caruby-tissue 1.2.2 → 1.2.3

data/lib/catissue/database/annotation/annotatable_service.rb

@@ -1,25 +0,0 @@
-require 'delegate'
-require 'caruby/database/persistence_service'
-
-module CaTissue
-  module Annotation
-    # An AnnotatableService queries and saves domain classes which hold annotation attributes.
-    class AnnotatableService < DelegateClass(CaRuby::PersistenceService)
-      def initialize(database, app_service, integration_service)
-        super(app_service)
-        @database = database
-        @integration_service = integration_service
-      end
-#
-#       def create(obj)
-#        super
-#        # TODO - refactor CaRuby::Database to remove Annotation cases; iterate over each annotation attribute here
-#      end
-#
-#      def update(obj)
-#        super
-#        # TODO - refactor CaRuby::Database to remove Annotation cases; iterate over each annotation attribute here
-#      end
-    end
-  end
-end

data/lib/catissue/database/annotation/entity_manager.rb

@@ -1,10 +0,0 @@
-require 'caruby/import/java'
-
-module CaTissue
-  module Annotation
-    # EntityManager dependencies
-    java_import('edu.wustl.common.security.exceptions.UserNotAuthorizedException')
-    # EntityManager is the caTissue singleton Winnebago object for persisting annotations.
-    java_import('edu.common.dynamicextensions.entitymanager.EntityManager')
-  end
-end

data/lib/galena/cli/seed.rb

@@ -1,43 +0,0 @@
-#!/usr/bin/env jruby
-#
-# == Synopsis
-#
-# catissue-seed-galena.rb: seeds the Galena example administrative objects in the database
-#
-# == Usage
-#
-# catissue-seed-galena.rb [options] file
-#
-# --help, -h:
-# print this help message and exit
-#
-# --log file, -l file:
-# log file (default ./log/migration.log)
-#
-# --debug, -d:
-# print debug messages to log (optional)
-#
-# == License
-#
-# This program is licensed under the terms of the +LEGAL+ file in
-# the source distribution.
-
-# load the required gems
-require 'rubygems'
-begin
-  gem 'caruby-tissue'
-rescue LoadError
-  # if the gem is not available, then try a local source
-  $:.unshift File.join(File.dirname(__FILE__), '..', 'lib')
-  $:.unshift File.join(File.dirname(__FILE__), '..', 'examples', 'galena', 'lib')
-end
-
-# the default log file
-DEF_LOG_FILE = 'log/migration.log'
-
-require 'catissue'
-require 'catissue/cli/command'
-
-require 'galena/seed/defaults'
-
-CaTissue::Command.new.execute { Galena::Seed.defaults.ensure_exists }

data/lib/galena/migration/filter_shims.rb

@@ -1,43 +0,0 @@
-require 'uom'
-
-module CaTissue
-
-  # Declares the classes modified for migration.
-  shims Participant, TissueSpecimen, SpecimenCollectionGroup
-
-  class Participant
-    # Extracts the Participant first name from the +Initials+ input field.
-    def migrate_first_name(value, row)
-      self.first_name = value[0, 1]
-    end
-
-    # Extracts the Participant last name from the +Initials+ input field.
-    def migrate_last_name(value, row)
-      self.last_name = value[-1, 1]
-    end
-  end
-
-  class TissueSpecimen
-    # Transforms the +Frozen?+ flag input field to the caTissue specimen type +Frozen Tissue+ value.
-    def migrate_specimen_type(value, row)
-      'Frozen Tissue' if value =~ /TRUE/i
-    end
-
-    # Parses the source field as a UOM::Measurement if it is a string.
-    # Otherwises, returns the source value.
-    def migrate_initial_quantity(value, row)
-      # if value is not a string, then use it as is
-      return value unless value.is_a?(String)
-      # the value has a unit qualifier; parse the measurement.
-      # the unit is normalized to the Specimen standard unit.
-      value.to_measurement_quantity(standard_unit)
-    end
-  end
-
-  class SpecimenCollectionGroup
-    # Returns whether this SCG has a SPN.
-    def migration_valid?
-      surgical_pathology_number
-    end
-  end
-end

data/lib/galena/migration/frozen_shims.rb

@@ -1,53 +0,0 @@
-# load the defaults file in the seed directory
-require File.join(File.dirname(__FILE__), '..', 'seed', 'defaults')
-
-module CaTissue
-  # Declares the classes modified for migration.
-  shims TissueSpecimen, CollectionProtocolRegistration, StorageContainer 
-
-  class TissueSpecimen
-    # Sets the specimen type to +Frozen Tissue+.
-    #
-    # @param (see CaRuby::Migratable#migrate)
-    def migrate(row, migrated)
-      super
-      self.specimen_type = 'Frozen Tissue'
-    end
-  end
-  
-  class CollectionProtocolRegistration
-    # Sets this CPR's protocol to the pre-defined {Galena::Migration::Defaults#protocol}.
-    #
-    # @param (see CaRuby::Migratable#migrate)
-    def migrate(row, migrated)
-      super
-      self.protocol = Galena::Seed.defaults.protocol
-    end
-  end
-
-  class StorageContainer
-    # Creates the migrated box in the database, if necessary.
-    #
-    # @param (see CaRuby::Migratable#migrate)
-    def migrate(row, migrated)
-      super
-      find or create_box
-    end
-    
-    private
-    
-    # Creates a new box of type {Galena::Seed::Defaults#box_type} in a freezer of type
-    # {Galena::Seed::Defaults#freezer_type}.
-    # 
-    # @return [StorageContainer] the new box
-    def create_box
-      defs = Galena::Seed.defaults
-      self.storage_type = defs.box_type
-      # A freezer with a spot for the box
-      frz = defs.freezer_type.find_available(site, :create)
-      if frz.nil? then raise CaRuby::MigrationError.new("Freezer not available to place #{self}") end
-      # Add this box to the first open slot in the first unfilled rack in the freezer.
-      frz << self
-    end
-  end
-end

data/lib/galena/seed/defaults.rb

@@ -1,109 +0,0 @@
-require 'singleton'
-require 'catissue'
-
-module Galena
-  # Creates the {Galena::Seed::Defaults} administrative objects as necessary.
-  def self.seed
-    Seed.defaults.ensure_exists
-  end
-  
-  # Galena example utility module to populate the database with pre-defined administrative objects.
-  module Seed
-    # @return [Defaults] the defaults instance
-    def self.defaults
-      Defaults.instance
-    end
-  
-    # Pre-defined Galena example administrative objects. If the Galena example is already set up
-    # in the caTissue database, then the default object secondary key attributes can be used as a
-    # {CaRuby::Persistable#find} template to retrieve the existing objects. Otherwise, the Defaults
-    # attributes can be created by calling {CaRuby::Persistable#create}.
-    #
-    # In a real-world use case, the administrative objects are typically built in the UI before-hand.
-    # In that case, it is only necessary to define the object secondary key rather than content, e.g.:
-    #   pcl = CaTissue::CollectionProtocol.new(:short_title => 'Galena CP')
-    # The complete definitions are included in this method for convenience in order to seed the
-    # example in a test database. A real-world migration might find it useful to create a similar
-    # defaults file in order to rapidly seed an empty test or staging database.
-    class Defaults
-      include Singleton
-  
-      attr_reader :protocol, :hospital, :tissue_bank, :freezer_type, :box_type
-  
-      # Creates the Galena example Defaults singleton and populates the attributes.
-      def initialize
-        super
-        populate
-      end
-      
-      # Creates the Galena example administrative objects as necessary.
-      def ensure_exists
-        @protocol.find(:create)
-        @hospital.find(:create)
-        @surgeon.find(:create)
-        @box.find(:create)
-      end
-  
-      private
-  
-      # Sets the Galena example Defaults attributes to new objects.
-      def populate
-        galena = CaTissue::Institution.new(:name => 'Galena University')
-  
-        addr = CaTissue::Address.new(
-          :city => 'Galena', :state => 'Illinois', :country => 'United States', :zipCode => '37544',
-          :street => '411 Basin St', :phoneNumber => '311-555-5555')
-  
-        dept = CaTissue::Department.new(:name => 'Pathology')
-  
-        crg = CaTissue::CancerResearchGroup.new(:name => 'Don Thomas Cancer Center')
-  
-        coord = CaTissue::User.new(
-          :email_address => 'corey.nator@galena.edu',
-          :last_name => 'Nator', :first_name => 'Corey', :address => addr.copy,
-          :institution => galena, :department => dept, :cancer_research_group => crg)
-  
-        @hospital = CaTissue::Site.new(
-            :site_type => CaTissue::Site::SiteType::COLLECTION, :name => 'Galena Hospital', 
-            :address => addr, :coordinator => coord)
-  
-        @tissue_bank = CaTissue::Site.new(
-            :site_type => CaTissue::Site::SiteType::REPOSITORY, :name => 'Galena Tissue Bank', 
-            :address => addr, :coordinator => coord)
-  
-        pi = CaTissue::User.new(
-          :email_address => 'vesta.gator@galena.edu',
-          :last_name => 'Gator', :first_name => 'Vesta', :address => addr.copy,
-          :institution => galena, :department => dept, :cancer_research_group => crg)
-  
-        @surgeon = CaTissue::User.new(
-          :email_address => 'serge.on@galena.edu',
-          :first_name => 'Serge', :last_name => 'On', :address => addr.copy,
-          :institution => galena, :department => dept, :cancer_research_group => crg)
-  
-        @protocol = CaTissue::CollectionProtocol.new(:short_title => 'Galena Migration', 
-          :principal_investigator => pi, :sites => [@tissue_bank])
-  
-        # CPE has default 1.0 event point and label
-        cpe = CaTissue::CollectionProtocolEvent.new(:collection_protocol => @protocol)
-        
-        # the sole specimen requirement. Setting the requirement collection_event attribute to a CPE automatically
-        # sets the CPE requirement inverse attribute in caRuby.
-        CaTissue::TissueSpecimenRequirement.new(:collection_event => cpe, :specimen_type => 'Fixed Tissue')
-  
-        # the storage container type hierarchy
-        @freezer_type = CaTissue::StorageType.new(:name => 'GTB Freezer', :columns => 10, :rows => 1, :column_label => 'Rack')
-        rack_type = CaTissue::StorageType.new(:name => 'GTB Rack', :columns => 10, :rows => 10)
-        @box_type = CaTissue::StorageType.new(:name => 'GTB Box', :columns => 10, :rows => 10)
-        @freezer_type << rack_type
-        rack_type << box_type
-        @box_type << 'Tissue'
-        
-        # a sample freezer and box
-        frz = CaTissue::StorageContainer.new(:name => 'GTB Freezer 1', :storage_type=>@freezer_type, :site=>@tissue_bank)
-        @box = CaTissue::StorageContainer.new(:name => 'GTB Box 1', :storage_type=>@box_type)
-        frz << @box
-      end
-    end
-  end
-end