gem to handle Darwin Core Archive files
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dwc-archive.gemspec

README.md

Darwin Core Archive

Gem Version Continuous Integration Status Coverage Status CodePolice Dependency Status

Darwin Core Archive format is a current standard for information exchange between Global Names Architecture modules. This gem allows to work with Darwin Core Archive data compressed to either zip or tar.gz files. More information about Darwing Core Archive can be found on a GBIF page:

Installation

sudo gem install dwc-archive

System Requirements

You need Redis Server and unzip library installed

Usage

require 'rubygems'
require 'dwc-archive'

dwc = DarwinCore.new('/path_to_file/archive_file.tar.gz')
dwc.archive.files      # the archive file list
dwc.metadata.data      # summary of metadata from eml.xml if it exists
dwc.metadata.authors   # authors of the archive
dwc.core.data          # summary of DarwinCore main file
dwc.core.file_path     # path to the DarwinCore main file
dwc.extensions         # array of DarwinCore Star extensions
dwc.extensions[0].data # summary for an extension

# read content of the core data file into memory or used with a block
# it returns array of arrays of data
# rows that had a wrong encoding will be collected into errors array
data, errors = dwc.core.read

# read content using a block, getting back results in sets of 100 rows each
results = []
tail_data, tail_errors = dwc.core.read(100) do |data, errors|
  results << [data, errors]
end
results << [tail_data, tail_errors]

# read content of an extension data file into memory
data, errors = dwc.core.extensions[0].read

# read content of an extension data using block
results = []
tail_data, tail_errors = dwc.core.extensions[0](100) do |data, errors|
  results << [data, errors]
end
results << [tail_data, tail_errors]

# normalize names in classification collecting together synonyms,
# canonical names, vernacular names and associating paths to taxons
# in a classification distributed as DwCA file

result = dwc.normalize_classification

# for a finer control over normalization:

cn = DarwinCore::ClassificationNormalizer.new(dwc)
cn.normalize
# if you don't want to generate path consisting of canonical forms
# of ancestors to a taxon
cn.normalize(:with_canonical_names => false)

# if you don't want to ingest information from extensions
cn.normalize(:with_extensions => false)

# to get a flat hash of nodes with attached vernacular names and synonyms
normalized_data = cn.normalized_data

# to get a representation of tree organization as a hash
classification_tree = cn.tree

# to get list of all name strings used as scientific or vernacular names
all_name_strings = cn.name_strings

# to get list of errors generated during the normalization
errors = cn.error_names

DarwinCore.clean_all   # remove all expanded archives

Creating a DarwinCore Archive file

gen = DarwinCore::Generator.new('/tmp/dwc_birches.tar.gz')

core = [
  ["http://rs.tdwg.org/dwc/terms/taxonID",
   "http://rs.tdwg.org/dwc/terms/parentNameUsageID",
   "http://rs.tdwg.org/dwc/terms/scientificName",
   "http://rs.tdwg.org/dwc/terms/taxonRank"],
  [1, 0, "Plantae", "kingdom"],
  [2, 1, "Betula", "genus"],
  [3, 2, "Betula verucosa", "species"]
]

vernacular_names = [
  ["http://rs.tdwg.org/dwc/terms/TaxonID",
  "http://rs.tdwg.org/dwc/terms/vernacularName"],
  [1, "Plants"],
  [1, "Растения"],
  [2, "Birch"],
  [2, "Береза"],
  [3, "Wheeping Birch"],
  [3, "Береза плакучая"]
]

eml = {
  :id => '1234',
  :license => 'http://creativecommons.org/licenses/by-sa/3.0/',
  :title => 'Test Classification',
  :authors => [
    { :first_name => 'John',
      :last_name => 'Doe',
      :email => 'jdoe@example.com',
      :organization => 'Example',
      :position => 'Assistant Professor',
      :url => 'http://example.org' },
      { :first_name => 'Jane',
        :last_name => 'Doe',
        :email => 'jane@example.com' }
],
  :metadata_providers => [
    { :first_name => 'Jim',
      :last_name => 'Doe',
      :email => 'jimdoe@example.com',
      :url => 'http://aggregator.example.org' }],
  :abstract => 'test classification',
  :citation =>
    'Test classification: Doe John, Doe Jane, Taxnonmy, 10, 1, 2010',
  :url => 'http://example.com'
}

gen.add_core(core, 'core.txt')
gen.add_extension(vernacular_names,
                  'vernacular_names.txt',
                  true, 'http://rs.gbif.org/terms/1.0/VernacularName')
gen.add_meta_xml
gen.add_eml_xml(eml)
gen.pack

Logging

Gem has ability to show logs of it's events:

require 'dwc-archive'
DarwinCore.logger = Logger.new($stdout)

Note on Patches/Pull Requests

  • Fork the project.
  • Make your feature addition or bug fix.
  • Add tests for it. This is important so I don't break it in a future version unintentionally.
  • Commit, do not mess with rakefile, version, or history. (if you want to have your own version, that is fine but bump version in a commit by itself I can ignore when I pull)
  • Send me a pull request. Bonus points for topic branches.

Copyright

Author -- Dmitry Mozzherin

Contributors -- Matt Yoder

Copyright (c) 2010-2014 Marine Biological Laboratory. See LICENSE for details.