gn_crossmap 3.0.0 → 3.0.1

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: 143661fa671afbd77e8f666ef883df2e127356fa
-  data.tar.gz: a809d9b2472bb8577fffc9df78b72557f7ff3200
+  metadata.gz: 622626c52d655a7b098dc7d6f6e36bb861f2efa3
+  data.tar.gz: f28718b24dada45b2caeafd6f9a86b2807910e48
 SHA512:
-  metadata.gz: 6dbc394ee6ae8e673f455dba4f789bc0ccded1b5c68ca51e19d1549233effeac417b26f7faa6fcac8a7b7db06f4a4d26e7f0944b5f9553673f82a752452e9048
-  data.tar.gz: 6e4be322cbd94e014ee70c9f009fe28c2da4f1b9012cf5cdfa2c0c8b62772dd69ed41ae1c42e917d2648ba3852a3c819add1f2813f85800156dff93f0d7111c0
+  metadata.gz: 302d0ece173f9d542aeaeabdff469656528a682696ab7cfac5de13d40a55a81f4de691cc6a1948989f40418e6a566751f5c7a8efecbe8fe92cb00ae2bd1dcaad
+  data.tar.gz: a91e936f6e8e003b99fb24a9036f7d64e789780ca57cb7a3bf22ef69274e23dc802c3698dac6255782f4fe82723a9e25ec50aef4b53f4dd18fcddb2228d3e7ae

data/.gitignore

@@ -12,3 +12,4 @@ output.csv
 t
 gn_crossmap-*.gem
 .byebug_history
+.nvimlog

data/.rubocop.yml

@@ -7,7 +7,7 @@ AllCops:
     - exe/crossmap
     - "**/Gemfile"
     - "**/Rakefile"
+Layout/DotPosition:
+  EnforcedStyle: trailing
 Style/StringLiterals:
   EnforcedStyle: double_quotes
-Style/DotPosition:
-  EnforcedStyle: trailing

data/CHANGELOG.md

@@ -1,5 +1,10 @@
 # ``gn_crossmap`` CHANGELOG
 
+## 3.0.1
+
+* @dimus - fixes #31 bug: prevent csv row to get  squashed
+           when original or alternative headers are not unique to each other
+
 ## 3.0.0
 
 * @dimus - allow lists without taxonID

data/Rakefile

@@ -8,4 +8,4 @@ end
 
 RuboCop::RakeTask.new
 
-task default: %i(rubocop rspec)
+task default: %i[rubocop rspec]

data/gn_crossmap.gemspec

@@ -41,6 +41,7 @@ Gem::Specification.new do |gem|
   gem.add_development_dependency "rspec", "~> 3.2"
   gem.add_development_dependency "rubocop", "~> 0.31"
   gem.add_development_dependency "coveralls", "~> 0.8"
+  gem.add_development_dependency "byebug", "~> 9.0"
 end
 
 # rubocop:enable Metrics/BlockLength:

data/lib/gn_crossmap/collector.rb

@@ -30,15 +30,16 @@ module GnCrossmap
     end
 
     def collect_data
-      @row = @fields.zip(@row).to_h
-      data = @collector.id_name_rank(@row)
+      @row = @fields.zip(@row)
+      @row_hash = @row.to_h
+      data = @collector.id_name_rank(@row_hash)
       return unless data
       data[:original] = prepare_original
       @data << data
     end
 
     def prepare_original
-      @skip_original ? [@row[:taxonid]] : @row.values
+      @skip_original ? [@row_hash[:taxonid]] : @row.map(&:last)
     end
 
     def collector_factory

data/lib/gn_crossmap/column_collector.rb

@@ -1,11 +1,11 @@
 module GnCrossmap
   # Assemble data from CSV reader by checking column fields
   class ColumnCollector
-    RANKS = %i(kingdom subkingdom phylum subphylum superclass class
+    RANKS = %i[kingdom subkingdom phylum subphylum superclass class
                subclass cohort superorder order suborder infraorder superfamily
                family subfamily tribe subtribe genus subgenus section species
-               subspecies variety form).freeze
-    SPECIES_RANKS = %i(genus species subspecies variety form).freeze
+               subspecies variety form].freeze
+    SPECIES_RANKS = %i[genus species subspecies variety form].freeze
 
     def initialize(fields)
       @fields = fields

data/lib/gn_crossmap/reader.rb

@@ -70,10 +70,20 @@ module GnCrossmap
 
     def process_headers(row)
       @original_fields = headers(row)
-      row = @alt_headers unless @alt_headers.empty?
+      row = produce_alt_headers(row) if @alt_headers && !@alt_headers.empty?
       row
     end
 
+    def produce_alt_headers(row)
+      tail_size = row.size - @alt_headers.size
+      if tail_size <= 0
+        @alt_headers = @alt_headers[0..row.size - 1]
+      else
+        tail_size.times { @alt_headers << "" }
+      end
+      @alt_headers = @alt_headers.map { |h| h.nil? ? "" : h }
+    end
+
     def log_progress(count)
       return false unless (count % 1_000).zero?
       GnCrossmap.log("Ingesting csv row #{count + 1}")

data/lib/gn_crossmap/version.rb

@@ -1,6 +1,6 @@
 # Namespace module for crossmapping checklists to GN sources
 module GnCrossmap
-  VERSION = "3.0.0".freeze
+  VERSION = "3.0.1".freeze
 
   def self.version
     VERSION

data/lib/gn_crossmap/writer.rb

@@ -22,10 +22,10 @@ module GnCrossmap
     private
 
     def output_fields(original_fields)
-      original_fields + %i(matchedType inputName matchedName
+      original_fields + %i[matchedType inputName matchedName
                            matchedCanonicalForm inputRank matchedRank
                            synonymStatus acceptedName matchedEditDistance
-                           matchedScore matchTaxonID)
+                           matchedScore matchTaxonID]
     end
   end
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: gn_crossmap
 version: !ruby/object:Gem::Version
-  version: 3.0.0
+  version: 3.0.1
 platform: ruby
 authors:
 - Dmitry Mozzherin
 autorequire: 
 bindir: exe
 cert_chain: []
-date: 2017-03-31 00:00:00.000000000 Z
+date: 2017-07-17 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: trollop
@@ -150,6 +150,20 @@ dependencies:
     - - "~>"
       - !ruby/object:Gem::Version
         version: '0.8'
+- !ruby/object:Gem::Dependency
+  name: byebug
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '9.0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '9.0'
 description: Gem uses a checklist in a comma-separated format as an input, and returns
   back a new comma-separated list crossmapping the scientific names to one of the
   data sources from http://resolver.globalnames.org
@@ -204,7 +218,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 2.5.1
+rubygems_version: 2.6.11
 signing_key: 
 specification_version: 4
 summary: Crossmaps a list of scientific names to names from a data source in GN Index