gn_crossmap 0.1.8 → 0.2.0

checksums.yaml

@@ -1,7 +1,7 @@
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data/.gitignore

@@ -8,3 +8,6 @@
 /spec/reports/
 /tmp/
 output.csv
+.vim.custom
+t
+gn_crossmap-*.gem

data/CHANGELOG.md

@@ -1,15 +1,17 @@
-gn_crossmap CHANGELOG
-=====================
-0.1.8
------
+# ``gn_crossmap`` CHANGELOG
+
+## 0.2.0
+
+* @dimus - #17 - change in API - use of STDIN and STDOUT for input and output
+
+## 0.1.8
 
 * @dimus - #14 - show synonym status
 
-0.1.7
------
+## 0.1.7
 
 * @dimus - #13 - make it possible wo ingest field names like dwc:scientificName
-                 or http://example.org/term/sommeTerm
+                 or ``http://example.org/term/sommeTerm``
 
 * @dimus - #12 - fix a bug which prevents so salvage most of the names from a
                  failing batch (if a batch of names has one name that breaks
@@ -22,13 +24,11 @@ gn_crossmap CHANGELOG
 
 * @dimus - #9 - fixed another problem with rank inffering
 
-0.1.6
------
+## 0.1.6
 
 * @dimus - #8 - catching "No Method Found" exception at inferring rank
 
-0.1.5
------
+## 0.1.5
 
 * @dimus - #5 - All original fields are now preserved in the output file.
 
@@ -42,25 +42,23 @@ gn_crossmap CHANGELOG
 
 * @dimus - #1 Bug - Add missing rest-client gem
 
-0.1.4
------
-- [Dmitry Mozzherin][dimus] - Bug fixes
+## 0.1.4
+
+* @dimus - Bug fixes
+
+## 0.1.3
+
+* @dimus - README and gemspec changes
+
+## 0.1.2
 
-0.1.3
------
-- [Dmitry Mozzherin][dimus] - README and gemspec changes
+* @dimus - clean up docs, and remove junk code
 
-0.1.2
------
-- [Dmitry Mozzherin][dimus] - clean up docs, and remove junk code
+## 0.1.1
 
-0.1.1
------
-- [Dmitry Mozzherin][dimus] - first official release -- works for full names
+* @dimus - first official release -- works for full names
                               and names entered in rank fields
 
-0.1.0
------
-- [Dmitry Mozzherin][dimus] - initial version
+## 0.1.0
 
-[dimus]: https://github.com/dimus
+* @dimus - initial version

data/LICENSE

@@ -1,4 +1,4 @@
-Copyright (c) 2015 Marine Biological Laboratory
+Copyright (c) 2015-2016 Marine Biological Laboratory
 
 Permission is hereby granted, free of charge, to any person obtaining
 a copy of this software and associated documentation files (the

data/README.md

@@ -1,9 +1,10 @@
 # GnCrossmap
-[![Gem Version][gem_badge]][gem_link]
-[![Continuous Integration Status][ci_badge]][ci_link]
-[![Coverage Status][cov_badge]][cov_link]
-[![CodeClimate][code_badge]][code_link]
-[![Dependency Status][dep_badge]][dep_link]
+
+[![Gem Version][gem-badge]][gem-link]
+[![Continuous Integration Status][ci-badge]][ci-link]
+[![Coverage Status][cov-badge]][cov-link]
+[![CodeClimate][code-badge]][code-link]
+[![Dependency Status][dep-badge]][dep-link]
 
 This gem crossmaps a checklist of scientific names to names from a data source
 in [GN Resolver][resolver].
@@ -12,13 +13,11 @@ Checklist has to be in a CSV format.
 
 [Issues on waffle.io][waffle]
 
-Compatibility
--------------
+## Compatibility
 
 This gem is compatible with Ruby versions higher or equal to 2.1.0
 
-Installation
-------------
+## Installation
 
 Add this line to your application's Gemfile:
 
@@ -28,25 +27,27 @@ gem 'gn_crossmap'
 
 And then execute:
 
-    $ bundle
+    bundle
 
 Or install it yourself as:
 
-    $ gem install gn_crossmap
+    gem install gn_crossmap
 
-Usage
------
+## Usage
 
 ### Usage from command line
 
     # to see help
-    $ crossmap --help
+    crossmap --help
 
     # to compare with default source (Catalogue of Life)
-    $ crossmap -i my_list.csv -o my_list_col.csv
+    crossmap -i my_list.csv -o my_list_col.csv
 
     # to compare with other source (Index Fungorum in this example)
-    $ crossmap -i my_list.csv -o my_list_if.csv -d 5
+    crossmap -i my_list.csv -o my_list_if.csv -d 5
+
+    # to use standard intput and/or output
+    cat my_list.csv | crossmap -i - -o - > output
 
 ### Usage as Ruby Library
 
@@ -59,7 +60,6 @@ GnCrossmap.logger = MyCustomLogger.new
 GnCrossmap.run("path/to/input.csv", "path/to/output.csv", 5)
 ```
 
-
 ### Input file format
 
 - Comma Separated File with names of fields in first row.
@@ -108,7 +108,6 @@ GnCrossmap.run("path/to/input.csv", "path/to/output.csv", 5)
     TaxonId;kingdom;subkingdom;phylum;subphylum;superclass;class;subclass;cohort;superorder;order;suborder;infraorder;superfamily;family;subfamily;tribe;subtribe;genus;subgenus;section;species;subspecies;variety;form;ScientificNameAuthorship
     1;Animalia;;Tardigrada;;;Eutardigrada;;;;Parachela;;;Macrobiotoidea;Macrobiotidae;;;;Macrobiotus;;;harmsworthi;obscurus;;;Dastych, 1985
 
-
 TaxonId|kingdom|subkingdom|phylum|subphylum|superclass|class|subclass|cohort|superorder|order|suborder|infraorder|superfamily|family|subfamily|tribe|subtribe|genus|subgenus|section|species|subspecies|variety|form|ScientificNameAuthorship
 -------|-------|----------|------|---------|----------|-----|--------|------|----------|-----|--------|----------|-----------|------|---------|-----|--------|-----|--------|-------|-------|----------|-------|----|------------------------
 136021|Animalia||Pogonophora||||||||||||||||||||||
@@ -145,8 +144,7 @@ The output fomat returns 7 possible types of matches:
 6. **Exact match by genus part of a canonical form** - The genus part of the canonical form of the species name returned an exact match
 7. **[Blank]** - No match
 
-Development
------------
+## Development
 
 After checking out the repo, run `bin/setup` to install dependencies. Then, run
 `bin/console` for an interactive prompt that will allow you to experiment.
@@ -157,33 +155,31 @@ release a new version, update the version number in `version.rb`, and then run
 commits and tags, and push the `.gem` file to
 [rubygems.org][rubygems]
 
-Contributing
-------------
+## Contributing
 
-1. Fork it ( https://github.com/[my-github-username]/gn_crossmap/fork )
+1. Fork it ( ``https://github.com/[my-github-username]/gn_crossmap/fork`` )
 2. Create your feature branch (`git checkout -b my-new-feature`)
 3. Commit your changes (`git commit -am 'Add some feature'`)
 4. Push to the branch (`git push origin my-new-feature`)
 5. Create a new Pull Request
 
-Copyright
----------
+## Copyright
 
 Author -- [Dmitry Mozzherin][dimus]
 
-Copyright (c) 2015 [Marine Biological Laboratory][mbl].
+Copyright (c) 2015-2016 [Marine Biological Laboratory][mbl].
 See [LICENSE][license] for details.
 
-[gem_badge]: https://badge.fury.io/rb/gn_crossmap.svg
-[gem_link]: http://badge.fury.io/rb/gn_crossmap
-[ci_badge]: https://secure.travis-ci.org/GlobalNamesArchitecture/gn_crossmap.svg
-[ci_link]: http://travis-ci.org/GlobalNamesArchitecture/gn_crossmap
-[cov_badge]: https://coveralls.io/repos/GlobalNamesArchitecture/gn_crossmap/badge.svg?branch=master
-[cov_link]: https://coveralls.io/r/GlobalNamesArchitecture/gn_crossmap?branch=master
-[code_badge]: https://codeclimate.com/github/GlobalNamesArchitecture/gn_crossmap/badges/gpa.svg
-[code_link]: https://codeclimate.com/github/GlobalNamesArchitecture/gn_crossmap
-[dep_badge]: https://gemnasium.com/GlobalNamesArchitecture/gn_crossmap.png
-[dep_link]: https://gemnasium.com/GlobalNamesArchitecture/gn_crossmap
+[gem-badge]: https://badge.fury.io/rb/gn_crossmap.svg
+[gem-link]: http://badge.fury.io/rb/gn_crossmap
+[ci-badge]: https://secure.travis-ci.org/GlobalNamesArchitecture/gn_crossmap.svg
+[ci-link]: http://travis-ci.org/GlobalNamesArchitecture/gn_crossmap
+[cov-badge]: https://coveralls.io/repos/GlobalNamesArchitecture/gn_crossmap/badge.svg?branch=master
+[cov-link]: https://coveralls.io/r/GlobalNamesArchitecture/gn_crossmap?branch=master
+[code-badge]: https://codeclimate.com/github/GlobalNamesArchitecture/gn_crossmap/badges/gpa.svg
+[code-link]: https://codeclimate.com/github/GlobalNamesArchitecture/gn_crossmap
+[dep-badge]: https://gemnasium.com/GlobalNamesArchitecture/gn_crossmap.png
+[dep-link]: https://gemnasium.com/GlobalNamesArchitecture/gn_crossmap
 [resolver]: http://resolver.globalnames.org/data_sources
 [rubygems]: https://rubygems.org
 [dimus]: https://github.com/dimus

data/exe/crossmap

@@ -5,20 +5,23 @@ require "gn_crossmap"
 puts "This program requires Ruby >= v. 2.1.0" if RUBY_VERSION < "2.1.0"
 
 CATALOGUE_OF_LIFE = 1
-OUTPUT = "output.csv"
+OUTPUT = "output.csv".freeze
 opts = Trollop.options do
   banner "Compares a list of scientific names to scientific names from a " \
     "data source from Global Names Resolver\n\n " \
-    "Usage:\n  crossmap [options]\n\noptions:"
+    "Usage:\n  crossmap [options]\n\noptions:" \
+    "\n\n  ('-i -' reads from STDIN; '-o -' writes to STDOUT)\n\n"
 
-  opt(:input, "Path to intput file", type: :string)
+  opt(:input, "Path to input file", type: :string)
   opt(:output, "Path to output file", default: OUTPUT)
   opt(:data_source_id, "Data source id from GN Resolver",
       default: CATALOGUE_OF_LIFE)
 end
 
 Trollop.die :input, "must be set" if opts[:input].nil?
-Trollop.die :input, "file must exist" unless File.exist?(opts[:input])
+unless File.exist?(opts[:input]) || opts[:input] == "-"
+  Trollop.die :input, "file must exist"
+end
 
 begin
   GnCrossmap.run(opts[:input], opts[:output], opts[:data_source_id])

data/gn_crossmap.gemspec

@@ -19,15 +19,16 @@ Gem::Specification.new do |gem|
                       "data sources from http://resolver.globalnames.org"
   gem.homepage      = "https://github.com/GlobalNamesArchitecture/gn_crossmap"
 
-  gem.files         = `git ls-files -z`.split("\x0").
-    reject { |f| f.match(%r{^(test|spec|features)/}) }
+  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 "trollop", "~> 2.1"
   gem.add_dependency "biodiversity", "~> 3.1"
-  gem.add_dependency "rest-client", "~> 1.8"
+  gem.add_dependency "rest-client", "~> 2.0"
   gem.add_dependency "logger-colors", "~> 1.0"
 
   gem.add_development_dependency "bundler", "~> 1.7"

data/lib/gn_crossmap.rb

@@ -1,5 +1,6 @@
 require "csv"
 require "rest_client"
+require "tempfile"
 require "logger"
 require "logger/colors"
 require "biodiversity"
@@ -15,23 +16,61 @@ require "gn_crossmap/result_processor"
 
 # Namespace module for crossmapping checklists wth GN sources
 module GnCrossmap
+  INPUT_MODE = "r:utf-8".freeze
+  OUTPUT_MODE = "w:utf-8".freeze
+
   class << self
     attr_writer :logger
 
     def run(input, output, data_source_id)
-      reader = Reader.new(input)
+      input_io, output_io = io(input, output)
+      reader = Reader.new(input_io, input_name(input))
       data = reader.read
-      writer = Writer.new(output, reader.original_fields)
+      writer = Writer.new(output_io, reader.original_fields,
+                          output_name(output))
       Resolver.new(writer, data_source_id).resolve(data)
       output
     end
 
     def logger
-      @logger ||= Logger.new($stdout)
+      @logger ||= Logger.new(STDERR)
     end
 
     def log(message)
       logger.info(message)
     end
+
+    private
+
+    def io(input, output)
+      io_in = iogen(input, INPUT_MODE)
+      io_out = iogen(output, OUTPUT_MODE)
+      [io_in, io_out]
+    end
+
+    def iogen(arg, mode)
+      if arg.nil? || arg == "-"
+        mode == INPUT_MODE ? stdin : STDOUT
+      else
+        fd_i = IO.sysopen(arg, mode)
+        IO.new(fd_i, mode)
+      end
+    end
+
+    def stdin
+      temp = Tempfile.open("stdin")
+      return STDIN if File.file?(STDIN)
+      IO.copy_stream(STDIN, temp)
+      fd_i = IO.sysopen(temp, INPUT_MODE)
+      IO.new(fd_i, INPUT_MODE)
+    end
+
+    def input_name(input)
+      input.nil? || input == "-" ? "STDIN" : input
+    end
+
+    def output_name(output)
+      output.nil? || output == "-" ? "STDOUT" : output
+    end
   end
 end

data/lib/gn_crossmap/collector.rb

@@ -20,11 +20,11 @@ module GnCrossmap
       @fields = @row.map { |f| prepare_field(f) }
       @collector = collector_factory
       err = "taxonID must be present in the csv header"
-      fail GnCrossmapError, err unless @fields.include?(:taxonid)
+      raise GnCrossmapError, err unless @fields.include?(:taxonid)
     end
 
     def prepare_field(field)
-      field = field.to_s.gsub(":", "/")
+      field = field.to_s.tr(":", "/")
       field.split("/")[-1].strip.downcase.to_sym
     end
 

data/lib/gn_crossmap/column_collector.rb

@@ -4,14 +4,14 @@ module GnCrossmap
     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)
-    SPECIES_RANKS = %i(genus species subspecies variety form)
+               subspecies variety form).freeze
+    SPECIES_RANKS = %i(genus species subspecies variety form).freeze
 
     def initialize(fields)
       @fields = fields
       err = "At least some of these fields must exist in " \
         "the CSV header: '#{RANKS.join('\', \'')}'"
-      fail GnCrossmapError, err if (RANKS - @fields).size == RANKS.size
+      raise GnCrossmapError, err if (RANKS - @fields).size == RANKS.size
     end
 
     def id_name_rank(row)
@@ -29,7 +29,7 @@ module GnCrossmap
 
     def find_rank
       name_rank = nil
-      RANKS.reverse_each do  |rank|
+      RANKS.reverse_each do |rank|
         next if @row[rank].to_s.strip == ""
         name_rank = rank
         break

data/lib/gn_crossmap/reader.rb

@@ -4,32 +4,35 @@ module GnCrossmap
   class Reader
     attr_reader :original_fields
 
-    def initialize(csv_path)
-      @csv_file = csv_path
+    def initialize(csv_io, input_name)
+      @csv_io = csv_io
       @col_sep = col_sep
       @original_fields = nil
+      @input_name = input_name
     end
 
     def read
-      GnCrossmap.log("Read input file '#{File.basename(@csv_file)}'")
+      GnCrossmap.log("Read input from #{@input_name}")
       parse_input
     end
 
     private
 
     def col_sep
-      line = open(@csv_file, &:readline)
+      line = @csv_io.first
+      @csv_io.rewind
       [";", ",", "\t"].map { |s| [line.count(s), s] }.sort.last.last
     end
 
     def parse_input
       dc = Collector.new
-      CSV.open(@csv_file, col_sep: @col_sep).each_with_index do |row, i|
+      csv = CSV.new(@csv_io, col_sep: col_sep)
+      csv.each_with_index do |row, i|
         @original_fields = row.dup if @original_fields.nil?
         i += 1
-        GnCrossmap.log("Ingesting #{i}th csv row") if i % 10_000 == 0
+        GnCrossmap.log("Ingesting #{i}th csv row") if (i % 10_000).zero?
         dc.process_row(row)
-      end
+      end && @csv_io.close
       dc.data
     end
   end

data/lib/gn_crossmap/resolver.rb

@@ -1,7 +1,7 @@
 module GnCrossmap
   # Sends data to GN Resolver and collects results
   class Resolver
-    URL = "http://resolver.globalnames.org/name_resolvers.json"
+    URL = "http://resolver.globalnames.org/name_resolvers.json".freeze
 
     def initialize(writer, data_source_id)
       @processor = GnCrossmap::ResultProcessor.new(writer)

data/lib/gn_crossmap/result_processor.rb

@@ -9,7 +9,7 @@ module GnCrossmap
       4 => "Partial canonical form match",
       5 => "Partial canonical form fuzzy match",
       6 => "Genus part match"
-    }
+    }.freeze
 
     attr_reader :input, :writer
 

data/lib/gn_crossmap/sci_name_collector.rb

@@ -12,7 +12,7 @@ module GnCrossmap
       name = find_name
       rank = @row[:taxonrank]
       rank = parse_rank if rank.nil?
-      (id && name) ? { id: id, name: name, rank: rank } : nil
+      id && name ? { id: id, name: name, rank: rank } : nil
     end
 
     private

data/lib/gn_crossmap/version.rb

@@ -1,6 +1,6 @@
 # Namespace module for crossmapping checklists to GN sources
 module GnCrossmap
-  VERSION = "0.1.8"
+  VERSION = "0.2.0".freeze
 
   def self.version
     VERSION

data/lib/gn_crossmap/writer.rb

@@ -1,12 +1,13 @@
 module GnCrossmap
   # Saves output from GN Resolver to disk
   class Writer
-    def initialize(output_path, original_fields)
-      @path = output_path
+    def initialize(output_io, original_fields, output_name)
+      @output_io = output_io
       @output_fields = output_fields(original_fields)
-      @output = CSV.open(@path, "w:utf-8")
+      @output = CSV.new(@output_io)
       @output << @output_fields
-      GnCrossmap.log("Open output file '#{@path}'")
+      @output_name = output_name
+      GnCrossmap.log("Open output to #{@output_name}")
     end
 
     def write(record)
@@ -14,8 +15,8 @@ module GnCrossmap
     end
 
     def close
-      GnCrossmap.log("Close output file '#{@path}'")
-      @output.close
+      GnCrossmap.log("Close #{@output_name}")
+      @output_io.close
     end
 
     private

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: gn_crossmap
 version: !ruby/object:Gem::Version
-  version: 0.1.8
+  version: 0.2.0
 platform: ruby
 authors:
 - Dmitry Mozzherin
 autorequire: 
 bindir: exe
 cert_chain: []
-date: 2015-07-20 00:00:00.000000000 Z
+date: 2016-11-07 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: trollop
@@ -44,14 +44,14 @@ dependencies:
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '1.8'
+        version: '2.0'
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '1.8'
+        version: '2.0'
 - !ruby/object:Gem::Dependency
   name: logger-colors
   requirement: !ruby/object:Gem::Requirement
@@ -203,7 +203,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 2.4.5
+rubygems_version: 2.5.1
 signing_key: 
 specification_version: 4
 summary: Crossmaps a list of scientific names to names from a data source in GN Index