dwca_hunter 0.5.3 → 0.7.2

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: c3fbae125e5aa2c8891a3fa045eb3c628c7c53b7b3957a5b0f8153e6d6b3cbbb
-  data.tar.gz: 71f2c5579faf193f9a2b81378b2a437c5e0b3a4f4152fa8496bc0233ed27f225
+  metadata.gz: 26106d03a805f473871c3092a84b8d0498f991ff809a7e3f259f1e20d29bca80
+  data.tar.gz: 28ac068cf264870f67ffdc6697801c683ffec0e101c582ddbd50aa77b7831b8f
 SHA512:
-  metadata.gz: 371304bc1e3a0c5b2862b4213e494f713b27895237d5226430001a98b17c122b5924ad815c9b8c3e164d19ae22997e2c955e8812600c230c011bed484d1b4bd2
-  data.tar.gz: 0f97ed3b3230161bf03ad0976785eaded15e500fd2fa8443c85144a90d6439faaa1c33eaa5aa0aad4355aef8882ade0c661d1ee3f25144f82436926f9e3581a7
+  metadata.gz: 3a1e49e6db3aa0bb79616a512feb8c05438f3534d6c7bdd43a0ae32981e32f83ccd74bdcd682130bdf044dd893e0017eeddf533b170109338bb8d95f0379e2b7
+  data.tar.gz: 35bb769a822639d26380ad70db0b7aeed22483ce7184e62b7fad38c8d5c3b7ab5ea3b82e3dce00bb012bcc18e719077c2c3bb4a2b53830f7babd693c26aa2caf

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: 3.0.0
   Exclude:
     - bin/**/*
     - db/**/*
@@ -27,7 +28,15 @@ Metrics/ClassLength:
 Metrics/MethodLength:
   Enabled: false
 
+Metrics/AbcSize:
+  Enabled: false
+
+Metrics/PerceivedComplexity:
+  Enabled: false
+
+
+
 Naming/FileName:
   Exclude:
     - Gemfile
-    - Rakefile
+    - Rakefile

data/.ruby-version

@@ -1 +1 @@
-2.5.3
+3.0.0

data/Gemfile.lock

@@ -1,140 +1,146 @@
 PATH
   remote: .
   specs:
-    dwca_hunter (0.5.2)
-      biodiversity (~> 3.5)
-      dwc-archive (~> 1.0)
+    dwca_hunter (0.7.2)
+      biodiversity (~> 5.1.2)
+      dwc-archive (~> 1.1.3)
       gn_uuid (~> 0.5)
       htmlentities (~> 4.3)
-      nokogiri (~> 1.8)
-      rest-client (~> 2.0)
+      nokogiri (~> 1.11)
+      rest-client (~> 2.1)
       ruby-xz (~> 1.0)
-      thor (~> 0.19)
+      rubyzip (~> 2.3)
+      thor (~> 1.1)
 
 GEM
   remote: http://rubygems.org/
   specs:
-    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)
-    byebug (10.0.2)
-    coveralls (0.8.22)
+    ast (2.4.2)
+    backport (1.1.2)
+    benchmark (0.1.1)
+    biodiversity (5.1.2)
+      ffi (~> 1.14)
+    byebug (11.1.3)
+    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)
-    diff-lcs (1.3)
-    docile (1.3.1)
+    diff-lcs (1.4.4)
+    docile (1.3.5)
     domain_name (0.5.20190701)
       unf (>= 0.0.5, < 1.0.0)
-    dwc-archive (1.0.1)
-      nokogiri (~> 1.8)
-      parsley-store (~> 0.3)
+    dwc-archive (1.1.3)
+      biodiversity (~> 5.1.2)
+      nokogiri (~> 1.11)
+    e2mmap (0.1.0)
+    ffi (1.14.2)
     gn_uuid (0.5.1)
     htmlentities (4.3.4)
     http-accept (1.7.0)
     http-cookie (1.0.3)
       domain_name (~> 0.5)
-    jaro_winkler (1.5.2)
-    json (2.2.0)
-    kramdown (1.17.0)
-    mime-types (3.3)
+    jaro_winkler (1.5.4)
+    json (2.5.1)
+    kramdown (2.3.0)
+      rexml
+    kramdown-parser-gfm (1.1.0)
+      kramdown (~> 2.0)
+    mime-types (3.3.1)
       mime-types-data (~> 3.2015)
-    mime-types-data (3.2019.1009)
-    mini_portile2 (2.4.0)
+    mime-types-data (3.2020.1104)
+    mini_portile2 (2.5.0)
     netrc (0.11.0)
-    nokogiri (1.10.5)
-      mini_portile2 (~> 2.4.0)
-    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)
+    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)
+    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)
-    reverse_markdown (1.1.0)
+    reverse_markdown (2.0.0)
       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 (1.9.0)
       parallel (~> 1.10)
-      parser (>= 2.5, != 2.5.1.1)
-      powerpack (~> 0.1)
-      psych (>= 3.1.0)
+      parser (>= 3.0.0.0)
       rainbow (>= 2.2.2, < 4.0)
+      regexp_parser (>= 1.8, < 3.0)
+      rexml
+      rubocop-ast (>= 1.2.0, < 2.0)
       ruby-progressbar (~> 1.7)
-      unicode-display_width (~> 1.4.0)
-    ruby-progressbar (1.10.0)
+      unicode-display_width (>= 1.4.0, < 3.0)
+    rubocop-ast (1.4.1)
+      parser (>= 2.7.1.5)
+    ruby-progressbar (1.11.0)
     ruby-xz (1.0.0)
+    rubyzip (2.3.0)
     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)
+    solargraph (0.40.2)
+      backport (~> 1.1)
+      benchmark
+      bundler (>= 1.17.2)
+      e2mmap
       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)
+      kramdown (~> 2.3)
+      kramdown-parser-gfm (~> 1.1)
+      parser (~> 3.0)
+      reverse_markdown (>= 1.0.5, < 3)
+      rubocop (>= 0.52)
+      thor (~> 1.0)
       tilt (~> 2.0)
-      yard (~> 0.9)
+      yard (~> 0.9, >= 0.9.24)
+    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)
+    thor (1.1.0)
+    tilt (2.0.10)
+    tins (1.28.0)
+      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 (0.9.20)
+    unf_ext (0.0.7.7)
+    unicode-display_width (2.0.0)
+    yard (0.9.26)
 
 PLATFORMS
   ruby
 
 DEPENDENCIES
-  bundler (~> 2.0)
-  byebug (~> 10.0)
+  bundler (~> 2.2)
+  byebug (~> 11.1)
   coveralls (~> 0.8)
   dwca_hunter!
-  rake (~> 12.3)
-  rspec (~> 3.7)
-  rubocop (~> 0.58)
-  solargraph (~> 0.23)
+  rake (~> 13.0)
+  rspec (~> 3.10)
+  rubocop (~> 1.9)
+  solargraph (~> 0.40)
 
 BUNDLED WITH
-   2.0.1
+   2.2.7

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 = ">= 3.0.0"
   gem.name          = "dwca_hunter"
   gem.version       = DwcaHunter.version
   gem.license       = "MIT"
@@ -26,20 +26,21 @@ 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", "~> 5.1.2"
+  gem.add_dependency "dwc-archive", "~> 1.1.3"
   gem.add_dependency "gn_uuid", "~> 0.5"
   gem.add_dependency "htmlentities", "~> 4.3"
-  gem.add_dependency "nokogiri", "~> 1.8"
-  gem.add_dependency "rest-client", "~> 2.0"
+  gem.add_dependency "nokogiri", "~> 1.11"
+  gem.add_dependency "rest-client", "~> 2.1"
   gem.add_dependency "ruby-xz", "~> 1.0"
-  gem.add_dependency "thor", "~> 0.19"
+  gem.add_dependency "rubyzip", "~> 2.3"
+  gem.add_dependency "thor", "~> 1.1"
 
-  gem.add_development_dependency "bundler", "~> 2.0"
-  gem.add_development_dependency "byebug", "~> 10.0"
+  gem.add_development_dependency "bundler", "~> 2.2"
+  gem.add_development_dependency "byebug", "~> 11.1"
   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", "~> 3.10"
+  gem.add_development_dependency "rubocop", "~> 1.9"
+  gem.add_development_dependency "solargraph", "~> 0.40"
 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
@@ -53,7 +51,6 @@ class DwcaHunterCLI < Thor
                 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)
@@ -61,7 +58,6 @@ class DwcaHunterCLI < Thor
     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|

data/lib/dwca_hunter.rb

@@ -7,11 +7,13 @@ require "dwca_hunter/resource"
 require "fileutils"
 require "htmlentities"
 require "json"
+require "zip"
 require "logger"
 require "net/http"
 require "rest_client"
 require "tmpdir"
 require "uri"
+require "cgi"
 
 Dir[File.join(__dir__, "dwca_hunter", "*.rb")].
   each { |f| require f }
@@ -51,5 +53,36 @@ 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]}"
+        else
+          res << a
+        end
+      end
+      res.size == 1 ? res[0] : "#{res[0..-2].join(', ')} & #{res[-1]}"
+    end
   end
 end