6ae
+  data.tar.gz: e714a158d2e1388dec94482c1fa858a2ee29a6eca6e0f9004658446801088476
 SHA512:
-  metadata.gz: 6c0072f1cd34f7bd192a4231b6c496e81d4ce380edaf08cd5fb997b240ad64b09c8ce94ed4083a65f812c11971b1e11eadf2d8099edb898226d904a8e58c3d17
-  data.tar.gz: 71aa7a0ff75185089d2a7705a13635b67b0fbaa600b438a35fde7f75a4bd83061f050b1c4eeef98162e38b64a66e6c23e3f45748bde93b5de42acaee32fadf9e
+  metadata.gz: 251925f9e4c45f20f6ae4270fc73adfe9f4645689bda08ebd42c2b707909177ab575e0427c83e321c2ebc039c735f9bc141b29037f28cb65249c25bd9e76d520
+  data.tar.gz: '053391d53a3a3a46bbfedce8e7a04ea0f28a7f5c43689c2bde3c1901f9303eae7356d507904ec1892d9da61f2d4c9c6e58ed3fec894985e19b9ab85dd5fa65fd'

data/lib/moab.rb

@@ -1,3 +1,5 @@
+# frozen_string_literal: true
+
 # Moab is a module that provides a distintive namespace for the collection of classes it contains.
 #
 # ====Data Model
@@ -29,11 +31,10 @@
 # @note Copyright (c) 2012 by The Board of Trustees of the Leland Stanford Junior University.
 #   All rights reserved.  See {file:LICENSE.rdoc} for details.
 module Moab
-  DEFAULT_CHECKSUM_TYPES = [:md5, :sha1, :sha256].freeze
+  DEFAULT_CHECKSUM_TYPES = %i[md5 sha1 sha256].freeze
 end
 
 require 'serializer'
-require 'confstruct/configuration'
 require 'moab/config'
 require 'moab/utc_time'
 require 'moab/file_signature'

data/lib/moab/bagger.rb

@@ -1,3 +1,5 @@
+# frozen_string_literal: true
+
 module Moab
   # A class used to create a BagIt package from a version inventory and a set of source files.
   # The {#fill_bag} method is called with a package_mode parameter that specifies
@@ -25,7 +27,7 @@ module Moab
       @version_inventory = version_inventory
       @signature_catalog = signature_catalog
       @bag_pathname = Pathname.new(bag_pathname)
-      create_bagit_txt()
+      create_bagit_txt
     end
 
     # @return [FileInventory] The complete inventory of the files comprising a digital object version
@@ -54,7 +56,7 @@ module Moab
 
     # @api internal
     # @return [void] Generate the bagit.txt tag file
-    def create_bagit_txt()
+    def create_bagit_txt
       bag_pathname.mkpath
       bag_pathname.join("bagit.txt").open('w') do |f|
         f.puts "Tag-File-Character-Encoding: UTF-8"
@@ -63,13 +65,13 @@ module Moab
     end
 
     # @return [NilClass] Delete the bagit files
-    def delete_bag()
+    def delete_bag
       # make sure this looks like a bag before deleting
       if bag_pathname.join('bagit.txt').exist?
         if bag_pathname.join('data').exist?
           bag_pathname.rmtree
         else
-          bag_pathname.children.each { |file| file.delete }
+          bag_pathname.children.each(&:delete)
           bag_pathname.rmdir
         end
       end
@@ -77,7 +79,7 @@ module Moab
     end
 
     # @param tar_pathname [Pathname] The location of the tar file (default is based on bag location)
-    def delete_tarfile()
+    def delete_tarfile
       bag_name = bag_pathname.basename
       bag_parent = bag_pathname.parent
       tar_pathname = bag_parent.join("#{bag_name}.tar")
@@ -140,7 +142,8 @@ module Moab
     #    Return true if successful or nil if the group was not found in the inventory
     def deposit_group(group_id, source_dir)
       group = bag_inventory.group(group_id)
-      return nil? if group.nil? or group.files.empty?
+      return nil? if group.nil? || group.files.empty?
+
       target_dir = bag_pathname.join('data', group_id)
       group.path_list.each do |relative_path|
         source = source_dir.join(relative_path)
@@ -157,7 +160,8 @@ module Moab
     #    Return true if successful or nil if the group was not found in the inventory
     def reconstuct_group(group_id, storage_object_dir)
       group = bag_inventory.group(group_id)
-      return nil? if group.nil? or group.files.empty?
+      return nil? if group.nil? || group.files.empty?
+
       target_dir = bag_pathname.join('data', group_id)
       group.files.each do |file|
         catalog_entry = signature_catalog.signature_hash[file.signature]
@@ -165,7 +169,7 @@ module Moab
         file.instances.each do |instance|
           target = target_dir.join(instance.path)
           target.parent.mkpath
-          FileUtils.symlink source, target
+          FileUtils.symlink source, target unless target.exist?
         end
       end
       true
@@ -183,8 +187,8 @@ module Moab
     # @api internal
     # @return [void] Using the checksum information from the inventory, create BagIt manifest files for the payload
     def create_payload_manifests
-      manifest_pathname = Hash.new
-      manifest_file = Hash.new
+      manifest_pathname = {}
+      manifest_file = {}
       DEFAULT_CHECKSUM_TYPES.each do |type|
         manifest_pathname[type] = bag_pathname.join("manifest-#{type}.txt")
         manifest_file[type] = manifest_pathname[type].open('w')
@@ -205,7 +209,7 @@ module Moab
         if manifest_file[type]
           manifest_file[type].close
           manifest_pathname[type].delete if
-              manifest_pathname[type].exist? and manifest_pathname[type].size == 0
+              manifest_pathname[type].exist? && manifest_pathname[type].size == 0
         end
       end
     end
@@ -222,9 +226,9 @@ module Moab
 
     # @api internal
     # @return [void] create BagIt tag manifest files containing checksums for all files in the bag's root directory
-    def create_tagfile_manifests()
-      manifest_pathname = Hash.new
-      manifest_file = Hash.new
+    def create_tagfile_manifests
+      manifest_pathname = {}
+      manifest_file = {}
       DEFAULT_CHECKSUM_TYPES.each do |type|
         manifest_pathname[type] = bag_pathname.join("tagmanifest-#{type}.txt")
         manifest_file[type] = manifest_pathname[type].open('w')
@@ -243,7 +247,7 @@ module Moab
         if manifest_file[type]
           manifest_file[type].close
           manifest_pathname[type].delete if
-              manifest_pathname[type].exist? and manifest_pathname[type].size == 0
+              manifest_pathname[type].exist? && manifest_pathname[type].size == 0
         end
       end
     end
@@ -259,8 +263,9 @@ module Moab
       rescue
         shell_execute(tar_cmd.sub('--force-local', ''))
       end
-      raise "Unable to create tarfile #{tar_pathname}" unless tar_pathname.exist?
-      return true
+      raise(MoabRuntimeError, "Unable to create tarfile #{tar_pathname}") unless tar_pathname.exist?
+
+      true
     end
 
     # Executes a system command in a subprocess
@@ -273,12 +278,12 @@ module Moab
         stdout
       else
         msg = "Shell command failed: [#{command}] caused by <STDERR = #{stderr}>"
-        msg << " STDOUT = #{stdout}" if stdout && stdout.length.positive?
-        raise(StandardError, msg)
+        msg << " STDOUT = #{stdout}" if stdout&.length&.positive?
+        raise(MoabStandardError, msg)
       end
     rescue SystemCallError => e
       msg = "Shell command failed: [#{command}] caused by #{e.inspect}"
-      raise(StandardError, msg)
+      raise(MoabStandardError, msg)
     end
   end
 end

data/lib/moab/config.rb

@@ -1,12 +1,43 @@
-require 'moab'
+# frozen_string_literal: true
 
 module Moab
-  # @return [Confstruct::Configuration] the configuration data
-  Config = Confstruct::Configuration.new do
-    storage_roots nil
-    storage_trunk nil
-    deposit_trunk nil
-    path_method :druid_tree
-    checksum_algos [:md5, :sha1, :sha256]
+  # A place to store configuration for the gem
+  class Configuration
+    def initialize
+      @path_method = :druid_tree
+      @checksum_algos = [:md5, :sha1, :sha256]
+    end
+
+    def configure(&block)
+      instance_eval(&block)
+    end
+
+    def storage_roots(new_value = nil)
+      @storage_roots = new_value if new_value
+      @storage_roots
+    end
+
+    def storage_trunk(new_value = nil)
+      @storage_trunk = new_value if new_value
+      @storage_trunk
+    end
+
+    def deposit_trunk(new_value = nil)
+      @deposit_trunk = new_value if new_value
+      @deposit_trunk
+    end
+
+    def path_method(new_value = nil)
+      @path_method = new_value if new_value
+      @path_method
+    end
+
+    def checksum_algos(new_value = nil)
+      @checksum_algos = new_value if new_value
+      @checksum_algos
+    end
   end
+
+  # @return [Moab::Configuration] the configuration data
+  Config = Configuration.new
 end

data/lib/moab/deposit_bag_validator.rb

@@ -1,3 +1,5 @@
+# frozen_string_literal: true
+
 module Moab
   # Given a deposit bag, ensures the contents valid for becoming a StorageObjectVersion
   # this is a Shameless Green implementation, combining code from:
@@ -30,23 +32,23 @@ module Moab
       VERSION_MISSING_FROM_FILE => "Version xml file %{version_file} missing data at %{xpath} containing version id"
     }.freeze
 
-    REQUIRED_MANIFEST_CHECKSUM_TYPE = 'sha256'.freeze
-    RECOGNIZED_CHECKSUM_ALGORITHMS = [:md5, :sha1, :sha256, :sha384, :sha512].freeze
+    REQUIRED_MANIFEST_CHECKSUM_TYPE = 'sha256'
+    RECOGNIZED_CHECKSUM_ALGORITHMS = %i[md5 sha1 sha256 sha384 sha512].freeze
 
-    TAGMANIFEST = 'tagmanifest'.freeze
-    MANIFEST = 'manifest'.freeze
-    DATA_DIR_BASENAME = 'data'.freeze
-    BAG_INFO_TXT_BASENAME = 'bag-info.txt'.freeze
-    VERSION_ADDITIONS_BASENAME = 'versionAdditions.xml'.freeze
-    VERSION_INVENTORY_BASENAME = 'versionInventory.xml'.freeze
-    VERSION_METADATA_PATH = "#{DATA_DIR_BASENAME}/metadata/versionMetadata.xml".freeze
+    TAGMANIFEST = 'tagmanifest'
+    MANIFEST = 'manifest'
+    DATA_DIR_BASENAME = 'data'
+    BAG_INFO_TXT_BASENAME = 'bag-info.txt'
+    VERSION_ADDITIONS_BASENAME = 'versionAdditions.xml'
+    VERSION_INVENTORY_BASENAME = 'versionInventory.xml'
+    VERSION_METADATA_PATH = "#{DATA_DIR_BASENAME}/metadata/versionMetadata.xml"
 
     REQUIRED_BAG_FILES = [
       DATA_DIR_BASENAME,
-      'bagit.txt'.freeze,
+      'bagit.txt',
       BAG_INFO_TXT_BASENAME,
-      "#{MANIFEST}-#{REQUIRED_MANIFEST_CHECKSUM_TYPE}.txt".freeze,
-      "#{TAGMANIFEST}-#{REQUIRED_MANIFEST_CHECKSUM_TYPE}.txt".freeze,
+      "#{MANIFEST}-#{REQUIRED_MANIFEST_CHECKSUM_TYPE}.txt",
+      "#{TAGMANIFEST}-#{REQUIRED_MANIFEST_CHECKSUM_TYPE}.txt",
       VERSION_ADDITIONS_BASENAME,
       VERSION_INVENTORY_BASENAME,
       VERSION_METADATA_PATH
@@ -64,6 +66,7 @@ module Moab
     def validation_errors
       return [single_error_hash(BAG_DIR_NOT_FOUND, bag_dir: deposit_bag_pathname)] unless deposit_bag_pathname.exist?
       return result_array unless required_bag_files_exist?
+
       verify_version
       verify_tagmanifests
       verify_payload_size
@@ -112,6 +115,7 @@ module Moab
       doc = Nokogiri::XML(File.open(pathname.to_s), &:strict)
       version_id = doc.xpath(xpath).last.text unless doc.xpath(xpath).empty?
       return version_id.to_i if version_id
+
       err_data = {
         version_file: pathname,
         xpath: xpath
@@ -129,6 +133,7 @@ module Moab
 
     def verify_version_from_xml_file(file_pathname, found)
       return if found == expected_new_version
+
       err_data = {
         file_pathname: file_pathname,
         new_version: expected_new_version,
@@ -186,7 +191,7 @@ module Moab
       home_dir_pathnames = deposit_bag_pathname.children.reject { |file| file.basename.to_s.start_with?(TAGMANIFEST) }
       hash_with_full_pathnames = generate_checksums_hash(home_dir_pathnames, types_to_generate)
       # return hash keys as basenames only
-      hash_with_full_pathnames.map { |k, v| [Pathname.new(k).basename.to_s, v] }.to_h
+      hash_with_full_pathnames.transform_keys { |k| Pathname.new(k).basename.to_s }
     end
 
     # generate hash of checksums by file name for bag data dir files
@@ -194,7 +199,7 @@ module Moab
       data_pathnames = deposit_bag_pathname.join(DATA_DIR_BASENAME).find
       hash_with_full_pathnames = generate_checksums_hash(data_pathnames, types_to_generate)
       # return hash keys beginning with 'data/'
-      hash_with_full_pathnames.map { |k, v| [Pathname.new(k).relative_path_from(deposit_bag_pathname).to_s, v] }.to_h
+      hash_with_full_pathnames.transform_keys { |k| Pathname.new(k).relative_path_from(deposit_bag_pathname).to_s }
     end
 
     def generate_checksums_hash(pathnames, types_to_generate)
@@ -251,6 +256,7 @@ module Moab
         end
       end
       return if diff_hash.empty?
+
       err_data = {
         manifest_type: manifest_type,
         diffs: diff_hash
@@ -266,9 +272,7 @@ module Moab
       checksum_types_to_compare.each do |type|
         left_checksum = left_checksums[type]
         right_checksum = right_checksums[type]
-        if left_checksum != right_checksum
-          diff_hash[type] = { left_label => left_checksum, right_label => right_checksum }
-        end
+        diff_hash[type] = { left_label => left_checksum, right_label => right_checksum } if left_checksum != right_checksum
       end
       diff_hash.empty? ? nil : diff_hash
     end
@@ -277,6 +281,7 @@ module Moab
       sizes_from_bag_info_file = bag_info_payload_size
       generated_sizes = generated_payload_size
       return if sizes_from_bag_info_file == generated_sizes
+
       err_data = {
         bag_info_sizes: sizes_from_bag_info_file,
         generated_sizes: generated_sizes

data/lib/moab/exceptions.rb

@@ -1,13 +1,15 @@
+# frozen_string_literal: true
+
 module Moab
-  class ObjectNotFoundException < RuntimeError
-  end
+  class MoabRuntimeError < RuntimeError; end
+
+  class MoabStandardError < StandardError; end
+
+  class FileNotFoundException < MoabRuntimeError; end
 
-  class FileNotFoundException < RuntimeError
-  end
+  class InvalidMetadataException < MoabRuntimeError; end
 
-  class InvalidMetadataException < RuntimeError
-  end
+  class InvalidSuriSyntaxError < MoabRuntimeError; end
 
-  class ValidationException < RuntimeError
-  end
+  class ObjectNotFoundException < MoabRuntimeError; end
 end

data/lib/moab/file_group.rb

@@ -1,4 +1,4 @@
-require 'moab'
+# frozen_string_literal: true
 
 module Moab
   # A container for a standard subset of a digital objects {FileManifestation} objects
@@ -22,22 +22,23 @@ module Moab
 
     # (see Serializable#initialize)
     def initialize(opts = {})
-      @signature_hash = Hash.new
+      @signature_hash = {}
       @data_source = ""
+      @signatures_from_bag = nil # prevents later warning: instance variable @signatures_from_bag not initialized
       super(opts)
     end
 
     # @attribute
     # @return [String] The name of the file group
-    attribute :group_id, String, :tag => 'groupId', :key => true
+    attribute :group_id, String, tag: 'groupId', key: true
 
     # @attribute
     # @return [String] The directory location or other source of this groups file data
-    attribute :data_source, String, :tag => 'dataSource'
+    attribute :data_source, String, tag: 'dataSource'
 
     # @attribute
     # @return [Integer] The total number of data files (dynamically calculated)
-    attribute :file_count, Integer, :tag => 'fileCount', :on_save => Proc.new { |i| i.to_s }
+    attribute :file_count, Integer, tag: 'fileCount', on_save: proc { |i| i.to_s }
 
     def file_count
       files.inject(0) { |sum, manifestation| sum + manifestation.file_count }
@@ -45,7 +46,7 @@ module Moab
 
     # @attribute
     # @return [Integer] The total size (in bytes) of all data files (dynamically calculated)
-    attribute :byte_count, Integer, :tag => 'byteCount', :on_save => Proc.new { |i| i.to_s }
+    attribute :byte_count, Integer, tag: 'byteCount', on_save: proc { |i| i.to_s }
 
     def byte_count
       files.inject(0) { |sum, manifestation| sum + manifestation.byte_count }
@@ -53,7 +54,7 @@ module Moab
 
     # @attribute
     # @return [Integer] The total disk usage (in 1 kB blocks) of all data files (estimating du -k result) (dynamically calculated)
-    attribute :block_count, Integer, :tag => 'blockCount', :on_save => Proc.new { |i| i.to_s }
+    attribute :block_count, Integer, tag: 'blockCount', on_save: proc { |i| i.to_s }
 
     def block_count
       files.inject(0) { |sum, manifestation| sum + manifestation.block_count }
@@ -61,12 +62,12 @@ module Moab
 
     # @return [Array<String>] The data fields to include in summary reports
     def summary_fields
-      %w{group_id file_count byte_count block_count}
+      %w[group_id file_count byte_count block_count]
     end
 
     # @attribute
     # @return [Array<FileManifestation>] The set of files comprising the group
-    has_many :files, FileManifestation, :tag => 'file'
+    has_many :files, FileManifestation, tag: 'file'
 
     def files
       signature_hash.values
@@ -80,7 +81,7 @@ module Moab
     # @return [Hash<String,FileSignature>] An index of file paths,
     #   used to test for existence of a filename in this file group
     def path_hash
-      path_hash = Hash.new
+      path_hash = {}
       signature_hash.each do |signature, manifestation|
         manifestation.instances.each do |instance|
           path_hash[instance.path] = signature
@@ -91,14 +92,14 @@ module Moab
 
     # @return [Array<String>] The list of file paths in this group
     def path_list
-      files.collect { |file| file.instances.collect { |instance| instance.path } }.flatten
+      files.collect { |file| file.instances.collect(&:path) }.flatten
     end
 
     # @api internal
     # @param signature_subset [Array<FileSignature>] The signatures used to select the entries to return
     # @return [Hash<String,FileSignature>] A pathname,signature hash containing a subset of the filenames in this file group
     def path_hash_subset(signature_subset)
-      path_hash = Hash.new
+      path_hash = {}
       signature_subset.each do |signature|
         manifestation = signature_hash[signature]
         manifestation.instances.each do |instance|
@@ -132,7 +133,7 @@ module Moab
     # @return [void] Add a single {FileSignature},{FileInstance} key/value pair to this group.
     #   Data is actually stored in the {#signature_hash}
     def add_file_instance(signature, instance)
-      if signature_hash.has_key?(signature)
+      if signature_hash.key?(signature)
         manifestation = signature_hash[signature]
       else
         manifestation = FileManifestation.new
@@ -146,7 +147,7 @@ module Moab
     # @return [void] Remove a file from the inventory
     # for example, the manifest inventory does not contain a file entry for itself
     def remove_file_having_path(path)
-      signature = self.path_hash[path]
+      signature = path_hash[path]
       signature_hash.delete(signature)
     end
 
@@ -161,10 +162,12 @@ module Moab
     # @param pathname [Pathname] The file path to be tested
     # @return [Boolean] Test whether the given path is contained within the {#base_directory}
     def is_descendent_of_base?(pathname)
-      raise("base_directory has not been set") if @base_directory.nil?
+      raise(MoabRuntimeError, "base_directory has not been set") if @base_directory.nil?
+
       is_descendent = false
       pathname.expand_path.ascend { |ancestor| is_descendent ||= (ancestor == @base_directory) }
-      raise("#{pathname} is not a descendent of #{@base_directory}") unless is_descendent
+      raise(MoabRuntimeError, "#{pathname} is not a descendent of #{@base_directory}") unless is_descendent
+
       is_descendent
     end
 
@@ -203,9 +206,9 @@ module Moab
       pathname = Pathname.new(path).expand_path
       validated ||= is_descendent_of_base?(pathname)
       pathname.children.sort.each do |child|
-        if child.basename.to_s == ".DS_Store"
-          next
-        elsif child.directory?
+        next if child.basename.to_s == '.DS_Store'
+
+        if child.directory?
           harvest_directory(child, recursive, validated) if recursive
         else
           add_physical_file(child, validated)
@@ -224,9 +227,7 @@ module Moab
       instance = FileInstance.new.instance_from_file(pathname, @base_directory)
       if @signatures_from_bag && @signatures_from_bag[pathname]
         signature = @signatures_from_bag[pathname]
-        unless signature.complete?
-          signature = signature.normalized_signature(pathname)
-        end
+        signature = signature.normalized_signature(pathname) unless signature.complete?
       else
         signature = FileSignature.new.signature_from_file(pathname)
       end