Class: DwcaHunter::ResourceOpenTree

Inherits:
Resource
  • Object
show all
Defined in:
lib/dwca_hunter/resources/opentree.rb

Overview

Harvesting resource for Open Tree of Life

Instance Attribute Summary

Attributes inherited from Resource

#abbr, #command, #download_path, #title, #url, #uuid

Instance Method Summary collapse

Methods inherited from Resource

gunzip, #needs_download?, #needs_unpack?, unzip

Constructor Details

#initialize(opts = {}) ⇒ ResourceOpenTree

Returns a new instance of ResourceOpenTree.



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# File 'lib/dwca_hunter/resources/opentree.rb', line 6

def initialize(opts = {})
  @command = "open-tree"
  @title = "Open Tree of Life Reference Taxonomy"
  @uuid = "e10865e2-cdd9-4f97-912f-08f3d5ef49f7"
  @data = []
  @extensions = []
  @count = 1
  @clades = {}
  @core = [["http://rs.tdwg.org/dwc/terms/taxonId",
            "http://globalnames.org/terms/localID",
            "http://purl.org/dc/terms/scientificName",
            "http://purl.org/dc/terms/parentNameUsageId",
            "http://purl.org/dc/terms/taxonRank",
            "http://globalnames.org/ottCrossMaps",
            "http://globalnames.org/ottNotes"]]
  @eml = {
    id: @uuid,
    title: @title,
    authors: [{ url: "https://tree.opentreeoflife.org" }],
    abstract: "Open Tree of Life aims to construct a comprehensive, " \
              "dynamic and digitally-available tree of life by " \
              "synthesizing published phylogenetic trees along with" \
              "taxonomic data. The project is a collaborative effort" \
              "between 11 PIs across 10 institutions.",
    metadata_providers: [
      { first_name: "Dmitry",
        last_name: "Mozzherin",
        email: "[email protected]" }
    ],
    url: @url
  }
  @url = "http://opendata.globalnames.org/id-crossmap/ott3.0.tgz"
  @download_path = File.join(Dir.tmpdir, "dwca_hunter",
                             "opentree", "data.tar.gz")
  super
end

Instance Method Details

#download ⇒ Object 



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# File 'lib/dwca_hunter/resources/opentree.rb', line 53

def download
  return unless @needs_download
  DwcaHunter.logger_write(object_id, "Downloading file -- "\
                           "it will take some time...")
  dlr = DwcaHunter::Downloader.new(url, @download_path)
  dlr.download
end

#make_dwca ⇒ Object 



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# File 'lib/dwca_hunter/resources/opentree.rb', line 47

def make_dwca
  DwcaHunter.logger_write(object_id, "Extracting data")
  collect_data
  generate_dwca
end

#unpack ⇒ Object 



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# File 'lib/dwca_hunter/resources/opentree.rb', line 43

def unpack
  unpack_tar if @needs_unpack
end