Class: Moab::Bagger

Inherits:
Object
  • Object
show all
Defined in:
lib/moab/bagger.rb

Overview

Note:

Copyright © 2012 by The Board of Trustees of the Leland Stanford Junior University. All rights reserved. See LICENSE for details.

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 whether the bag is being created for deposit into the repository or is to contain the output of a version reconstruction.

  • In :depositor mode, the version inventory is filtered using the digital object’s signature catalog so that only

new files are included

  • In :reconstructor mode, the version inventory and signature catalog are used together to regenerate the complete

set of files for the version.

Data Model

  • StorageRepository = represents a digital object repository storage node

    • StorageServices = supports application layer access to the repository’s objects, data, and metadata

    • StorageObject = represents a digital object’s repository storage location and ingest/dissemination methods

      • StorageObjectVersion [1..*] = represents a version subdirectory within an object’s home directory

        • Bagger [1] = utility for creating bagit packages for ingest or dissemination

Instance Attribute Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(version_inventory, signature_catalog, bag_pathname) ⇒ Bagger

Returns a new instance of Bagger.

Parameters:

  • version_inventory (FileInventory) —

    The complete inventory of the files comprising a digital object version

  • signature_catalog (SignatureCatalog) —

    The signature catalog, used to specify source paths (in :reconstructor mode), or to filter the version inventory (in :depositor mode)

  • bag_pathname (Pathname, String) —

    The location of the Bagit bag to be created



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# File 'lib/moab/bagger.rb', line 29

def initialize(version_inventory, signature_catalog, bag_pathname)
  @version_inventory = version_inventory
  @signature_catalog = signature_catalog
  @bag_pathname = Pathname.new(bag_pathname)
  create_bagit_txt()
end

Instance Attribute Details

#bag_inventory ⇒ FileInventory

Returns The actual inventory of the files to be packaged (derived from @version_inventory in #fill_bag).

Returns:

  • (FileInventory) —

    The actual inventory of the files to be packaged (derived from @version_inventory in #fill_bag)



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# File 'lib/moab/bagger.rb', line 47

def bag_inventory
  @bag_inventory
end

#bag_pathname ⇒ Pathname

Returns The location of the Bagit bag to be created.

Returns:

  • (Pathname) —

    The location of the Bagit bag to be created



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# File 'lib/moab/bagger.rb', line 44

def bag_pathname
  @bag_pathname
end

#package_mode ⇒ Symbol

Returns The operational mode controlling what gets bagged #fill_bag and the full path of source files #fill_payload.

Returns:



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# File 'lib/moab/bagger.rb', line 51

def package_mode
  @package_mode
end

#signature_catalog ⇒ SignatureCatalog

Returns The signature catalog, used to specify source paths (in :reconstructor mode), or to filter the version inventory (in :depositor mode).

Returns:

  • (SignatureCatalog) —

    The signature catalog, used to specify source paths (in :reconstructor mode), or to filter the version inventory (in :depositor mode)



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# File 'lib/moab/bagger.rb', line 41

def signature_catalog
  @signature_catalog
end

#version_inventory ⇒ FileInventory

Returns The complete inventory of the files comprising a digital object version.

Returns:

  • (FileInventory) —

    The complete inventory of the files comprising a digital object version



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# File 'lib/moab/bagger.rb', line 37

def version_inventory
  @version_inventory
end

Instance Method Details

#create_bag_info_txt ⇒ void

This method returns an undefined value.

Returns Generate the bag-info.txt tag file.



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# File 'lib/moab/bagger.rb', line 218

def create_bag_info_txt
  @bag_pathname.join("bag-info.txt").open('w') do |f|
    f.puts "External-Identifier: #{@bag_inventory.package_id}"
    f.puts "Payload-Oxum: #{@bag_inventory.byte_count}.#{@bag_inventory.file_count}"
    f.puts "Bag-Size: #{@bag_inventory.human_size}"
  end
end

#create_bag_inventory(package_mode) ⇒ FileInventory

Returns Create, write, and return the inventory of the files that will become the payload.

Parameters:

  • package_mode (Symbol) —

    The operational mode controlling what gets bagged and the full path of source files (Bagger#fill_payload)

Returns:

  • (FileInventory) —

    Create, write, and return the inventory of the files that will become the payload



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# File 'lib/moab/bagger.rb', line 107

def create_bag_inventory(package_mode)
  @package_mode = package_mode
  @bag_pathname.mkpath
  case package_mode
    when :depositor
      @version_inventory.write_xml_file(@bag_pathname, 'version')
      @bag_inventory = @signature_catalog.version_additions(@version_inventory)
      @bag_inventory.write_xml_file(@bag_pathname, 'additions')
    when :reconstructor
      @bag_inventory = @version_inventory
      @bag_inventory.write_xml_file(@bag_pathname, 'version')
  end
  @bag_inventory
end

#create_bagit_txt ⇒ void

This method returns an undefined value.

Returns Generate the bagit.txt tag file.



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# File 'lib/moab/bagger.rb', line 62

def create_bagit_txt()
  @bag_pathname.mkpath
  @bag_pathname.join("bagit.txt").open('w') do |f|
    f.puts "Tag-File-Character-Encoding: UTF-8"
    f.puts "BagIt-Version: 0.97"
  end
end

#create_payload_manifests ⇒ void

This method returns an undefined value.

Returns Using the checksum information from the inventory, create BagIt manifest files for the payload.



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# File 'lib/moab/bagger.rb', line 187

def create_payload_manifests
  manifest_pathname = Hash.new
  manifest_file = Hash.new
  manifest_types =  [:md5, :sha1, :sha256]
  manifest_types.each do |type|
    manifest_pathname[type] = @bag_pathname.join("manifest-#{type.to_s}.txt")
    manifest_file[type] = manifest_pathname[type].open('w')
  end
  @bag_inventory.groups.each do |group|
    group.files.each do |file|
      fixity = file.signature.fixity
      file.instances.each do |instance|
        data_path = File.join('data', group.group_id, instance.path)
        manifest_types.each do |type|
          manifest_file[type].puts("#{fixity[type]} #{data_path}") if fixity[type]
        end
      end
    end
  end
ensure
  manifest_types.each do |type|
    if manifest_file[type]
      manifest_file[type].close
      manifest_pathname[type].delete if
          manifest_pathname[type].exist? and manifest_pathname[type].size == 0
    end
  end
end

#create_tagfile_manifests ⇒ void

This method returns an undefined value.

Returns create BagIt tag manifest files containing checksums for all files in the bag’s root directory.



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# File 'lib/moab/bagger.rb', line 228

def create_tagfile_manifests()
  manifest_pathname = Hash.new
  manifest_file = Hash.new
  manifest_types =  [:md5, :sha1, :sha256]
  manifest_types.each do |type|
    manifest_pathname[type] = @bag_pathname.join("tagmanifest-#{type.to_s}.txt")
    manifest_file[type] = manifest_pathname[type].open('w')
  end
  @bag_pathname.children.each do |file|
    unless file.directory? || file.basename.to_s[0, 11] == 'tagmanifest'
      signature = FileSignature.new.signature_from_file(file)
      fixity = signature.fixity
      manifest_types.each do |type|
        manifest_file[type].puts("#{fixity[type]} #{file.basename}") if fixity[type]
      end
    end
  end
ensure
  manifest_types.each do |type|
    if manifest_file[type]
      manifest_file[type].close
      manifest_pathname[type].delete if
          manifest_pathname[type].exist? and manifest_pathname[type].size == 0
    end
  end
end

#create_tagfiles ⇒ Boolean

Returns create BagIt manifests and tag files. Return true if successful.

Returns:

  • (Boolean) —

    create BagIt manifests and tag files. Return true if successful



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# File 'lib/moab/bagger.rb', line 177

def create_tagfiles
  create_payload_manifests
  create_bag_info_txt
  create_bagit_txt
  create_tagfile_manifests
  true
end

#create_tarfile(tar_pathname = nil) ⇒ Boolean

Returns Create a tar file containing the bag.

Returns:

  • (Boolean) —

    Create a tar file containing the bag



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# File 'lib/moab/bagger.rb', line 256

def create_tarfile(tar_pathname=nil)
  bag_name = @bag_pathname.basename
  bag_parent = @bag_pathname.parent
  tar_pathname ||= bag_parent.join("#{bag_name}.tar")
  tar_cmd="cd '#{bag_parent}'; tar --dereference --force-local -cf  '#{tar_pathname}' '#{bag_name}'"
  begin
    shell_execute(tar_cmd)
  rescue
    shell_execute(tar_cmd.sub('--force-local',''))
  end
  raise "Unable to create tarfile #{tar_pathname}" unless tar_pathname.exist?
  return true

end

#delete_bag ⇒ NilClass

Returns Delete the bagit files.

Returns:

  • (NilClass) —

    Delete the bagit files



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# File 'lib/moab/bagger.rb', line 71

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.rmdir
    end
  end
  nil
end

#delete_tarfile ⇒ Object

Parameters:

  • tar_pathname (Pathname) —

    The location of the tar file (default is based on bag location)



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# File 'lib/moab/bagger.rb', line 85

def delete_tarfile()
  bag_name = @bag_pathname.basename
  bag_parent = @bag_pathname.parent
  tar_pathname = bag_parent.join("#{bag_name}.tar")
  tar_pathname.delete if tar_pathname.exist?
end

#deposit_group(group_id, source_dir) ⇒ Boolean

Copy all the files listed in the group inventory to the bag. Return true if successful or nil if the group was not found in the inventory

Parameters:

  • group_id (String) —

    The name of the data group being copied to the bag

  • source_dir (Pathname) —

    The location from which files should be copied

Returns:

  • (Boolean) —

    Copy all the files listed in the group inventory to the bag. Return true if successful or nil if the group was not found in the inventory



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# File 'lib/moab/bagger.rb', line 143

def deposit_group(group_id, source_dir)
  group = @bag_inventory.group(group_id)
  return nil? if group.nil? or group.files.empty?
  target_dir = @bag_pathname.join('data',group_id)
  group.path_list.each do |relative_path|
    source = source_dir.join(relative_path)
    target = target_dir.join(relative_path)
    target.parent.mkpath
    FileUtils.symlink source, target
  end
  true
end

#fill_bag(package_mode, source_base_pathname) ⇒ Bagger

Returns Perform all the operations required to fill the bag payload, write the manifests and tagfiles, and checksum the tagfiles.

Examples:

Parameters:

  • package_mode (Symbol) —

    The operational mode controlling what gets bagged and the full path of source files (Bagger#fill_payload)

  • source_base_pathname (Pathname) —

    The home location of the source files

Returns:

  • (Bagger) —

    Perform all the operations required to fill the bag payload, write the manifests and tagfiles, and checksum the tagfiles



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# File 'lib/moab/bagger.rb', line 97

def fill_bag(package_mode, source_base_pathname)
  create_bag_inventory(package_mode)
  fill_payload(source_base_pathname)
  create_tagfiles
  self
end

#fill_payload(source_base_pathname) ⇒ void

This method returns an undefined value.

This method uses Unix hard links in order to greatly speed up the process. Hard links, however, require that the target bag must be created within the same filesystem as the source files

Parameters:

  • source_base_pathname (Pathname) —

    The home location of the source files



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# File 'lib/moab/bagger.rb', line 127

def fill_payload(source_base_pathname)
  @bag_inventory.groups.each do |group|
    group_id = group.group_id
    case @package_mode
      when :depositor
        deposit_group(group_id, source_base_pathname.join(group_id))
      when :reconstructor
        reconstuct_group(group_id, source_base_pathname)
    end
  end
end

#reconstuct_group(group_id, storage_object_dir) ⇒ Boolean

Copy all the files listed in the group inventory to the bag. Return true if successful or nil if the group was not found in the inventory

Parameters:

  • group_id (String) —

    The name of the data group being copied to the bag

  • storage_object_dir (Pathname) —

    The home location of the object store from which files should be copied

Returns:

  • (Boolean) —

    Copy all the files listed in the group inventory to the bag. Return true if successful or nil if the group was not found in the inventory



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# File 'lib/moab/bagger.rb', line 160

def reconstuct_group(group_id, storage_object_dir)
  group = @bag_inventory.group(group_id)
  return nil? if group.nil? or group.files.empty?
  target_dir = @bag_pathname.join('data',group_id)
  group.files.each do |file|
    catalog_entry = @signature_catalog.signature_hash[file.signature]
    source = storage_object_dir.join(catalog_entry.storage_path)
    file.instances.each do |instance|
      target = target_dir.join(instance.path)
      target.parent.mkpath
      FileUtils.symlink source, target
    end
  end
  true
end

#reset_bag ⇒ void

This method returns an undefined value.

Returns Delete any existing bag data and re-initialize the bag directory.



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# File 'lib/moab/bagger.rb', line 54

def reset_bag
  delete_bag
  delete_tarfile
  create_bagit_txt
end

#shell_execute(command) ⇒ String

Executes a system command in a subprocess. The method will return stdout from the command if execution was successful. The method will raise an exception if if execution fails. The exception’s message will contain the explaination of the failure.

Parameters:

  • command (String) —

    the command to be executed

Returns:

  • (String) —

    stdout from the command if execution was successful



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# File 'lib/moab/bagger.rb', line 277

def shell_execute(command)
  status, stdout, stderr = systemu(command)
  if (status.exitstatus != 0)
    raise stderr
  end
  return stdout
rescue
  msg = "Command failed to execute: [#{command}] caused by <STDERR = #{stderr.split($/).join('; ')}>"
  msg << " STDOUT = #{stdout.split($/).join('; ')}" if (stdout && (stdout.length > 0))
  raise msg
end