dwca_hunter 0.5.2 → 0.7.1

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: fb05e834a8403ae6b6cce3fc9c913b38d7111808ec355f4ad659d74b3960697f
-  data.tar.gz: cb30906b445212fa52d4ab536610d77050bcfa417fdbb0546c93d5f004a266d9
+  metadata.gz: 60327e105c53c226f322e3a7272bdc5747d73fac0124887b024f99e3c39c985b
+  data.tar.gz: '09660f8b5feccfaf4caeaec277db4dc4729a973196a77bb02860947ef55bd272'
 SHA512:
-  metadata.gz: 8ee016bf36ca9bab6ed6d65475b52e231c13cae276482ac34787b5680d3953ca5672b73428b33e1834823ad90411464567617b9a7bf25f359a09e5f6f7a8122c
-  data.tar.gz: 233dd03050a99fc016e1c78326d76476f0fbf3f81743a28c1ec842e4b5755a2162eb1951035192149b9da537811dedad20c046b31e962eeeabd89550b146cec5
+  metadata.gz: 9b0a621f85535f421eef5a8550ce653c4f3483f563c7b19934a76e8f30b0cdf17e7a8c59945ea31455c57a350a14d345993f5fe6b91d656f5eb40317da6b1af9
+  data.tar.gz: 00a54b23a8588e6d304d35bb8756f633fb409777f07908525d257f4b1a23c5956a9683863b491f50e8d772c8b41343f909e6cb252a326d4f2e662f96f37826ed

data/.byebug_history

@@ -1,3 +1,40 @@
+q
+row
+data
+cc
+c
+data
+c
+data
+c
+data
+c
+data
+c
+data
+q
+p n
+n
+q
+@name_id_json[n]
+n = row[:acc_name].to_sym
+row[:acc_name].to_sym
+row[:acc_name]
+acc_id
+vi acc_id
+q
+@name_id
+acc_id
+id
+q
+DwcaHunter.resources
+q
+DwcaHunter.resources
+q
+res.size
+res.len
+res
+trd
 exit
 pp row
 require "pp"

data/.gitignore

@@ -56,3 +56,8 @@ tags
 
 # vscode
 .vs
+
+# misc
+*.json
+*.csv
+*.txt

data/.rubocop.yml

@@ -1,5 +1,6 @@
 AllCops:
-  TargetRubyVersion: 2.4
+  NewCops: disable
+  TargetRubyVersion: 2.6.6
   Exclude:
     - bin/**/*
     - db/**/*
@@ -30,4 +31,4 @@ Metrics/MethodLength:
 Naming/FileName:
   Exclude:
     - Gemfile
-    - Rakefile
+    - Rakefile

data/.ruby-version

@@ -1 +1 @@
-2.5.3
+2.6.6

data/Gemfile.lock

@@ -1,13 +1,12 @@
 PATH
   remote: .
   specs:
-    dwca_hunter (0.5.2)
-      biodiversity (~> 3.5)
-      dwc-archive (~> 1.0)
+    dwca_hunter (0.7.0)
+      biodiversity (~> 4)
+      dwc-archive (~> 1.1.1)
       gn_uuid (~> 0.5)
-      google-cloud-storage (~> 1.23)
       htmlentities (~> 4.3)
-      nokogiri (~> 1.8)
+      nokogiri (~> 1.11)
       rest-client (~> 2.0)
       ruby-xz (~> 1.0)
       thor (~> 0.19)
@@ -15,166 +14,92 @@ PATH
 GEM
   remote: http://rubygems.org/
   specs:
-    addressable (2.7.0)
-      public_suffix (>= 2.0.2, < 5.0)
-    ast (2.4.0)
-    backport (0.3.0)
-    biodiversity (3.5.1)
-      gn_uuid (~> 0.5)
-      parallel (~> 1.12)
-      treetop (~> 1.6)
-      unicode_utils (~> 1.4)
+    ast (2.4.1)
+    biodiversity (4.1.0)
+      ffi (~> 1.11)
     byebug (10.0.2)
-    coveralls (0.8.22)
+    coveralls (0.8.23)
       json (>= 1.8, < 3)
       simplecov (~> 0.16.1)
       term-ansicolor (~> 1.3)
-      thor (~> 0.19.4)
+      thor (>= 0.19.4, < 2.0)
       tins (~> 1.6)
-    declarative (0.0.10)
-    declarative-option (0.1.0)
-    diff-lcs (1.3)
-    digest-crc (0.4.1)
-    docile (1.3.1)
+    diff-lcs (1.4.4)
+    docile (1.3.4)
     domain_name (0.5.20190701)
       unf (>= 0.0.5, < 1.0.0)
-    dwc-archive (1.0.1)
-      nokogiri (~> 1.8)
-      parsley-store (~> 0.3)
-    faraday (0.17.0)
-      multipart-post (>= 1.2, < 3)
+    dwc-archive (1.1.1)
+      biodiversity (~> 4)
+      nokogiri (~> 1.10)
+    ffi (1.14.2)
     gn_uuid (0.5.1)
-    google-api-client (0.34.1)
-      addressable (~> 2.5, >= 2.5.1)
-      googleauth (~> 0.9)
-      httpclient (>= 2.8.1, < 3.0)
-      mini_mime (~> 1.0)
-      representable (~> 3.0)
-      retriable (>= 2.0, < 4.0)
-      signet (~> 0.12)
-    google-cloud-core (1.4.1)
-      google-cloud-env (~> 1.0)
-    google-cloud-env (1.3.0)
-      faraday (~> 0.11)
-    google-cloud-storage (1.23.0)
-      addressable (~> 2.5)
-      digest-crc (~> 0.4)
-      google-api-client (~> 0.33)
-      google-cloud-core (~> 1.2)
-      googleauth (~> 0.9)
-      mini_mime (~> 1.0)
-    googleauth (0.10.0)
-      faraday (~> 0.12)
-      jwt (>= 1.4, < 3.0)
-      memoist (~> 0.16)
-      multi_json (~> 1.11)
-      os (>= 0.9, < 2.0)
-      signet (~> 0.12)
     htmlentities (4.3.4)
     http-accept (1.7.0)
     http-cookie (1.0.3)
       domain_name (~> 0.5)
-    httpclient (2.8.3)
-    jaro_winkler (1.5.2)
-    json (2.2.0)
-    jwt (2.2.1)
-    kramdown (1.17.0)
-    memoist (0.16.1)
-    mime-types (3.3)
+    json (2.5.1)
+    mime-types (3.3.1)
       mime-types-data (~> 3.2015)
-    mime-types-data (3.2019.1009)
-    mini_mime (1.0.2)
-    mini_portile2 (2.4.0)
-    multi_json (1.14.1)
-    multipart-post (2.1.1)
+    mime-types-data (3.2020.1104)
+    mini_portile2 (2.5.0)
     netrc (0.11.0)
-    nokogiri (1.10.1)
-      mini_portile2 (~> 2.4.0)
-    os (1.0.1)
-    parallel (1.14.0)
-    parser (2.6.0.0)
-      ast (~> 2.4.0)
-    parsley-store (0.3.6)
-      biodiversity (~> 3.1)
-      redis (~> 3.0)
-    polyglot (0.3.5)
-    powerpack (0.1.2)
-    psych (3.1.0)
-    public_suffix (4.0.1)
+    nokogiri (1.11.1)
+      mini_portile2 (~> 2.5.0)
+      racc (~> 1.4)
+    parallel (1.20.1)
+    parser (3.0.0.0)
+      ast (~> 2.4.1)
+    racc (1.5.2)
     rainbow (3.0.0)
-    rake (12.3.2)
-    redis (3.3.5)
-    representable (3.0.4)
-      declarative (< 0.1.0)
-      declarative-option (< 0.2.0)
-      uber (< 0.2.0)
+    rake (13.0.3)
+    regexp_parser (2.0.3)
     rest-client (2.1.0)
       http-accept (>= 1.7.0, < 2.0)
       http-cookie (>= 1.0.2, < 2.0)
       mime-types (>= 1.16, < 4.0)
       netrc (~> 0.8)
-    retriable (3.1.2)
-    reverse_markdown (1.1.0)
-      nokogiri
-    rspec (3.8.0)
-      rspec-core (~> 3.8.0)
-      rspec-expectations (~> 3.8.0)
-      rspec-mocks (~> 3.8.0)
-    rspec-core (3.8.0)
-      rspec-support (~> 3.8.0)
-    rspec-expectations (3.8.2)
+    rexml (3.2.4)
+    rspec (3.10.0)
+      rspec-core (~> 3.10.0)
+      rspec-expectations (~> 3.10.0)
+      rspec-mocks (~> 3.10.0)
+    rspec-core (3.10.1)
+      rspec-support (~> 3.10.0)
+    rspec-expectations (3.10.1)
       diff-lcs (>= 1.2.0, < 2.0)
-      rspec-support (~> 3.8.0)
-    rspec-mocks (3.8.0)
+      rspec-support (~> 3.10.0)
+    rspec-mocks (3.10.1)
       diff-lcs (>= 1.2.0, < 2.0)
-      rspec-support (~> 3.8.0)
-    rspec-support (3.8.0)
-    rubocop (0.65.0)
-      jaro_winkler (~> 1.5.1)
+      rspec-support (~> 3.10.0)
+    rspec-support (3.10.1)
+    rubocop (0.93.1)
       parallel (~> 1.10)
-      parser (>= 2.5, != 2.5.1.1)
-      powerpack (~> 0.1)
-      psych (>= 3.1.0)
+      parser (>= 2.7.1.5)
       rainbow (>= 2.2.2, < 4.0)
+      regexp_parser (>= 1.8)
+      rexml
+      rubocop-ast (>= 0.6.0)
       ruby-progressbar (~> 1.7)
-      unicode-display_width (~> 1.4.0)
-    ruby-progressbar (1.10.0)
+      unicode-display_width (>= 1.4.0, < 2.0)
+    rubocop-ast (1.4.0)
+      parser (>= 2.7.1.5)
+    ruby-progressbar (1.11.0)
     ruby-xz (1.0.0)
-    signet (0.12.0)
-      addressable (~> 2.3)
-      faraday (~> 0.9)
-      jwt (>= 1.5, < 3.0)
-      multi_json (~> 1.10)
     simplecov (0.16.1)
       docile (~> 1.1)
       json (>= 1.8, < 3)
       simplecov-html (~> 0.10.0)
     simplecov-html (0.10.2)
-    solargraph (0.31.3)
-      backport (~> 0.3)
-      htmlentities (~> 4.3, >= 4.3.4)
-      jaro_winkler (~> 1.5)
-      kramdown (~> 1.16)
-      parser (~> 2.3)
-      reverse_markdown (~> 1.0, >= 1.0.5)
-      rubocop (~> 0.52)
-      thor (~> 0.19, >= 0.19.4)
-      tilt (~> 2.0)
-      yard (~> 0.9)
+    sync (0.5.0)
     term-ansicolor (1.7.1)
       tins (~> 1.0)
-    thor (0.19.4)
-    tilt (2.0.9)
-    tins (1.20.2)
-    treetop (1.6.10)
-      polyglot (~> 0.3)
-    uber (0.1.0)
+    thor (0.20.3)
+    tins (1.26.0)
+      sync
     unf (0.1.4)
       unf_ext
-    unf_ext (0.0.7.6)
-    unicode-display_width (1.4.1)
-    unicode_utils (1.4.0)
-    yard (0.9.18)
+    unf_ext (0.0.7.7)
+    unicode-display_width (1.7.0)
 
 PLATFORMS
   ruby
@@ -184,10 +109,9 @@ DEPENDENCIES
   byebug (~> 10.0)
   coveralls (~> 0.8)
   dwca_hunter!
-  rake (~> 12.3)
-  rspec (~> 3.7)
-  rubocop (~> 0.58)
-  solargraph (~> 0.23)
+  rake (~> 13.0)
+  rspec (~> 3.9)
+  rubocop (~> 0.84)
 
 BUNDLED WITH
-   2.0.1
+   2.1.4

data/LICENSE.txt

@@ -1,4 +1,4 @@
-Copyright (c) 2011 Marine Biological Laboratory
+Copyright (c) 2011-2020 Dmitry Mozzherin
 
 Permission is hereby granted, free of charge, to any person obtaining
 a copy of this software and associated documentation files (the

data/README.md

@@ -32,7 +32,7 @@ See dwca_hunter/bin/dwca-hunt.rb as a example how to use the code.
 
 ## Copyright
 
-Copyright (c) 2011-2016 Dmitry Mozzherin. See LICENSE.txt for further details.
+Copyright (c) 2011-2020 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

data/dwca_hunter.gemspec

@@ -6,7 +6,7 @@ $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.required_ruby_version = ">= 2.6.6"
   gem.name          = "dwca_hunter"
   gem.version       = DwcaHunter.version
   gem.license       = "MIT"
@@ -26,11 +26,11 @@ Gem::Specification.new do |gem|
   gem.executables   = gem.files.grep(%r{^exe/}) { |f| File.basename(f) }
   gem.require_paths = ["lib"]
 
-  gem.add_dependency "biodiversity", "~> 3.5"
-  gem.add_dependency "dwc-archive", "~> 1.0"
+  gem.add_dependency "biodiversity", "~> 4"
+  gem.add_dependency "dwc-archive", "~> 1.1.1"
   gem.add_dependency "gn_uuid", "~> 0.5"
   gem.add_dependency "htmlentities", "~> 4.3"
-  gem.add_dependency "nokogiri", "~> 1.8"
+  gem.add_dependency "nokogiri", "~> 1.11"
   gem.add_dependency "rest-client", "~> 2.0"
   gem.add_dependency "ruby-xz", "~> 1.0"
   gem.add_dependency "thor", "~> 0.19"
@@ -38,8 +38,7 @@ Gem::Specification.new do |gem|
   gem.add_development_dependency "bundler", "~> 2.0"
   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"
+  gem.add_development_dependency "rake", "~> 13.0"
+  gem.add_development_dependency "rspec", "~> 3.9"
+  gem.add_development_dependency "rubocop", "~> 0.84"
 end

data/exe/dwcahunter

@@ -37,9 +37,7 @@ class DwcaHunterCLI < Thor
     res = []
     DwcaHunter.resources.each do |resource|
       r = resource.new
-      if add_resource?(search, r)
-        res << { n: nil, command: r.command, resource: r.title }
-      end
+      res << { n: nil, command: r.command, resource: r.title } if add_resource?(search, r)
     end
     res.sort_by { |r| r[:command] }.each_with_object([]) do |r, a|
       r[:n] = a.size + 1

data/lib/dwca_hunter.rb

@@ -1,17 +1,17 @@
 # frozen_string_literal: true
 
+require "base64"
 require "biodiversity"
-require "logger"
-require "fileutils"
-require "uri"
-require "tmpdir"
-require "net/http"
-require "json"
-require "htmlentities"
 require "dwc_archive"
 require "dwca_hunter/resource"
+require "fileutils"
+require "htmlentities"
+require "json"
+require "logger"
+require "net/http"
 require "rest_client"
-require "base64"
+require "tmpdir"
+require "uri"
 
 Dir[File.join(__dir__, "dwca_hunter", "*.rb")].
   each { |f| require f }
@@ -51,5 +51,36 @@ module DwcaHunter
         c < Resource
       end
     end
+
+    def normalize_authors(auth)
+      reg = Regexp.new(/^([\(]?)(.*?)(([\s,\)][^[:upper:]]*)?$)/)
+      auth = auth.gsub(/duPont/, 'du Pont')
+      match = reg.match(auth)
+      return auth if match.nil?
+      a1, a2, a3 = match[1..3]
+      a2mod = a2.gsub('&', ',')
+      ary2 = a2mod.split(',').map(&:strip)
+      a2 = move_initials(ary2) if ary2.size > 1
+      "#{a1}#{a2}#{a3}"
+    end
+
+    def move_initials(ary)
+      res = []
+      ary.each do |a|
+        if res.empty?
+          res << a
+          next
+        end
+        match = /^([[:upper:]]{1,4})(\sJr)?$/.match(a)
+        if !match.nil?
+          initialls = match[1].split('').join('. ')
+          res[-1] = "#{initialls}. #{res[-1]}#{match[2].to_s}"
+        else
+          res << a
+        end
+      end
+      res.size == 1 ? res[0] : "#{res[0..-2].join(', ')} & #{res[-1]}"
+    end
   end
 end
+