Class: DarwinCore

Inherits:
Object
  • Object
show all
Defined in:
lib/dwc_archive.rb,
lib/dwc_archive/core.rb,
lib/dwc_archive/errors.rb,
lib/dwc_archive/archive.rb,
lib/dwc_archive/version.rb,
lib/dwc_archive/expander.rb,
lib/dwc_archive/ingester.rb,
lib/dwc_archive/metadata.rb,
lib/dwc_archive/extension.rb,
lib/dwc_archive/generator.rb,
lib/dwc_archive/gnub_taxon.rb,
lib/dwc_archive/xml_reader.rb,
lib/dwc_archive/taxon_normalized.rb,
lib/dwc_archive/generator_eml_xml.rb,
lib/dwc_archive/generator_meta_xml.rb,
lib/dwc_archive/classification_normalizer.rb

Overview

Version constant of the class

Defined Under Namespace

Modules: Ingester, XmlReader Classes: Archive, ClassificationNormalizer, Core, CoreFileError, EncodingError, Error, Expander, Extension, ExtensionFileError, FileNotFoundError, Generator, GeneratorError, GnubTaxon, InvalidArchiveError, Metadata, ParentNotCurrentError, SynonymNormalized, TaxonNormalized, UnpackingError, VernacularNormalized

Constant Summary collapse

DEFAULT_TMP_DIR = 
"/tmp"
VERSION = 
"1.1.9"

Class Attribute Summary collapse

Instance Attribute Summary collapse

Class Method Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(dwc_path, tmp_dir = DEFAULT_TMP_DIR) ⇒ DarwinCore

Returns a new instance of DarwinCore.



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# File 'lib/dwc_archive.rb', line 79

def initialize(dwc_path, tmp_dir = DEFAULT_TMP_DIR)
  @dwc_path = dwc_path
  @archive = DarwinCore::Archive.new(@dwc_path, tmp_dir)
  @core = DarwinCore::Core.new(self)
  @metadata = DarwinCore::Metadata.new(@archive)
  extensions
end

Class Attribute Details

.logger ⇒ Object 



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# File 'lib/dwc_archive.rb', line 67

def self.logger
  @logger ||= Logger.new(nil)
end

Instance Attribute Details

#archive ⇒ Object (readonly)

Returns the value of attribute archive.



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# File 'lib/dwc_archive.rb', line 51

def archive
  @archive
end

#classification_normalizer ⇒ Object (readonly)

Returns the value of attribute classification_normalizer.



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# File 'lib/dwc_archive.rb', line 51

def classification_normalizer
  @classification_normalizer
end

#core ⇒ Object (readonly)

Returns the value of attribute core.



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# File 'lib/dwc_archive.rb', line 51

def core
  @core
end

#metadata ⇒ Object (readonly) Also known as: eml

Returns the value of attribute metadata.



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# File 'lib/dwc_archive.rb', line 51

def metadata
  @metadata
end

Class Method Details

.clean(path) ⇒ Object 



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# File 'lib/dwc_archive.rb', line 36

def clean(path)
  FileUtils.rm_rf(path) if FileTest.exist?(path)
end

.clean_all(tmp_dir = DEFAULT_TMP_DIR) ⇒ Object 



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# File 'lib/dwc_archive.rb', line 60

def self.clean_all(tmp_dir = DEFAULT_TMP_DIR)
  Dir.entries(tmp_dir).each do |entry|
    path = File.join(tmp_dir, entry)
    FileUtils.rm_rf(path) if FileTest.directory?(path) && entry.match(/^dwc_\d+$/)
  end
end

.files(path) ⇒ Object 



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# File 'lib/dwc_archive.rb', line 40

def files(path)
  return nil unless path && FileTest.exist?(path)

  Dir.entries(path).reject { |e| e.match(/[.]{1,2}$/) }.sort
end

.logger_reset ⇒ Object 



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# File 'lib/dwc_archive.rb', line 71

def self.logger_reset
  self.logger = Logger.new(nil)
end

.logger_write(obj_id, message, method = :info) ⇒ Object 



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# File 'lib/dwc_archive.rb', line 75

def self.logger_write(obj_id, message, method = :info)
  logger.send(method, "|#{obj_id}|#{message}|")
end

.nil_field?(field) ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/dwc_archive.rb', line 54

def self.nil_field?(field)
  return true if [nil, "", "/N"].include?(field)

  false
end

.random_path(tmp_dir) ⇒ Object 



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# File 'lib/dwc_archive.rb', line 46

def random_path(tmp_dir)
  File.join(tmp_dir, "dwc_#{rand(10_000_000_000)}")
end

Instance Method Details

#checksum ⇒ Object 



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# File 'lib/dwc_archive.rb', line 110

def checksum
  Digest::SHA1.hexdigest(File.read(@dwc_path))
end

#extensions ⇒ Object 



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# File 'lib/dwc_archive.rb', line 114

def extensions
  return @extensions if @extensions

  root_key = @archive.meta.keys[0]
  ext = @archive.meta[root_key][:extension]
  return @extensions = [] unless ext

  ext = [ext] if ext.class != Array
  @extensions = ext.map { |e| DarwinCore::Extension.new(self, e) }
end

#file_name ⇒ Object 



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# File 'lib/dwc_archive.rb', line 87

def file_name
  File.split(@dwc_path).last
end

#normalize_classification ⇒ Object

generates a hash from a classification data with path to each node, list of synonyms and vernacular names.



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# File 'lib/dwc_archive.rb', line 97

def normalize_classification
  return nil unless parent_id?

  @classification_normalizer ||=
    DarwinCore::ClassificationNormalizer.new(self)
  @classification_normalizer.normalize
end

#parent_id? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/dwc_archive.rb', line 105

def parent_id?
  !@core.fields.join("|").
    downcase.match(/highertaxonid|parentnameusageid/).nil?
end

#path ⇒ Object 



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# File 'lib/dwc_archive.rb', line 91

def path
  File.expand_path(@dwc_path)
end