casento 1.0.0

checksums.yaml

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+---
+SHA1:
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+  data.tar.gz: ea2fc21a6de595bff9cb824ae187e1f29d9a9e09
+SHA512:
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data/.gitignore

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+/.bundle/
+/.yardoc
+/Gemfile.lock
+/_yardoc/
+/coverage/
+/doc/
+/pkg/
+/spec/reports/
+/tmp/

data/Gemfile

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+source 'https://rubygems.org'
+
+# Specify your gem's dependencies in bugguide.gemspec
+gemspec

data/LICENSE

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+The MIT License (MIT)
+
+Copyright (c) 2016 Ken-ichi Ueda
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

data/README.md

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+# Description
+The California Academy of Sciences has databased a great deal of their
+entomological specimen data, but it's generally only available through
+their own [website](http://researcharchive.calacademy.org/research/entomology/EntInv/index.asp)
+with no API and no machine-readable export functionality. This gem attempts to
+ameliorate the situation by scraping data and presenting it in a machine-
+readable format.
+
+Since it is just a scraper it is brittle, but still, better than nothing.
+
+# Installation
+
+This is a Ruby gem, so you'll need [Ruby](https://www.ruby-lang.org) and [RubyGems](https://rubygems.org/) installed. Then:
+
+`gem install casento`
+
+or if you just want to build and install locally:
+
+```bash
+git clone git@github.com:kueda/casento.git
+cd casento
+gem build casento.gemspec
+gem install casento-x.x.x.gem
+```
+
+# Examples
+
+`casento help` should get you started, but here are some ways I use it:
+
+```bash
+# List all records of Hemipenthes in California
+casento checklist Hemipenthes --state California --country U.S.A.
+
+# Export a checklist of all bee fly genera from California to CSV
+casento checklist Bombyliidae --state California --country U.S.A. --rank genus -f csv > bombyliidae-genera-ca.csv
+```

data/Rakefile

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+require "bundler/gem_tasks"
+require "rake/testtask"
+
+Rake::TestTask.new(:test) do |t|
+  t.libs << "test"
+  t.libs << "lib"
+  t.test_files = FileList['test/**/*_test.rb', 'test/**/*_spec.rb']
+end
+
+task :default => :test

data/bin/casento

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+#!/usr/bin/env ruby
+require 'commander/import'
+require 'casento'
+
+program :name, 'Casento'
+program :version, Casento::VERSION
+program :description, <<-EOT
+
+  Command-line tool for scraping data from
+  http://researcharchive.calacademy.org/research/entomology/EntInv. The only
+  option that isn't mostly self-explanatory is the taxon name. It will be
+  smart about matching names ending in "-dae" to families, names enting in
+  "-ptera" to orders, but otherwise it will assume a name in the "Genus
+  species subspecies" format.
+
+  One major caveat: the CAS website is super fussy about certain place names,
+  e.g. "U.S.A.", which must be the acronym, and must have all three periods.
+  Play with the underlying web page and check the URL parameters to resolve
+  problems like that.
+
+EOT
+
+global_option "--name NAME", String
+global_option "--family FAMILY", String
+global_option "--genus GENUS", String
+global_option "--species SPECIES", String
+global_option "-n", '--country COUNTRY', String, "Country / Nation, e.g. U.S.A"
+global_option "-s", '--state STATE', String, "Full name of state-level political body, e.g. California"
+global_option "-c", '--county COUNTY', String, "Full name of county-level political body, e.g. Alameda"
+global_option "-f", '--format table|csv', String, "Output format"
+
+def search(args, opts)
+  params = {}
+  if name = (opts.delete(:name) || args[0])
+    if name =~ /dae$/
+      params[:family] = name
+    elsif name =~ /ptera$/
+      params[:order] = name
+    else
+      params[:genus], params[:species], params[:subspecies] = name.split
+    end
+  end
+  params[:family] ||= opts.family
+  params[:genus] ||= opts.genus
+  params[:species] ||= opts.species
+  params[:country] ||= opts.country
+  params[:state] ||= opts.state
+  params[:county] ||= opts.county
+  Casento.search(params)
+end
+
+command :occurrences do |c|
+  c.syntax = "casento occurrences [taxon name]"
+  c.description "List occurrences matching the search parameters."
+  c.action do |args, opts|
+    occurrences = search(args, opts)
+    longest_name = occurrences.map(&:name).sort_by(&:size).last || ""
+    fields = %w(order family genus species country state county)
+    if opts.format == "csv"
+      puts fields.join(',')
+      occurrences.each do |o|
+        puts fields.map{|f| o.send(f)}.join(",")
+      end
+    else
+      puts "Found #{occurrences.size} occurrences:"
+      puts
+      puts fields.map{|f| f.ljust(longest_name.size) }.join(' ')
+      occurrences.each do |o|
+        puts fields.map{|f| o.send(f).to_s.ljust(longest_name.size)}.join(' ')
+      end
+    end
+  end
+end
+
+command :checklist do |c|
+  c.syntax = "casento checklist [taxon name]"
+  c.description "Generate a checklist of unique taxa from occurrences matching the search parameters."
+  c.option "--rank RANK", String, "Generate a checklist for names at this rank"
+  c.action do |args, opts|
+    occurrences = search(args, opts)
+    longest_name = ""
+    unique_name = if opts.rank == "species" || opts.rank.blank?
+      "scientific_name"
+    else
+      opts.rank
+    end
+    uniques = occurrences.uniq{|o|
+      longest_name = o.send(unique_name) if o.send(unique_name).size > longest_name.size
+      o.send(unique_name)
+    }.reject{|o|
+      o.send(unique_name).blank? || (opts.rank == "species" && o.species.blank?)
+    }.sort{|a,b|
+      a.send(unique_name) <=> b.send(unique_name)
+    }
+    fields = %w(order)
+    fields += case opts.rank
+    when "family"
+      %w(family)
+    when "genus"
+      %w(family genus)
+    when "species"
+      %w(family genus species)
+    else
+      %w(family genus species infraspecific_epithet)
+    end
+    if opts.format == "csv"
+      puts fields.join(',')
+      uniques.each do |o|
+        puts fields.map{|f| o.send(f)}.join(",")
+      end
+    else
+      puts "Found #{occurrences.size} occurrences of #{uniques.size} taxa:"
+      puts
+      puts fields.map{|f| f.ljust(longest_name.size)}.join(" ")
+      uniques.each do |o|
+        puts fields.map{|f| o.send(f).to_s.ljust(longest_name.size)}.join(" ")
+      end
+    end
+  end
+end

data/casento.gemspec

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+#encoding: utf-8
+lib = File.expand_path('../lib', __FILE__)
+$LOAD_PATH.unshift(lib) unless $LOAD_PATH.include?(lib)
+require 'casento/version'
+
+Gem::Specification.new do |spec|
+  spec.name          = "casento"
+  spec.version       = Casento::VERSION
+  spec.authors       = ["Ken-ichi Ueda"]
+  spec.email         = ["kenichi.ueda@gmail.com"]
+
+  spec.summary       = "Tool reading the Entomology General Collection Database at the California Academy of Sciences"
+  spec.description   = %q{
+    The California Academy of Sciences has databased a great deal of their
+    entomological specimen data, but it's generally only available through
+    their own website with no API and no machine-readable export
+    functionality. This gem attempts to ameliorate the situation by scraping
+    data and presenting it in a machine-readable format.
+  }
+  spec.homepage      = "https://github.com/kueda/casento"
+  spec.license       = "MIT"
+
+  spec.files         = `git ls-files -z`.split("\x0").reject { |f| f.match(%r{^(test|spec|features)/}) }
+  spec.bindir        = "bin"
+  spec.executables   = spec.files.grep(%r{^bin/}) { |f| File.basename(f) }
+  spec.require_paths = ["lib"]
+
+  spec.add_development_dependency "bundler", "~> 1.10"
+  spec.add_development_dependency "rake", "~> 10.0"
+  spec.add_development_dependency "minitest", "~> 5.8"
+  spec.add_development_dependency "m", "~> 1.4"
+  spec.add_runtime_dependency 'nokogiri', "~> 1.6"
+  spec.add_runtime_dependency 'activesupport', "~> 4.2"
+  spec.add_runtime_dependency 'commander', "~> 4.3"
+end

data/lib/casento.rb

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+# encoding: utf-8
+require "uri"
+require "ostruct"
+require "nokogiri"
+require "open-uri"
+require "active_support/core_ext/object/blank"
+require "active_support/core_ext/hash"
+require "active_support/inflector"
+require "casento/version"
+require "casento/occurrence"
+
+module Casento
+  def self.search( opts = {} )
+    occurrences = []
+    page = 1
+    loop do
+      page_results = get_page( page, opts )
+      break if page_results.blank?
+      occurrences += page_results
+      page += 1
+    end
+    occurrences
+  end
+
+  def self.get_page( page, opts )
+    opts.symbolize_keys!
+    # puts "opts: #{opts.inspect}"
+    url = "http://researcharchive.calacademy.org/research/entomology/EntInv/index.asp?"
+    params = {
+      "Page" => page,
+      "xAction" => "Search"
+    }
+    params["Country"] = opts[:country] if opts[:country]
+    params["StateProv"] = opts[:state] if opts[:state]
+    params["County"] = opts[:county] if opts[:county]
+    params["Ord"] = opts[:order] if opts[:order]
+    %w(Family Genus Species Subspecies).each do |rank|
+      val = opts[rank.to_sym] || opts[rank.downcase.to_sym]
+      params[rank] = val if val
+    end
+    url = "#{url}#{URI.encode_www_form( params )}"
+    # puts "opening #{url}"
+    headers = %w(
+      order
+      family
+      genus
+      species
+      subspecies
+      country
+      state
+      county
+      url
+    )
+    occurrences = []
+    open( url ) do |response|
+      # puts "response: #{response}"
+      html = Nokogiri::HTML(response.read)
+      html.xpath("//tr[td[@class='tdata']]").each do |tr|
+        occ = Occurrence.new
+        tr.css("td").each_with_index do |td, i|
+          # puts "td: #{td}"
+          val = if headers[i] == "url"
+            td.at("a")[:href]
+          else
+            td.inner_text.to_s
+          end
+          val = val.gsub(/[[:space:]]+$/, "").strip
+          next if val.blank?
+          next if val =~ /not entered/
+          # puts "setting #{headers[i]} to #{val}"
+          occ.send("#{headers[i]}=", val)
+        end
+        occurrences << occ
+      end
+    end
+    occurrences
+  end
+end

data/lib/casento/occurrence.rb

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+#encoding: utf-8
+module Casento
+  class Occurrence < OpenStruct
+    def kingdom
+      "Animalia"
+    end
+
+    def phylum
+      "Arthropoda"
+    end
+    
+    def dwc_class
+      "Insecta"
+    end
+
+    def specificEpithet
+      species
+    end
+
+    def infraspecificEpithet
+      subspecies
+    end
+
+    def scientificName
+      name
+    end
+
+    def state
+      super.gsub(/\(state of\)/i, "").strip
+    end
+
+    def stateProvince
+      state
+    end
+
+    %w(
+      kingdom
+      phylum
+      order
+      family
+      genus
+      specificEpithet
+      infraspecificEpithet
+      scientificName
+      stateProvince
+    ).each do |m|
+      define_method "dwc_#{m}" do
+        send(m)
+      end
+      if m.to_s.underscore != m.to_s
+        define_method m.to_s.underscore do
+          send(m)
+        end
+      end
+    end
+
+    def name
+      [genus, species, subspecies].compact.join(" ").strip
+    end
+
+    def species
+      super =~ /spp/ ? nil : super      
+    end
+  end
+end

data/lib/casento/version.rb

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+#encoding: utf-8
+module Casento
+  VERSION = "1.0.0"
+end

metadata

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+--- !ruby/object:Gem::Specification
+name: casento
+version: !ruby/object:Gem::Version
+  version: 1.0.0
+platform: ruby
+authors:
+- Ken-ichi Ueda
+autorequire: 
+bindir: bin
+cert_chain: []
+date: 2016-05-08 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: bundler
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.10'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.10'
+- !ruby/object:Gem::Dependency
+  name: rake
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '10.0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '10.0'
+- !ruby/object:Gem::Dependency
+  name: minitest
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '5.8'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '5.8'
+- !ruby/object:Gem::Dependency
+  name: m
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.4'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.4'
+- !ruby/object:Gem::Dependency
+  name: nokogiri
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.6'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.6'
+- !ruby/object:Gem::Dependency
+  name: activesupport
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '4.2'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '4.2'
+- !ruby/object:Gem::Dependency
+  name: commander
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '4.3'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '4.3'
+description: "\n    The California Academy of Sciences has databased a great deal
+  of their\n    entomological specimen data, but it's generally only available through\n
+  \   their own website with no API and no machine-readable export\n    functionality.
+  This gem attempts to ameliorate the situation by scraping\n    data and presenting
+  it in a machine-readable format.\n  "
+email:
+- kenichi.ueda@gmail.com
+executables:
+- casento
+extensions: []
+extra_rdoc_files: []
+files:
+- ".gitignore"
+- Gemfile
+- LICENSE
+- README.md
+- Rakefile
+- bin/casento
+- casento.gemspec
+- lib/casento.rb
+- lib/casento/occurrence.rb
+- lib/casento/version.rb
+homepage: https://github.com/kueda/casento
+licenses:
+- MIT
+metadata: {}
+post_install_message: 
+rdoc_options: []
+require_paths:
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: '0'
+required_rubygems_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: '0'
+requirements: []
+rubyforge_project: 
+rubygems_version: 2.4.6
+signing_key: 
+specification_version: 4
+summary: Tool reading the Entomology General Collection Database at the California
+  Academy of Sciences
+test_files: []
+has_rdoc: