dwca_hunter 0.5.0

checksums.yaml

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+---
+SHA256:
+  metadata.gz: 2a7db63e8ed5cb5d28892c4f43adaa015e52ae012a0363b6fe50aaa230038f04
+  data.tar.gz: 3b8bde91aeec03e927ec7811c0ccfba4c411e5f1a3c7521415bc359add68b8e1
+SHA512:
+  metadata.gz: 2992334297d7add2ad3875180b080c7278b7ab934440a5376a8fffb6943bcef9c585187ec67e1bf8737405e7153222bd65df494e4805ace843cfbfd07adf73c1
+  data.tar.gz: 91218db042979509afd377008df68c82d04a08fe39b653119cdbe3b187a27202e5da11f173310617535c2acabc1aef65aec142d4e6226d0abb250dcec2d38eab

data/.byebug_history

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+q
+c
+q
+resource.title =>q
+resource.title
+resource
+search
+q
+n
+data
+q
+d.first.keys.map { |k| k.to_s.capitalize }
+d.first.keys.mtp { |k| k.to_s.capitalize }
+d.map(&:values)
+d.first.keys
+d.first
+d = res.sort_by { |r| r[:command] }
+res.sort_by { |r| r[:command] }
+res.sort_by(command)
+res.sort_by(&:command)
+res
+q
+ObjectSpace.each_object(Class) {|c| puts c}q
+ObjectSpace.each_object(Class) {|c| puts c}
+ObjectSpace
+c
+subject.version
+subject
+q
+subject
+q

data/.document

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+lib/**/*.rb
+bin/*
+- 
+features/**/*.feature
+LICENSE.txt

data/.gitignore

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+*.gem
+
+# rcov generated
+coverage
+binold
+
+# rdoc generated
+rdoc
+
+# yard generated
+doc
+.yardoc
+
+# bundler
+.bundle
+bundle_bin
+
+# jeweler generated
+pkg
+
+# Have editor/IDE/OS specific files you need to ignore? Consider using a global gitignore:
+#
+# * Create a file at ~/.gitignore
+# * Include files you want ignored
+# * Run: git config --global core.excludesfile ~/.gitignore
+#
+# After doing this, these files will be ignored in all your git projects,
+# saving you from having to 'pollute' every project you touch with them
+#
+# Not sure what to needs to be ignored for particular editors/OSes? Here's some ideas to get you started. (Remember, remove the leading # of the line)
+#
+For MacOS:
+
+.DS_Store
+.vim.custom
+
+# For TextMate
+#*.tmproj
+#tmtags
+
+# For emacs:
+#*~
+#\#*
+#.\#*
+
+For vim:
+*.swp
+
+# For redcar:
+#.redcar
+
+# For rubinius:
+#*.rbc
+problems.txt
+tags
+
+# vscode
+.vs

data/.rspec

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+--format documentation
+--color
+--require spec_helper

data/.rubocop.yml

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+AllCops:
+  TargetRubyVersion: 2.4
+  Exclude:
+    - bin/**/*
+    - db/**/*
+    - bundle_bin/**/*
+  Include:
+    - dwca_hunter.gemspec
+    - exe/dwcahunter
+
+Style/StringLiterals:
+  EnforcedStyle: double_quotes
+
+Layout/DotPosition:
+  EnforcedStyle: trailing
+
+Metrics/BlockLength:
+  Exclude:
+    - Rakefile
+    - "*.gemspec"
+    - "**/*.rake"
+    - "spec/**/*spec.rb"
+
+Metrics/ClassLength:
+  Enabled: false
+
+Metrics/MethodLength:
+  Enabled: false
+
+Naming/FileName:
+  Exclude:
+    - Gemfile
+    - Rakefile

data/.ruby-version

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+2.5.1

data/CHANGELOG.md

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+# Changelog
+
+## Unreleased (placeholder for the next version)
+
+## [v0.5.0]
+- Add [#8] convert project to a `Ruby gem`
+
+## Footnotes
+
+This document follows [changelog guidelines]
+
+[#8]: https://github.com/GlobalNamesArchitecture/dwca_hunter/issues/8
+[v0.5.0]: https://github.com/gnames/dwca_hunter/compare/v0.4.0...v0.5.0
+
+[changelog guidelines]: https://github.com/olivierlacan/keep-a-changelog

data/Gemfile

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+source "http://rubygems.org"
+
+gemspec

data/Gemfile.lock

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+PATH
+  remote: .
+  specs:
+    dwca_hunter (0.5.0)
+      dwc-archive (~> 1.0)
+      gn_uuid (~> 0.5)
+      nokogiri (~> 1.8)
+      rest-client (~> 2.0)
+      thor (~> 0.19)
+
+GEM
+  remote: http://rubygems.org/
+  specs:
+    ast (2.4.0)
+    biodiversity (3.5.0)
+      gn_uuid (~> 0.5)
+      parallel (~> 1.12)
+      treetop (~> 1.6)
+      unicode_utils (~> 1.4)
+    byebug (10.0.2)
+    coderay (1.1.2)
+    coveralls (0.8.22)
+      json (>= 1.8, < 3)
+      simplecov (~> 0.16.1)
+      term-ansicolor (~> 1.3)
+      thor (~> 0.19.4)
+      tins (~> 1.6)
+    diff-lcs (1.3)
+    docile (1.3.1)
+    domain_name (0.5.20180417)
+      unf (>= 0.0.5, < 1.0.0)
+    dwc-archive (1.0.1)
+      nokogiri (~> 1.8)
+      parsley-store (~> 0.3)
+    eventmachine (1.2.7)
+    gn_uuid (0.5.0)
+    htmlentities (4.3.4)
+    http-cookie (1.0.3)
+      domain_name (~> 0.5)
+    jaro_winkler (1.5.1)
+    json (2.1.0)
+    kramdown (1.17.0)
+    mime-types (3.1)
+      mime-types-data (~> 3.2015)
+    mime-types-data (3.2016.0521)
+    mini_portile2 (2.3.0)
+    netrc (0.11.0)
+    nokogiri (1.8.4)
+      mini_portile2 (~> 2.3.0)
+    parallel (1.12.1)
+    parser (2.5.1.2)
+      ast (~> 2.4.0)
+    parsley-store (0.3.6)
+      biodiversity (~> 3.1)
+      redis (~> 3.0)
+    polyglot (0.3.5)
+    powerpack (0.1.2)
+    rainbow (3.0.0)
+    rake (12.3.1)
+    redis (3.3.5)
+    rest-client (2.0.2)
+      http-cookie (>= 1.0.2, < 2.0)
+      mime-types (>= 1.16, < 4.0)
+      netrc (~> 0.8)
+    reverse_markdown (1.1.0)
+      nokogiri
+    rspec (3.7.0)
+      rspec-core (~> 3.7.0)
+      rspec-expectations (~> 3.7.0)
+      rspec-mocks (~> 3.7.0)
+    rspec-core (3.7.1)
+      rspec-support (~> 3.7.0)
+    rspec-expectations (3.7.0)
+      diff-lcs (>= 1.2.0, < 2.0)
+      rspec-support (~> 3.7.0)
+    rspec-mocks (3.7.0)
+      diff-lcs (>= 1.2.0, < 2.0)
+      rspec-support (~> 3.7.0)
+    rspec-support (3.7.1)
+    rubocop (0.58.1)
+      jaro_winkler (~> 1.5.1)
+      parallel (~> 1.10)
+      parser (>= 2.5, != 2.5.1.1)
+      powerpack (~> 0.1)
+      rainbow (>= 2.2.2, < 4.0)
+      ruby-progressbar (~> 1.7)
+      unicode-display_width (~> 1.0, >= 1.0.1)
+    ruby-progressbar (1.9.0)
+    simplecov (0.16.1)
+      docile (~> 1.1)
+      json (>= 1.8, < 3)
+      simplecov-html (~> 0.10.0)
+    simplecov-html (0.10.2)
+    solargraph (0.23.5)
+      coderay (~> 1.1)
+      eventmachine (~> 1.2, >= 1.2.5)
+      htmlentities (~> 4.3, >= 4.3.4)
+      kramdown (~> 1.16)
+      parser (~> 2.4)
+      reverse_markdown (~> 1.0, >= 1.0.5)
+      rubocop (~> 0.52)
+      thor (~> 0.19, >= 0.19.4)
+      tilt (~> 2.0)
+      yard (~> 0.9)
+    term-ansicolor (1.6.0)
+      tins (~> 1.0)
+    thor (0.19.4)
+    tilt (2.0.8)
+    tins (1.16.3)
+    treetop (1.6.10)
+      polyglot (~> 0.3)
+    unf (0.1.4)
+      unf_ext
+    unf_ext (0.0.7.5)
+    unicode-display_width (1.4.0)
+    unicode_utils (1.4.0)
+    yard (0.9.15)
+
+PLATFORMS
+  ruby
+
+DEPENDENCIES
+  bundler (~> 1.16)
+  byebug (~> 10.0)
+  coveralls (~> 0.8)
+  dwca_hunter!
+  rake (~> 12.3)
+  rspec (~> 3.7)
+  rubocop (~> 0.58)
+  solargraph (~> 0.23)
+
+BUNDLED WITH
+   1.16.3

data/LICENSE.txt

@@ -0,0 +1,20 @@
+Copyright (c) 2011 Marine Biological Laboratory
+
+Permission is hereby granted, free of charge, to any person obtaining
+a copy of this software and associated documentation files (the
+"Software"), to deal in the Software without restriction, including
+without limitation the rights to use, copy, modify, merge, publish,
+distribute, sublicense, and/or sell copies of the Software, and to
+permit persons to whom the Software is furnished to do so, subject to
+the following conditions:
+
+The above copyright notice and this permission notice shall be
+included in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
+LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
+OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
+WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

data/README.md

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+# DarwinCoreArchive Hunter
+
+[![dwca_hunter][code-climate-img]][code-climate]
+
+DarwinCoreArchive Hunter is an application designed for reformatting publicly
+accessable scientific name sources into [Dawrin Core Archive format][dwca]
+
+Currently we have DWCA generators for
+
+* NCBI
+* ITIS
+* Wikispecies
+* WoRMS
+* Freebase
+
+See dwca_hunter/bin/dwca-hunt.rb as a example how to use the code.
+
+## Contributing to dwca_hunter
+
+* Check out the latest master to make sure the feature hasn't been implemented
+  or the bug hasn't been fixed yet
+* Check out the issue tracker to make sure someone already hasn't requested it
+  and/or contributed it
+* Fork the project
+* Start a feature/bugfix branch
+* Commit and push until you are happy with your contribution
+* Make sure to add tests for it. This is important so I don't break it in a
+  future version unintentionally.
+* Please try not to mess with the Rakefile, version, or history. If you want to
+  have your own version, or is otherwise necessary, that is fine, but please
+  isolate to its own commit so I can cherry-pick around it.
+
+## Copyright
+
+Copyright (c) 2011-2016 Dmitry Mozzherin. See LICENSE.txt for further details.
+
+[code-climate-img]: https://codeclimate.com/badge.png
+[code-climate]: https://codeclimate.com/github/GlobalNamesArchitecture/dwca_hunter
+[dwca]: http://code.google.com/p/gbif-ecat/wiki/DwCArchive

data/Rakefile

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+# frozen_string_literal: true
+
+require "bundler/gem_tasks"
+require "rspec/core/rake_task"
+require "rubocop/rake_task"
+
+RSpec::Core::RakeTask.new(:rspec)
+
+RuboCop::RakeTask.new
+
+task default: %i[rubocop rspec]

data/dwca_hunter.gemspec

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+# frozen_string_literal: true
+
+lib = File.expand_path("lib", __dir__)
+
+$LOAD_PATH.unshift(lib) unless $LOAD_PATH.include?(lib)
+require "dwca_hunter/version"
+
+Gem::Specification.new do |gem|
+  gem.required_ruby_version = ">= 2.4"
+  gem.name          = "dwca_hunter"
+  gem.version       = DwcaHunter.version
+  gem.license       = "MIT"
+  gem.authors       = ["Dmitry Mozzherin"]
+  gem.email         = ["dmozzherin@gmail.com"]
+
+  gem.summary       = "Converts a variety of available online resources to " \
+                      "DarwinCore Archive files."
+  gem.description   = "Gem harvests data from a variety of formats and " \
+                      "converts incoming data to DwCA format."
+  gem.homepage      = "https://github.com/GlobalNamesArchitecture/dwca_hunter"
+
+  gem.files         = `git ls-files -z`.
+                      split("\x0").
+                      reject { |f| f.match(%r{^(test|spec|features)/}) }
+  gem.bindir        = "exe"
+  gem.executables   = gem.files.grep(%r{^exe/}) { |f| File.basename(f) }
+  gem.require_paths = ["lib"]
+
+  gem.add_dependency "dwc-archive", "~> 1.0"
+  gem.add_dependency "gn_uuid", "~> 0.5"
+  gem.add_dependency "nokogiri", "~> 1.8"
+  gem.add_dependency "rest-client", "~> 2.0"
+  gem.add_dependency "thor", "~> 0.19"
+
+  gem.add_development_dependency "bundler", "~> 1.16"
+  gem.add_development_dependency "byebug", "~> 10.0"
+  gem.add_development_dependency "coveralls", "~> 0.8"
+  gem.add_development_dependency "rake", "~> 12.3"
+  gem.add_development_dependency "rspec", "~> 3.7"
+  gem.add_development_dependency "rubocop", "~> 0.58"
+  gem.add_development_dependency "solargraph", "~> 0.23"
+end

data/exe/dwcahunter

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+#!/usr/bin/env ruby
+# frozen_string_literal: true
+
+require "thor"
+require "dwca_hunter"
+
+# DwcaHunterCLI determines command line interface to the gem functionality
+class DwcaHunterCLI < Thor
+  desc "list [SEARCH]", "lists available sources to convert filtered by search"
+  def list(search = nil)
+    printf("List of available resources to convert to DwCA.\n\n" \
+      "For conversion use 'dwcahunter convert resource_command'\n\n")
+    print_table(collect_resources(search))
+  end
+
+  desc "version", "returns version of the package"
+  def version
+    puts DwcaHunter.version
+  end
+
+  desc "convert source_command", "converts a datasource to a DarwinCore Archive"
+  def convert(command)
+    resource = DwcaHunter.resources.select { |r| r.new.command == command }
+    if resource.empty?
+      puts "Unknown data source. Use 'dwcahunter list [SEARCH]' command" \
+           "to see available data sources."
+    else
+      DwcaHunter.process(resource[0].new)
+    end
+  end
+
+  private
+
+  def collect_resources(search)
+    res = []
+    DwcaHunter.resources.each do |resource|
+      r = resource.new
+      if add_resource?(search, r)
+        res << { n: nil, command: r.command, resource: r.title }
+      end
+    end
+    res.sort_by { |r| r[:command] }.each_with_object([]) do |r, a|
+      r[:n] = a.size + 1
+      a << r
+    end
+  end
+
+  def add_resource?(search, resource)
+    !search || (resource.title =~ /#{search}/i ||
+                resource.command =~ /#{search}/i ||
+                resource.abbr =~ /#{search}/i)
+  end
+
+  # rubocop:disable Metrics/AbcSize
+  def print_table(data)
+    table = [data.first.keys.map { |k| k.to_s.capitalize }] + data.map(&:values)
+    widths = table_widths(table)
+    table.insert(1, widths.map { |n| "-" * n })
+    format = widths.collect { |n| "%-#{n}s" }.join("  ")
+    table.each { |line| printf "  #{format}  \n", *line }
+  end
+  # rubocop:enable Metrics/AbcSize
+
+  def table_widths(table)
+    table.each_with_object([]) do |line, widths|
+      c = 0
+      line.each do |col|
+        col = col.to_s
+        wide_enough = widths[c] && widths[c] > col.length
+        widths[c] = wide_enough ? widths[c] : col.length
+        c += 1
+      end
+    end
+  end
+end
+
+DwcaHunterCLI.start(ARGV)