rubyMorphbank 0.2.0

data/.document

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+README.rdoc
+lib/**/*.rb
+bin/*
+features/**/*.feature
+LICENSE

data/.gitignore

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+## MAC OS
+.DS_Store
+
+## TEXTMATE
+*.tmproj
+tmtags
+
+## EMACS
+*~
+\#*
+.\#*
+
+## VIM
+*.swp
+
+## PROJECT::GENERAL
+coverage
+rdoc
+pkg
+
+## PROJECT::SPECIFIC

data/README.rdoc

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+= rubyMorphbank
+
+A request/response library for the Morphbank (http://morphbank.net) API.
+
+== Note on Patches/Pull Requests
+ 
+* Fork the project.
+* Make your feature addition or bug fix.
+* Add tests for it. This is important so I don't break it in a
+  future version unintentionally.
+* Commit, do not mess with rakefile, version, or history.
+  (if you want to have your own version, that is fine but bump version in a commit by itself I can ignore when I pull)
+* Send me a pull request. Bonus points for topic branches.
+
+== Copyright
+
+Copyright (c) 2010 mjy. See LICENSE for details.

data/Rakefile

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+require 'rubygems'
+require 'rake'
+
+begin
+  require 'jeweler'
+  Jeweler::Tasks.new do |gem|
+    gem.name = "rubyMorphbank"
+    gem.summary = %Q{Simple Morphbank (http://morphbank.net) services accessor.}
+    gem.description = %Q{Uses the Morphbank API to query and return results from the Morphbank database.}
+    gem.email = "diapriid@gmail.com"
+    gem.homepage = "http://github.com/mjy/rubyMorphbank"
+    gem.authors = ["mjy"]
+    gem.add_development_dependency "thoughtbot-shoulda", ">= 0"
+    gem.files +=  FileList['init.rb', 'lib/**/*.rb'].to_a
+    # gem is a Gem::Specification... see http://www.rubygems.org/read/chapter/20 for additional settings
+  end
+  Jeweler::GemcutterTasks.new
+rescue LoadError
+  puts "Jeweler (or a dependency) not available. Install it with: gem install jeweler"
+end
+
+require 'rake/testtask'
+Rake::TestTask.new(:test) do |test|
+  test.libs << 'lib' << 'test'
+  test.pattern = 'test/**/test_*.rb'
+  test.verbose = true
+end
+
+begin
+  require 'rcov/rcovtask'
+  Rcov::RcovTask.new do |test|
+    test.libs << 'test'
+    test.pattern = 'test/**/test_*.rb'
+    test.verbose = true
+  end
+rescue LoadError
+  task :rcov do
+    abort "RCov is not available. In order to run rcov, you must: sudo gem install spicycode-rcov"
+  end
+end
+
+task :test => :check_dependencies
+
+task :default => :test
+
+require 'rake/rdoctask'
+Rake::RDocTask.new do |rdoc|
+  version = File.exist?('VERSION') ? File.read('VERSION') : ""
+
+  rdoc.rdoc_dir = 'rdoc'
+  rdoc.title = "rubyMorphbank #{version}"
+  rdoc.rdoc_files.include('README*')
+  rdoc.rdoc_files.include('lib/**/*.rb')
+end

data/VERSION

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+0.2.0

data/init.rb

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+require 'rubyMorphbank'

data/lib/request.rb

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+class Request
+
+  # defaults
+  METHOD = 'search' 
+  OBJECTTYPE = 'Image'
+  LIMIT = 10 
+  DEPTH = 1
+  FORMAT = 'id'
+
+  # a subset of VALID_OPTIONS, these are concatenated in the request
+  URI_PARAMS = [:limit, :format, :depth, :objecttype, :first_result, :keywords, :id]
+
+  # possible options for a Request instance 
+  VALID_OPTIONS = {'v3' => URI_PARAMS + [:version, :method] } 
+
+  attr_reader(:request_url, :request_options)
+
+  def initialize(options = {}) 
+    opt = {
+      :version => 'v3',
+      :method => METHOD,
+      :limit => LIMIT,
+      :format => FORMAT,                # 'id' (brief results) or 'svc' (schema based results)
+      :depth => DEPTH,
+      :objecttype => OBJECTTYPE,        #  [nil, Taxon, Image, Character, Specimen, View, Matrix, Locality, Collection, OTU ] (nil = all)
+      :first_result => 0,
+      :keywords => ''
+    }.merge!(options)
+
+    # check for legal parameters
+    opt.keys.each do |p|
+      raise RubyMorphbankError, "#{p} is not a valid parameter" if !VALID_OPTIONS[opt[:version]].include?(p)
+    end 
+
+
+    # create the request 
+    @request_url = SERVICES_URI + "method=#{opt[:method]}" +
+    opt.keys.sort{|a,b| a.to_s <=> b.to_s}.collect{
+      |k| ( (URI_PARAMS.include?(k) && (!opt[k].nil? || opt[k].empty?)) ? "&#{k.to_s}=#{opt[k]}" : '')
+    }.join
+
+    # and some housekeepers
+    @request_options = opt 
+  end
+
+  def get_response
+    Response.new(self)
+  end
+
+  # .root.elements.each(xpath){}.map do |row|
+
+    ## REXML::XPath.match(@xml, '//object/width').collect{|e| e.text.to_s}
+end

data/lib/response.rb

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+class Response
+  
+  attr_reader(
+              :response,              # the Net:HTTP response
+              :doc,                   # the REXML:Document for :response
+              :request                # cache the request object for reference in the response
+             )
+
+  # all the objects returned
+  attr :objects, true
+  attr :ids, true
+
+  attr :annotations
+  attr :images
+
+  def initialize(request = Request.new)
+
+   
+    begin 
+      @response = Net::HTTP.get_response(URI.parse(request.request_url)).body
+    rescue SocketError
+      raise "can not connect to socket, check SERVICES_URI"
+    end 
+
+    # TODO: check that we're getting a legit XML document back before trying to parse it
+    @doc = REXML::Document.new(@response)
+
+    @request = request # TODO: can this be aliased some how?
+    self
+  end
+
+  # return an Array of ids representing morphbankIds to images
+  def mb_image_ids
+    if request.request_options[:format] == 'id' 
+      REXML::XPath.match(@doc, "//id").collect{|e| e.text.to_s}
+    else
+      raise RubyMorphbankError, "you must use method='image' in requests to use the mb_image_ids method"
+    end
+  end
+
+  # get the Integer of the first match
+  def get_int(element_name)
+    REXML::XPath.first(@doc, "//#{element_name}").nil? ? 0 : REXML::XPath.first(@doc, "//#{element_name}").text.to_i
+  end
+
+  # get the String of the first match
+  def get_text(element_name)
+    REXML::XPath.first(@doc, "//#{element_name}").nil? ? 0 : REXML::XPath.first(@doc, "//#{element_name}").text
+  end
+
+  # return an Array of XML elements whose root is an object element
+  def objects
+    REXML::XPath.match(@doc, "//object") 
+  end
+
+  # TODO: the has conversion is NOT optimal (no attributes, children of root only), see extension in rubyMorpbank
+  def hashified_objects
+    self.doc.records("//object")
+  end
+
+  # pagination
+  def link_forward?
+    ((get_int('numResultsReturned') + get_int('firstResult')) < get_int('numResults')) and return true
+    false
+  end
+
+  # pagination
+  def link_back?
+    (get_int('firstResult') > @request.request_options[:limit]) and return true
+    false
+  end
+
+end
+

data/lib/rubyMorphbank.rb

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+# Written by Matt Yoder, 2010
+# see source on github
+
+require 'ruby-debug'
+require 'rexml/document'
+require 'net/http'
+
+module RubyMorphbank
+
+  # schema is at  http://morphbank.net/schema/mbsvc3.xsd  
+  # web interface to API is at http://services.morphbank.net/mb3
+
+  require File.expand_path(File.join(File.dirname(__FILE__), '../lib/Request'))
+  require File.expand_path(File.join(File.dirname(__FILE__), '../lib/Response'))
+
+  class RubyMorphbankError < StandardError
+  end
+
+  SERVICES_URI = 'http://services.morphbank.net/mb3/request?' 
+
+  class Rmb
+    attr_accessor :opt
+
+    def initialize(options = {}) 
+      opt = {
+      }.merge!(options)  
+    end
+
+    def request(options = {})
+      opt = {
+      }.merge!(options)
+      Request.new(opt)
+    end
+  end
+
+  # returns a Hash with properties set to values !! no attributes, nothing other than child elements of root (see extensions below) !!
+  def metadata_hash_for_one_image(image_id)
+    Rmb.new.request(:id => image_id, :format => 'svc', :objecttype => 'Image', :method => 'id', :limit => 1).get_response.doc.record('//object')
+  end
+
+end
+
+
+## Base/REXML extension ##
+
+# modified from http://snippets.dzone.com/posts/show/6181
+
+# convert an array into a hash
+class Array
+  def to_h
+    Hash[*self]
+  end
+end
+
+# neither of these extensions is particularly good, they don't recurse etc.
+class REXML::Document
+  def record(xpath)
+    self.root.elements.each(xpath + '/*'){}.inject([]) do |r,node|
+      r << node.name.to_s << node.text.to_s.strip
+    end.to_h
+  end
+
+  def records(xpath)
+    self.root.elements.each(xpath){}.map do |row|
+      row.elements.each{}.inject([]) do |r,node|
+        r << node.name.to_s << node.text.to_s.strip
+      end.to_h
+    end
+  end
+end
+

data/test/helper.rb

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+require 'rubygems'
+require 'test/unit'
+require 'shoulda'
+
+$LOAD_PATH.unshift(File.join(File.dirname(__FILE__), '..', 'lib'))
+$LOAD_PATH.unshift(File.dirname(__FILE__))
+require 'rubyMorphbank'
+
+class Test::Unit::TestCase
+end

data/test/test_rubyMorphbank.rb

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+require File.expand_path(File.join(File.dirname(__FILE__), 'helper'))
+require File.expand_path(File.join(File.dirname(__FILE__), '../lib/rubyMorphbank'))
+
+include RubyMorphbank
+
+
+class TestRubyMorphbank < Test::Unit::TestCase
+
+  should "initialize a new instance without parameters" do
+    assert @bhl = Rmb.new()
+  end
+
+  should "return an hash object using get_metadata_for_one_image" do
+    # WARNING: this XML to hash is not a terribly useful conversion, the process drops all children and attributes
+    hash = metadata_hash_for_one_image(195815) # It's fixed data, not the best test, but if it's gone something is seriously wrong anyways
+    assert_equal '1360', hash['width']
+  end
+
+end
+
+
+class TestRequest < Test::Unit::TestCase
+
+  should "return a properly formatted request url with no options" do
+    @rmb = Rmb.new
+    assert @request = @rmb.request
+    assert_equal   "http://services.morphbank.net/mb3/request?method=search&depth=1&first_result=0&format=id&keywords=&limit=10&objecttype=Image",  @request.request_url 
+  end
+
+end
+
+
+
+class TestResponse < Test::Unit::TestCase
+
+  should "return initialize with a unparameterized request" do
+    @request = Rmb.new.request
+    @response = @request.get_response
+    assert_equal 'mbresponse', @response.doc.elements.first.name 
+  end
+
+  should "return 10 results when unparameterized" do
+    @request = Rmb.new.request
+    assert_equal 10, @request.get_response.get_int('numResultsReturned')
+  end
+
+  should "return many more than 10 results in MB when unparameterized" do
+    @request = Rmb.new.request
+    assert (10 < @request.get_response.get_int('numResults'))
+  end
+
+  should "should link_forward when unparameterized" do
+    @request = Rmb.new.request
+    assert @request.get_response.link_forward?
+  end
+
+  should "should not link_back when unparameterized" do
+    @request = Rmb.new.request
+    assert !@request.get_response.link_back?
+  end
+
+  should "return an array of morphbank image ids when using :format => id and mb_image_ids" do
+    @request = Rmb.new.request(:format => 'id')
+    @response = @request.get_response
+    assert @response.mb_image_ids.size == 10 # not a good test, but variable data return on a vanilla request
+    # this is an array of ids like ["32029", ... "32038"]
+  end
+
+  # test get_int
+  should "return a fixnum using get_int for element numResultsReturned" do
+    @request = Rmb.new.request()
+    assert_equal 10, @request.get_response.get_int('numResultsReturned')
+  end
+
+  # test get_text
+  should "return a mbresponse of objecttypes == Image by default" do
+    @request = Rmb.new.request()
+    assert_equal 'Image', @request.get_response.get_text('objecttypes')
+  end
+
+  # return a link to a numbnail in a call for a single image
+  should "return a URI to a thumb for a single object query" do
+    foo =  Rmb.new.request(:format => 'svc', :id => 195815, :method => 'id')
+    assert_equal 'http://images.morphbank.net/?id=195815&imgType=thumb', foo.get_response.get_text('thumbUrl')
+  end
+
+  should "return an array of hashified array of Morphbank objects" do 
+    foo =  Rmb.new.request(:format => 'svc').get_response.hashified_objects
+    assert_equal 10, foo.size
+  end
+
+end
+

metadata

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+--- !ruby/object:Gem::Specification 
+name: rubyMorphbank
+version: !ruby/object:Gem::Version 
+  prerelease: false
+  segments: 
+  - 0
+  - 2
+  - 0
+  version: 0.2.0
+platform: ruby
+authors: 
+- mjy
+autorequire: 
+bindir: bin
+cert_chain: []
+
+date: 2010-05-12 00:00:00 -04:00
+default_executable: 
+dependencies: 
+- !ruby/object:Gem::Dependency 
+  name: thoughtbot-shoulda
+  prerelease: false
+  requirement: &id001 !ruby/object:Gem::Requirement 
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        segments: 
+        - 0
+        version: "0"
+  type: :development
+  version_requirements: *id001
+description: Uses the Morphbank API to query and return results from the Morphbank database.
+email: diapriid@gmail.com
+executables: []
+
+extensions: []
+
+extra_rdoc_files: 
+- README.rdoc
+files: 
+- .document
+- .gitignore
+- README.rdoc
+- Rakefile
+- VERSION
+- init.rb
+- lib/request.rb
+- lib/response.rb
+- lib/rubyMorphbank.rb
+- test/helper.rb
+- test/test_rubyMorphbank.rb
+has_rdoc: true
+homepage: http://github.com/mjy/rubyMorphbank
+licenses: []
+
+post_install_message: 
+rdoc_options: 
+- --charset=UTF-8
+require_paths: 
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement 
+  requirements: 
+  - - ">="
+    - !ruby/object:Gem::Version 
+      segments: 
+      - 0
+      version: "0"
+required_rubygems_version: !ruby/object:Gem::Requirement 
+  requirements: 
+  - - ">="
+    - !ruby/object:Gem::Version 
+      segments: 
+      - 0
+      version: "0"
+requirements: []
+
+rubyforge_project: 
+rubygems_version: 1.3.6
+signing_key: 
+specification_version: 3
+summary: Simple Morphbank (http://morphbank.net) services accessor.
+test_files: 
+- test/helper.rb
+- test/test_rubyMorphbank.rb