biopsy 0.1.0.alpha → 0.1.1.alpha

data/lib/biopsy/domain.rb

@@ -1,156 +0,0 @@
-# todo: ensure testing accounts for situation where there are multiple
-# input or output files defined in the spec
-module Biopsy
-
-  class DomainLoadError < Exception
-  end
-
-  class Domain
-
-    attr_reader :name
-    attr_reader :input_filetypes
-    attr_reader :output_filetypes
-    attr_reader :objectives
-    attr_reader :keep_intermediates
-    attr_reader :gzip_intermediates
-
-    require 'yaml'
-    require 'pp'
-
-    # Return a new Domain object containing the specification of the
-    # currently active domain.
-    def initialize domain=nil
-      @name = domain.nil? ? self.get_current_domain : domain
-
-      @keep_intermediates = false
-      @gzip_intermediates = false
-      self.load_by_name @name
-    end
-
-    # Return the name of the currently active domain.
-    def get_current_domain
-      Settings.instance.domain
-    rescue
-      raise "You must specify the domain to use in the biopsy settings file or at the command line."
-    end
-
-    # Return the path to the YAML definition file for domain with +:name+.
-    # All +:domain_dirs+ in Settings are searched and the first matching
-    # file is returned.
-    def locate_definition name
-      Settings.instance.locate_config :domain_dir, name
-    end
-
-    # Check and apply the settings in +:config+ (Hash).
-    def apply_config config
-      [:input_filetypes, :output_filetypes, :objectives].each do |key|
-        raise DomainLoadError.new("Domain definition is missing the required key #{key}") unless config.has_key? key 
-        self.instance_variable_set('@' + key.to_s, config[key])
-      end
-    end
-
-    # Load and apply the domain definition with +:name+
-    def load_by_name name
-      path = self.locate_definition name
-      raise DomainLoadError.new("Domain definition file does not exist for #{name}") if path.nil?
-      config = YAML::load_file(path)
-      raise DomainLoadError.new("Domain definition file #{path} is not valid YAML") if config.nil?
-      self.apply_config config.deep_symbolize
-    end
-
-    # Validate a Target, returning true if the target meets
-    # the specification of this Domain, and false otherwise.
-    # +:target+, the Target object to validate.
-    def target_valid? target
-      l = []
-      @input_filetypes.each do |input|
-        l << [target[:input_files], input]
-      end
-      @output_filetypes.each do |output|
-        l << [target[:output_files], output]
-      end
-      errors = []
-      l.each do |pair|
-        testcase, definition = pair
-        errors += self.validate_target_filetypes(testcase, definition)
-      end
-      errors
-    end
-
-    # Returns an empty array if +:testcase+ conforms to definition,
-    # otherwise returns an array of strings describing the
-    # errors found.
-    def validate_target_filetypes testcase, definition
-      errors = []
-      # check extensions
-      testcase.each_pair do |key, f|
-        ext = File.extname(f)
-        unless definition[:allowed_extensions].include? ext
-          errors << %Q{input file #{f} doesn't match any of the filetypes
-                       allowed for this domain}
-        end
-      end
-      # check number of files
-      in_count = testcase.size
-      if definition.has_key? :n
-        unless in_count == definition[:n]
-          errors << %Q{the number of input files (#{in_count}) doesn't 
-                      match the domain specification (#{definition[:n]})}
-        end
-      end
-      if definition.has_key? :min
-        unless in_count >= definition[:min]
-          errors << %Q{the number of input files (#{in_count}) is lower 
-                      than the minimum for this domain (#{definition[:n]})}
-        end
-      end
-      if definition.has_key? :max
-        unless in_count >= definition[:max]
-          errors << %Q{the number of input files (#{in_count}) is greater 
-                      than the maximum for this domain (#{definition[:n]})}
-        end
-      end
-      errors
-    end
-
-    # Write out a template Domain definition to +:filename+
-    def write_template filename
-      data = {
-        :input_filetypes => [
-          {
-            :min => 1,
-            :max => 2,
-            :allowed_extensions => [
-              'txt',
-              'csv',
-              'tsv'
-            ]
-          },
-          {
-            :n => 2,
-            :allowed_extensions => [
-              'png'
-            ]
-          }
-        ],
-        :output_filetypes => [
-          {
-            :n => 1,
-            :allowed_extensions => [
-              'pdf',
-              'xls'
-            ]
-          }
-        ],
-        :objectives => [
-          'objective1', 'objective2'
-        ]
-      }
-      ::File.open(filename, 'w') do |f|
-        f.puts data.to_yaml
-      end
-    end
-
-  end # end of class Domain
-
-end # end of module Biopsy

data/test/test_domain.rb

@@ -1,61 +0,0 @@
-require 'helper'
-
-class TestDomain < Test::Unit::TestCase
-
-  require 'fileutils'
-
-  context "Domain" do
-
-    setup do
-      @h = Helper.new
-      @h.setup_tmp_dir
-
-      # we need a domain
-      @h.setup_domain
-      domain_name = @h.create_valid_domain
-      @domain = Biopsy::Domain.new domain_name
-    end
-
-    teardown do
-      @h.cleanup
-    end
-
-    should "be able to find the current domain" do
-      assert_equal 'test_domain', @domain.get_current_domain
-    end
-
-    should "be able to find a definition" do
-      assert_equal @h.domain_path, @domain.locate_definition('test_domain')
-    end
-
-    should "fail to find a non-existent definition" do
-      assert_equal nil, @domain.locate_definition('fake_filename')
-    end
-
-    should "reject any invalid config" do
-      # generate all trivial invalid configs
-      @h.domain_data.keys.each do |key|
-        d = @h.domain_data.clone
-        d.delete key
-        filepath = File.join(@h.domain_dir, 'broken_thing.yml')
-        File.open(filepath, 'w') do |f|
-          f.puts d.to_yaml
-        end
-
-        assert_raise Biopsy::DomainLoadError do
-          @domain.load_by_name 'broken_thing'
-        end
-
-        File.delete filepath if File.exists? filepath
-      end
-    end
-    
-    should "write a template that can be loaded as a valid definition" do
-      @domain.write_template File.join(@h.domain_dir, 'template.yml')
-      @domain.load_by_name 'template'
-      assert_equal ['objective1', 'objective2'], @domain.objectives
-    end
-
-  end # Domain context
-
-end # TestDomain