dwca_hunter 0.7.0 → 0.7.1

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
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-  data.tar.gz: 33c8040ec605718963ee46eef4a2a4c27770ce3cfb53baf7486047a3d0528410
+  metadata.gz: 60327e105c53c226f322e3a7272bdc5747d73fac0124887b024f99e3c39c985b
+  data.tar.gz: '09660f8b5feccfaf4caeaec277db4dc4729a973196a77bb02860947ef55bd272'
 SHA512:
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-  data.tar.gz: 97a397e0fc24f5705e46287178f4dd1560621995a19b85007609eba4819127b0a98c49a9dd9ea2d946ead54bf5c4f17e2d85cea738f3c9fdf7ba3de3a5c92f93
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+  data.tar.gz: 00a54b23a8588e6d304d35bb8756f633fb409777f07908525d257f4b1a23c5956a9683863b491f50e8d772c8b41343f909e6cb252a326d4f2e662f96f37826ed

data/Gemfile.lock

@@ -6,7 +6,7 @@ PATH
       dwc-archive (~> 1.1.1)
       gn_uuid (~> 0.5)
       htmlentities (~> 4.3)
-      nokogiri (~> 1.10)
+      nokogiri (~> 1.11)
       rest-client (~> 2.0)
       ruby-xz (~> 1.0)
       thor (~> 0.19)
@@ -14,7 +14,7 @@ PATH
 GEM
   remote: http://rubygems.org/
   specs:
-    ast (2.4.0)
+    ast (2.4.1)
     biodiversity (4.1.0)
       ffi (~> 1.11)
     byebug (10.0.2)
@@ -24,62 +24,66 @@ GEM
       term-ansicolor (~> 1.3)
       thor (>= 0.19.4, < 2.0)
       tins (~> 1.6)
-    diff-lcs (1.3)
-    docile (1.3.2)
+    diff-lcs (1.4.4)
+    docile (1.3.4)
     domain_name (0.5.20190701)
       unf (>= 0.0.5, < 1.0.0)
     dwc-archive (1.1.1)
       biodiversity (~> 4)
       nokogiri (~> 1.10)
-    ffi (1.13.1)
+    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)
-    json (2.3.0)
+    json (2.5.1)
     mime-types (3.3.1)
       mime-types-data (~> 3.2015)
-    mime-types-data (3.2020.0512)
-    mini_portile2 (2.4.0)
+    mime-types-data (3.2020.1104)
+    mini_portile2 (2.5.0)
     netrc (0.11.0)
-    nokogiri (1.10.9)
-      mini_portile2 (~> 2.4.0)
-    parallel (1.19.1)
-    parser (2.7.1.3)
-      ast (~> 2.4.0)
+    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 (13.0.1)
+    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)
     rexml (3.2.4)
-    rspec (3.9.0)
-      rspec-core (~> 3.9.0)
-      rspec-expectations (~> 3.9.0)
-      rspec-mocks (~> 3.9.0)
-    rspec-core (3.9.2)
-      rspec-support (~> 3.9.3)
-    rspec-expectations (3.9.2)
+    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 (~> 3.9.0)
-    rspec-mocks (3.9.1)
+      rspec-support (~> 3.10.0)
+    rspec-mocks (3.10.1)
       diff-lcs (>= 1.2.0, < 2.0)
-      rspec-support (~> 3.9.0)
-    rspec-support (3.9.3)
-    rubocop (0.84.0)
+      rspec-support (~> 3.10.0)
+    rspec-support (3.10.1)
+    rubocop (0.93.1)
       parallel (~> 1.10)
-      parser (>= 2.7.0.1)
+      parser (>= 2.7.1.5)
       rainbow (>= 2.2.2, < 4.0)
+      regexp_parser (>= 1.8)
       rexml
-      rubocop-ast (>= 0.0.3)
+      rubocop-ast (>= 0.6.0)
       ruby-progressbar (~> 1.7)
       unicode-display_width (>= 1.4.0, < 2.0)
-    rubocop-ast (0.0.3)
-      parser (>= 2.7.0.1)
-    ruby-progressbar (1.10.1)
+    rubocop-ast (1.4.0)
+      parser (>= 2.7.1.5)
+    ruby-progressbar (1.11.0)
     ruby-xz (1.0.0)
     simplecov (0.16.1)
       docile (~> 1.1)
@@ -90,7 +94,7 @@ GEM
     term-ansicolor (1.7.1)
       tins (~> 1.0)
     thor (0.20.3)
-    tins (1.25.0)
+    tins (1.26.0)
       sync
     unf (0.1.4)
       unf_ext

data/dwca_hunter.gemspec

@@ -30,7 +30,7 @@ Gem::Specification.new do |gem|
   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", "~> 1.10"
+  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"

data/lib/dwca_hunter/resources/index-fungorum.rb

@@ -0,0 +1,131 @@
+# frozen_string_literal: true
+
+module DwcaHunter
+  class ResourceAOS < DwcaHunter::Resource
+    def initialize(opts = {})
+      @command = "index-fungorum"
+      @title = "Index Fungorum (Species Fungorum)"
+      @url = "https://uofi.box.com/shared/static/54l3b7h4q4pwqq4fgqvx42h3d328fl1c.csv"
+      @UUID = "af06816a-0b28-4a09-8219-bd1d63289858"
+      @download_path = File.join(Dir.tmpdir,
+                                 "dwca_hunter",
+                                 "index-fungorum",
+                                 "data.csv")
+      @synonyms = []
+      @names = []
+      @extensions = []
+      @synonyms_hash = {}
+      super(opts)
+    end
+
+    def download
+      puts "Downloading csv from remote"
+      `curl -s -L #{@url} -o #{@download_path}`
+    end
+
+    def unpack; end
+
+    def make_dwca
+      DwcaHunter.logger_write(object_id, "Extracting data")
+      get_names
+      generate_dwca
+    end
+
+    private
+
+    def get_names
+      Dir.chdir(@download_dir)
+      collect_names
+    end
+
+    def collect_names
+      @names_index = {}
+      file = CSV.open(File.join(@download_dir, "data.csv"),
+                      headers: true)
+      file.each_with_index do |row, _i|
+        taxon_id = row["RECORD NUMBER"]
+        current_id = row["CURRENT NAME RECORD NUMBER"]
+        name_string = row["NAME OF FUNGUS"]
+        authors = row["AUTHORS"]
+        year = row["YEAR OF PUBLICATION"]
+        kingdom = row["Kingdom name"]
+        phylum = row["Phylum name"]
+        sub_phylum = row["Subphylum name"]
+        klass = row["Class name"]
+        subklass = row["Subclass name"]
+        order = row["Order name"]
+        family = row["Family name"]
+        code = "ICN"
+
+        @names << {
+          taxon_id: taxon_id,
+          name_string: "#{name_string} #{authors} #{year}",
+          current_id: current_id,
+          kingdom: kingdom,
+          phylum: phylum,
+          klass: klass,
+          order: order,
+          family: family,
+          code: code
+        }
+      end
+    end
+
+    def generate_dwca
+      DwcaHunter.logger_write(object_id,
+                              "Creating DarwinCore Archive file")
+      @core = [["http://rs.tdwg.org/dwc/terms/taxonID",
+                "http://rs.tdwg.org/dwc/terms/scientificName",
+                "http://rs.tdwg.org/dwc/terms/acceptedNameUsageID",
+                "http://rs.tdwg.org/dwc/terms/kingdom",
+                "http://rs.tdwg.org/dwc/terms/phylum",
+                "http://rs.tdwg.org/dwc/terms/class",
+                "http://rs.tdwg.org/dwc/terms/order",
+                "http://rs.tdwg.org/dwc/terms/family",
+                "http://rs.tdwg.org/dwc/terms/nomenclaturalCode"]]
+      @names.each do |n|
+        @core << [n[:taxon_id], n[:name_string], n[:current_id],
+                  n[:kingdom], n[:phylum], n[:klass], n[:order], n[:family],
+                  n[:code]]
+      end
+
+      @eml = {
+        id: @uuid,
+        title: @title,
+        authors: [
+          { first_name: "Paul",
+            last_name: "Kirk" }
+        ],
+        metadata_providers: [
+          { first_name: "Dmitry",
+            last_name: "Mozzherin",
+            email: "dmozzherin@gmail.com" }
+        ],
+        abstract: "The Index Fungorum, the global fungal nomenclator " \
+          "coordinated and supported by the Index Fungorum Partnership, " \
+          "contains names of fungi (including yeasts, lichens, chromistan " \
+          "fungal analogues, protozoan fungal analogues and fossil forms) " \
+          "at all ranks.\n\n" \
+          "As a result of changes to the ICN (previously ICBN) relating to " \
+          "registration of names and following the lead taken by MycoBank, " \
+          "Index Fungorum now provides a mechanism to register names of " \
+          "new taxa, new names, new combinations and new typifications — no " \
+          "login is required. Names registered at Index Fungorum can be " \
+          "published immediately through the Index Fungorum e-Publication " \
+          "facility — an authorized login is required for this.\n\n" \
+          "Species Fungorum is currently an RBG Kew coordinated initiative " \
+          "to compile a global checklist of the fungi. You may search " \
+          "systematically defined and taxonomically complete datasets - " \
+          "global species databases - or the entire Species Fungorum. " \
+          "Species Fungorum contributes the fungal component to the Species " \
+          "2000 project and, in partnership with ITIS, to the Catalogue " \
+          "of Life (currently used in the GBIF and EoL portal); for more " \
+          "information regarding these global initiative visit their " \
+          "websites. Please contact Paul Kirk if you you would like to " \
+          "contribute to Species Fungorum.",
+        url: @url
+      }
+      super
+    end
+  end
+end

data/lib/dwca_hunter/resources/ion.rb

@@ -0,0 +1,98 @@
+# frozen_string_literal: true
+
+module DwcaHunter
+  class ResourceION < DwcaHunter::Resource
+    def initialize(opts = {})
+      @command = "ion"
+      @title = "Index to Organism Names"
+      @url = "https://uofi.box.com/shared/static/tklh8i6q2kb33g6ki33k6s3is06lo9np.gz"
+      @UUID = "1137dfa3-5b8c-487d-b497-dc0938605864"
+      @download_path = File.join(Dir.tmpdir,
+                                 "dwca_hunter",
+                                 "ion",
+                                 "data.tar.gz")
+      @names = []
+      @extensions = []
+      super(opts)
+    end
+
+    def download
+      puts "Downloading cached verion of the file. Ask Rod Page to make new."
+      `curl -s -L #{@url} -o #{@download_path}`
+    end
+
+    def unpack
+      unpack_tar
+    end
+
+    def make_dwca
+      DwcaHunter.logger_write(object_id, "Extracting data")
+      get_names
+      generate_dwca
+    end
+
+    private
+
+    def get_names
+      Dir.chdir(@download_dir)
+      collect_names
+    end
+
+    def collect_names
+      file = CSV.open(File.join(@download_dir, "ion.tsv"),
+                      headers: true, col_sep: "\t", quote_char: "щ")
+      file.each_with_index do |row, i|
+        id = row["id"]
+        name_string = row["nameComplete"]
+        auth = row["taxonAuthor"]
+
+        @names << { taxon_id: id,
+                    name_string: name_string,
+                    auth: auth }
+
+        puts "Processed %s names" % i if i % 10_000 == 0
+      end
+    end
+
+    def generate_dwca
+      DwcaHunter.logger_write(object_id,
+                              "Creating DarwinCore Archive file")
+      @core = [["http://rs.tdwg.org/dwc/terms/taxonID",
+                "http://rs.tdwg.org/dwc/terms/scientificName",
+                "http://rs.tdwg.org/dwc/terms/scientificNameAuthorship"]]
+      @names.each do |n|
+        @core << [n[:taxon_id], n[:name_string], n[:auth]]
+      end
+
+      @eml = {
+        id: @uuid,
+        title: @title,
+        authors: [
+          { first_name: "Nigel",
+            last_name: "Robinson",
+            email: "nigel.robinson@thomsonreuters.com" }
+        ],
+        metadata_providers: [
+          { first_name: "Dmitry",
+            last_name: "Mozzherin",
+            email: "dmozzherin@gmail.com" }
+        ],
+        abstract: "ION contains millions of animal names, both fossil and " \
+          "recent, at all taxonomic ranks, reported from the scientific " \
+          "literature. (Bacteria, plant and virus names will be added soon)." \
+          "\n\n" \
+          "These names are derived from premier Clarivate databases: " \
+          "Zoological Record®, BIOSIS Previews®, and Biological Abstracts®. " \
+          "All names are tied to at least one published article. Together, " \
+          "these resources cover every aspect of the life sciences - " \
+          "providing names from over 30 million scientific records, " \
+          "including approximately ,000 international journals, patents, " \
+          "books, and conference proceedings. They provide a powerful " \
+          "foundation for the most complete collection of organism names " \
+          "available today.",
+        url: @url
+      }
+      super
+    end
+  end
+end

data/lib/dwca_hunter/resources/itis.rb

@@ -4,7 +4,7 @@ module DwcaHunter
   class ResourceITIS < DwcaHunter::Resource
     def initialize(opts = {})
       @command = "itis"
-      @title = "ITIS"
+      @title = "Integrated Taxonomic Information SystemITIS"
       @url = "https://www.itis.gov/downloads/itisMySQLTables.tar.gz"
       @uuid = "5d066e84-e512-4a2f-875c-0a605d3d9f35"
       @download_path = File.join(Dir.tmpdir,

data/lib/dwca_hunter/resources/ncbi.rb

@@ -4,7 +4,7 @@ module DwcaHunter
   class ResourceNCBI < DwcaHunter::Resource
     def initialize(opts = {})
       @command = "ncbi"
-      @title = "NCBI"
+      @title = "National Center for Biotechnology Information"
       @url = "ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz"
       @uuid = "97d7633b-5f79-4307-a397-3c29402d9311"
       @download_path = File.join(Dir.tmpdir,

data/lib/dwca_hunter/version.rb

@@ -1,5 +1,5 @@
 module DwcaHunter
-  VERSION = "0.7.0"
+  VERSION = "0.7.1"
 
   def self.version
     VERSION

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: dwca_hunter
 version: !ruby/object:Gem::Version
-  version: 0.7.0
+  version: 0.7.1
 platform: ruby
 authors:
 - Dmitry Mozzherin
 autorequire:
 bindir: exe
 cert_chain: []
-date: 2020-06-15 00:00:00.000000000 Z
+date: 2021-01-07 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: biodiversity
@@ -72,14 +72,14 @@ dependencies:
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '1.10'
+        version: '1.11'
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '1.10'
+        version: '1.11'
 - !ruby/object:Gem::Dependency
   name: rest-client
   requirement: !ruby/object:Gem::Requirement
@@ -242,7 +242,9 @@ files:
 - lib/dwca_hunter/resources/freebase.rb
 - lib/dwca_hunter/resources/gnub.rb
 - lib/dwca_hunter/resources/how-moore-birds.rb
+- lib/dwca_hunter/resources/index-fungorum.rb
 - lib/dwca_hunter/resources/ioc_word_bird.rb
+- lib/dwca_hunter/resources/ion.rb
 - lib/dwca_hunter/resources/ipni.rb
 - lib/dwca_hunter/resources/itis.rb
 - lib/dwca_hunter/resources/mammal_divdb.rb