caruby-tissue 1.2.1

data/lib/catissue/util/log.rb

@@ -0,0 +1,30 @@
+module CaTissue
+  private
+
+  # Makes a log subdirectory to avoid a caTissue log initializer error. This method should be called
+  # before caTissue start-up.
+  #
+  # The caTissue log4j location is unfortunately hard-coded in a caTissue client configuration
+  # file, does not create the parent directory on demand, and issues an obscure error message if
+  # the directory does not exist. This method ensures that the current directory contains a log
+  # subdirectory.
+  def self.ensure_log4j_directory_exists
+    # caTissue alert - avoid caTissue error by creating log subdirectory
+    if File.directory?('log') then
+      unless File.writable?('log') then
+        raise StandardError.new("caTissue log subdirectory #{File.expand_path('log')} is not writable.")
+      end
+    elsif File.exists?('log') then
+      raise StandardError.new("Existing file #{File.expand_path('log')} prevents creation of the required caTissue log subdirectory.")
+    else
+      begin
+        Dir.mkdir('log')
+      rescue Exception => e
+        raise StandardError.new("Cannot create the log subdirectory required by the caTissue client: #{File.expand_path('log')}.")
+      end
+    end
+  end
+
+  # make the log4j directory, if necessary
+  ensure_log4j_directory_exists
+end

data/lib/catissue/util/person.rb

@@ -0,0 +1,31 @@
+require 'caruby/util/person'
+
+module CaTissue
+  # Mix-in for domain classes that define the +first_name+, +last_name+ and optional +middle_name+ attributes.
+  module Person
+    include CaRuby::Person
+
+    public
+
+    # Returns this Person's name as a Name structure, or nil if there is no last name.
+    def name
+      middle = middle_name if respond_to?(:middle_name)
+      Name.new(last_name, first_name, middle) if last_name
+    end
+
+    # Sets this Person's name to the name string or Name object.
+    # A string name argument is parsed using Name.parse.
+    def name=(value)
+      value = Name.parse(value) if String === value
+      # a missing name is equivalent to an empty name for our purposes here
+      value = Name.new(nil, nil) if value.nil?
+      unless Name === value then
+        raise ArgumentError.new("Name argument type invalid; expected <#{Name}>, found <#{value.class}>")
+      end
+      self.first_name = value.first
+      self.last_name = value.last
+      # caTissue alert - CaTissue person names are inconsistent: Participant has a middle name, User doesn't.
+      self.middle_name = value.middle if respond_to?(:middle_name)
+    end
+  end
+end

data/lib/catissue/util/position.rb

@@ -0,0 +1,54 @@
+require 'catissue/util/location'
+
+module CaTissue
+  # The Position mix-in encapsulates the location of an occupant in a holder.
+  # Classes which include Position are required to implement the column, row, occupant
+  # and holder methods.
+  module Position
+    include Comparable
+
+    # @param [Position] other the position to compare
+    # @return (see Location#<=>)
+    # @raise [ArgumentError] if other is not an instance of this Position's concrete class
+    def <=>(other)
+      raise ArgumentError.new("Can't compare #{qp} to #{other.qp}") unless self.class === other
+      equal?(other) ? 0 : location <=> other.location
+    end
+
+    # @return [Boolean] whether other is an instance of this position's class with the same
+    #   occupant and equal location
+    #
+    # @see Location#==
+    def ==(other)
+      self.class === other and occupant == other.occupant and location == other.location
+    end
+
+    # @return [Coordinate] the read-only coordinate with this AbstractPosition's #row and {#column}.
+    def coordinate
+      location.coordinate
+    end
+    
+    # @return [Location] the location of this Position.
+    def location
+      @location ||= Location.new
+      # always ensure that the location is consistent with the Java state
+      @location.holder = holder
+      @location.row = row
+      @location.column = column
+      @location
+    end
+
+    # @param [Location] the location value to set
+    def location=(value)
+      @location = value || Location.new
+      self.holder = @location.holder
+      self.row = @location.row
+      self.column = @location.column
+    end
+
+    # @return [(Integer, Integer)] this Position's zero-based ({#column}, {#row}) tuple.
+    def to_a
+      [column, row]
+    end
+  end
+end

data/lib/catissue/util/storable.rb

@@ -0,0 +1,34 @@
+require 'caruby/util/collection'
+
+module CaTissue
+  # The Storable mix-in adds methods for a domain class which can be stored and implements
+  # the +storable_type+, +position+ and +position_class+ methods.
+  module Storable
+    # Position is an alias for CaTissue::AbstractPosition.
+    Position = CaTissue::AbstractPosition
+
+    # Returns the Container which holds this Storable, or nil if none.
+    def container
+      position and position.container
+    end
+
+    # Moves this Storable from its current Position, if any, to the given container at the optional
+    # Coordinate coordinate. Returns the new position.
+    #
+    # @see Container#add
+    def move_to(container_or_location)
+      case container_or_location
+      when CaTissue::Container then
+        container_or_location.add(self)
+      when CaTissue::Location then
+        loc = container_or_location
+        loc.container.add(self, loc.coordinate)
+      else
+        raise ArgumentError.new("Target location is neither a Container nor a Location: #{container_or_location.class.qp}")
+      end
+      position
+    end
+
+    alias :>> :move_to
+  end
+end

data/lib/catissue/util/storage_type_holder.rb

@@ -0,0 +1,30 @@
+require 'caruby/util/collection'
+
+module CaTissue
+  # The StorageTypeHolder mix-in adds common methods for the StorageType or StorageContainer child type accessors.
+  module StorageTypeHolder
+    include PartialOrder
+
+    # Returns the {CaTissue::SpecimenArrayType}, {CaTissue::AbstractSpecimen#specimen_class} or {CaTissue::StorageType}
+    # children which this StorageTypeHolder can hold.
+    def child_types
+      @child_types ||= holds_storage_types.union(holds_specimen_classes).union(holds_specimen_array_types)
+    end
+
+    # Adds the given subtype to the list of subtypes which this StorageType can hold.
+    #
+    # @param [CaTissue::StorageType, CaTissue::SpecimenArrayType, String] the subcontainer type or
+    #   {CaTissue::AbstractSpecimen#specimen_class} which this StorageType can hold
+    # @return [StorageTypeHolder] self
+    # @raise [ArgumentError] if the type to add is not a supported parameter
+    def add_child_type(type)
+      case type
+      when CaTissue::StorageType then holds_storage_types << type
+      when CaTissue::SpecimenArrayType then holds_specimen_array_types << type
+      when String then holds_specimen_classes << type
+      else raise ArgumentError.new("Storage type child not supported - #{type}")
+      end
+      self
+    end
+  end
+end

data/lib/catissue/version.rb

@@ -0,0 +1,7 @@
+module CaTissue
+  # The version of this caRuby Tissue release.
+  VERSION = "1.2.1"
+  
+  # The supported caTissue release versions.
+  CATISSUE_VERSIONS = "1.1.2"
+end

metadata

@@ -0,0 +1,212 @@
+--- !ruby/object:Gem::Specification 
+extensions: []
+
+homepage: http://rubyforge.org/projects/caruby/tissue
+executables: 
+- crtdump
+- crtexample
+- crtextract
+- crtmigrate
+- crtsmoke
+version: !ruby/object:Gem::Version 
+  prerelease: false
+  version: 1.2.1
+  segments: 
+  - 1
+  - 2
+  - 1
+post_install_message: 
+date: 2010-09-30 07:00:00 +00:00
+files: 
+- bin/crtdump
+- bin/crtexample
+- bin/crtextract
+- bin/crtmigrate
+- bin/crtsmoke
+- examples/galena/README.md
+- examples/galena/bin/migrate.rb
+- examples/galena/bin/seed.rb
+- examples/galena/conf/extract/simple_fields.yaml
+- examples/galena/conf/migration/filter_fields.yaml
+- examples/galena/conf/migration/filter_migration.yaml
+- examples/galena/conf/migration/frozen_fields.yaml
+- examples/galena/conf/migration/frozen_migration.yaml
+- examples/galena/conf/migration/general_fields.yaml
+- examples/galena/conf/migration/general_migration.yaml
+- examples/galena/conf/migration/simple_fields.yaml
+- examples/galena/conf/migration/simple_migration.yaml
+- examples/galena/conf/migration/small_fields.yaml
+- examples/galena/conf/migration/small_migration.yaml
+- examples/galena/data/filter.csv
+- examples/galena/data/frozen.csv
+- examples/galena/data/general.csv
+- examples/galena/data/minimal.csv
+- examples/galena/data/simple.csv
+- examples/galena/data/small.csv
+- examples/galena/doc/_index.html
+- examples/galena/doc/CaTissue.html
+- examples/galena/doc/class_list.html
+- examples/galena/doc/file.README.html
+- examples/galena/doc/file_list.html
+- examples/galena/doc/frames.html
+- examples/galena/doc/Galena.html
+- examples/galena/doc/index.html
+- examples/galena/doc/method_list.html
+- examples/galena/doc/top-level-namespace.html
+- examples/galena/doc/CaTissue/CollectionProtocolRegistration.html
+- examples/galena/doc/CaTissue/Participant.html
+- examples/galena/doc/CaTissue/SpecimenCollectionGroup.html
+- examples/galena/doc/CaTissue/StorageContainer.html
+- examples/galena/doc/CaTissue/TissueSpecimen.html
+- examples/galena/doc/css/common.css
+- examples/galena/doc/css/full_list.css
+- examples/galena/doc/css/style.css
+- examples/galena/doc/Galena/Seed.html
+- examples/galena/doc/Galena/Seed/Defaults.html
+- examples/galena/doc/js/app.js
+- examples/galena/doc/js/full_list.js
+- examples/galena/doc/js/jquery.js
+- examples/galena/lib/galena.rb
+- examples/galena/lib/README.html
+- examples/galena/lib/galena/cli/seed.rb
+- examples/galena/lib/galena/migration/filter_shims.rb
+- examples/galena/lib/galena/migration/frozen_shims.rb
+- examples/galena/lib/galena/seed/defaults.rb
+- lib/catissue.rb
+- lib/catissue/database.rb
+- lib/catissue/resource.rb
+- lib/catissue/version.rb
+- lib/catissue/cli/command.rb
+- lib/catissue/cli/example.rb
+- lib/catissue/cli/migrate.rb
+- lib/catissue/cli/smoke.rb
+- lib/catissue/database/controlled_value_finder.rb
+- lib/catissue/database/controlled_values.rb
+- lib/catissue/database/annotation/annotatable_service.rb
+- lib/catissue/database/annotation/annotation_service.rb
+- lib/catissue/database/annotation/annotator.rb
+- lib/catissue/database/annotation/entity_manager.rb
+- lib/catissue/database/annotation/integration_service.rb
+- lib/catissue/domain/abstract_domain_object.rb
+- lib/catissue/domain/abstract_position.rb
+- lib/catissue/domain/abstract_specimen.rb
+- lib/catissue/domain/abstract_specimen_collection_group.rb
+- lib/catissue/domain/address.rb
+- lib/catissue/domain/cancer_research_group.rb
+- lib/catissue/domain/capacity.rb
+- lib/catissue/domain/check_in_check_out_event_parameter.rb
+- lib/catissue/domain/collection_event_parameters.rb
+- lib/catissue/domain/collection_protocol.rb
+- lib/catissue/domain/collection_protocol_event.rb
+- lib/catissue/domain/collection_protocol_registration.rb
+- lib/catissue/domain/consent_tier_response.rb
+- lib/catissue/domain/consent_tier_status.rb
+- lib/catissue/domain/container.rb
+- lib/catissue/domain/container_position.rb
+- lib/catissue/domain/container_type.rb
+- lib/catissue/domain/department.rb
+- lib/catissue/domain/disposal_event_parameters.rb
+- lib/catissue/domain/embedded_event_parameters.rb
+- lib/catissue/domain/external_identifier.rb
+- lib/catissue/domain/frozen_event_parameters.rb
+- lib/catissue/domain/institution.rb
+- lib/catissue/domain/new_specimen_array_order_item.rb
+- lib/catissue/domain/order_details.rb
+- lib/catissue/domain/participant.rb
+- lib/catissue/domain/participant_medical_identifier.rb
+- lib/catissue/domain/password.rb
+- lib/catissue/domain/race.rb
+- lib/catissue/domain/received_event_parameters.rb
+- lib/catissue/domain/scg_event_parameters.rb
+- lib/catissue/domain/site.rb
+- lib/catissue/domain/specimen.rb
+- lib/catissue/domain/specimen_array.rb
+- lib/catissue/domain/specimen_array_content.rb
+- lib/catissue/domain/specimen_array_type.rb
+- lib/catissue/domain/specimen_characteristics.rb
+- lib/catissue/domain/specimen_collection_group.rb
+- lib/catissue/domain/specimen_event_parameters.rb
+- lib/catissue/domain/specimen_position.rb
+- lib/catissue/domain/specimen_protocol.rb
+- lib/catissue/domain/specimen_requirement.rb
+- lib/catissue/domain/storage_container.rb
+- lib/catissue/domain/storage_type.rb
+- lib/catissue/domain/transfer_event_parameters.rb
+- lib/catissue/domain/user.rb
+- lib/catissue/extract/command.rb
+- lib/catissue/extract/delta.rb
+- lib/catissue/extract/extractor.rb
+- lib/catissue/migration/migrator.rb
+- lib/catissue/migration/shims.rb
+- lib/catissue/migration/uniquify.rb
+- lib/catissue/util/controlled_value.rb
+- lib/catissue/util/location.rb
+- lib/catissue/util/log.rb
+- lib/catissue/util/person.rb
+- lib/catissue/util/position.rb
+- lib/catissue/util/storable.rb
+- lib/catissue/util/storage_type_holder.rb
+- History.txt
+- LEGAL
+- LICENSE
+- README.md
+rubygems_version: 1.3.7
+rdoc_options: []
+
+signing_key: 
+cert_chain: []
+
+name: caruby-tissue
+has_rdoc: catissue
+platform: ruby
+summary: Ruby facade for caTissue.
+default_executable: 
+bindir: bin
+licenses: []
+
+required_rubygems_version: !ruby/object:Gem::Requirement 
+  none: false
+  requirements: 
+  - - '>='
+    - !ruby/object:Gem::Version 
+      version: "0"
+      segments: 
+      - 0
+required_ruby_version: !ruby/object:Gem::Requirement 
+  none: false
+  requirements: 
+  - - '>='
+    - !ruby/object:Gem::Version 
+      version: "0"
+      segments: 
+      - 0
+require_paths: 
+- lib
+specification_version: 3
+test_files: []
+
+dependencies: 
+- !ruby/object:Gem::Dependency 
+  prerelease: false
+  type: :runtime
+  name: caruby-core
+  version_requirements: &id001 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - '>='
+      - !ruby/object:Gem::Version 
+        version: "0"
+        segments: 
+        - 0
+  requirement: *id001
+description: "    The caruby-tissue gem applies the caRuby facade to the caTissue \
+  application.\n"
+email: caruby.org@gmail.com
+authors: 
+- OHSU
+extra_rdoc_files: []
+
+requirements: []
+
+rubyforge_project: caruby
+autorequire: