RubyGems - caruby-tissue - Versions diffs - 1.2.1 - Mend

caruby-tissue 1.2.1

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Files changed (133) hide show

data/History.txt +4 -0
data/LEGAL +5 -0
data/LICENSE +22 -0
data/README.md +44 -0
data/bin/crtdump +31 -0
data/bin/crtexample +18 -0
data/bin/crtextract +47 -0
data/bin/crtmigrate +17 -0
data/bin/crtsmoke +27 -0
data/examples/galena/README.md +53 -0
data/examples/galena/bin/migrate.rb +42 -0
data/examples/galena/bin/seed.rb +43 -0
data/examples/galena/conf/extract/simple_fields.yaml +4 -0
data/examples/galena/conf/migration/filter_fields.yaml +7 -0
data/examples/galena/conf/migration/filter_migration.yaml +9 -0
data/examples/galena/conf/migration/frozen_fields.yaml +11 -0
data/examples/galena/conf/migration/frozen_migration.yaml +9 -0
data/examples/galena/conf/migration/general_fields.yaml +42 -0
data/examples/galena/conf/migration/general_migration.yaml +9 -0
data/examples/galena/conf/migration/simple_fields.yaml +30 -0
data/examples/galena/conf/migration/simple_migration.yaml +7 -0
data/examples/galena/conf/migration/small_fields.yaml +24 -0
data/examples/galena/conf/migration/small_migration.yaml +9 -0
data/examples/galena/data/filter.csv +1 -0
data/examples/galena/data/frozen.csv +1 -0
data/examples/galena/data/general.csv +1 -0
data/examples/galena/data/minimal.csv +1 -0
data/examples/galena/data/simple.csv +1 -0
data/examples/galena/data/small.csv +1 -0
data/examples/galena/doc/CaTissue.html +93 -0
data/examples/galena/doc/CaTissue/CollectionProtocolRegistration.html +181 -0
data/examples/galena/doc/CaTissue/Participant.html +241 -0
data/examples/galena/doc/CaTissue/SpecimenCollectionGroup.html +190 -0
data/examples/galena/doc/CaTissue/StorageContainer.html +179 -0
data/examples/galena/doc/CaTissue/TissueSpecimen.html +320 -0
data/examples/galena/doc/Galena.html +290 -0
data/examples/galena/doc/Galena/Seed.html +203 -0
data/examples/galena/doc/Galena/Seed/Defaults.html +646 -0
data/examples/galena/doc/_index.html +188 -0
data/examples/galena/doc/class_list.html +36 -0
data/examples/galena/doc/css/common.css +1 -0
data/examples/galena/doc/css/full_list.css +53 -0
data/examples/galena/doc/css/style.css +307 -0
data/examples/galena/doc/file.README.html +108 -0
data/examples/galena/doc/file_list.html +38 -0
data/examples/galena/doc/frames.html +13 -0
data/examples/galena/doc/index.html +108 -0
data/examples/galena/doc/js/app.js +202 -0
data/examples/galena/doc/js/full_list.js +149 -0
data/examples/galena/doc/js/jquery.js +154 -0
data/examples/galena/doc/method_list.html +179 -0
data/examples/galena/doc/top-level-namespace.html +112 -0
data/examples/galena/lib/README.html +33 -0
data/examples/galena/lib/galena.rb +8 -0
data/examples/galena/lib/galena/cli/seed.rb +43 -0
data/examples/galena/lib/galena/migration/filter_shims.rb +43 -0
data/examples/galena/lib/galena/migration/frozen_shims.rb +54 -0
data/examples/galena/lib/galena/seed/defaults.rb +97 -0
data/lib/catissue.rb +26 -0
data/lib/catissue/cli/command.rb +51 -0
data/lib/catissue/cli/example.rb +31 -0
data/lib/catissue/cli/migrate.rb +60 -0
data/lib/catissue/cli/smoke.rb +45 -0
data/lib/catissue/database.rb +451 -0
data/lib/catissue/database/annotation/annotatable_service.rb +25 -0
data/lib/catissue/database/annotation/annotation_service.rb +79 -0
data/lib/catissue/database/annotation/annotator.rb +84 -0
data/lib/catissue/database/annotation/entity_manager.rb +10 -0
data/lib/catissue/database/annotation/integration_service.rb +87 -0
data/lib/catissue/database/controlled_value_finder.rb +43 -0
data/lib/catissue/database/controlled_values.rb +162 -0
data/lib/catissue/domain/abstract_domain_object.rb +8 -0
data/lib/catissue/domain/abstract_position.rb +22 -0
data/lib/catissue/domain/abstract_specimen.rb +288 -0
data/lib/catissue/domain/abstract_specimen_collection_group.rb +25 -0
data/lib/catissue/domain/address.rb +13 -0
data/lib/catissue/domain/cancer_research_group.rb +11 -0
data/lib/catissue/domain/capacity.rb +34 -0
data/lib/catissue/domain/check_in_check_out_event_parameter.rb +19 -0
data/lib/catissue/domain/collection_event_parameters.rb +13 -0
data/lib/catissue/domain/collection_protocol.rb +177 -0
data/lib/catissue/domain/collection_protocol_event.rb +108 -0
data/lib/catissue/domain/collection_protocol_registration.rb +108 -0
data/lib/catissue/domain/consent_tier_response.rb +13 -0
data/lib/catissue/domain/consent_tier_status.rb +29 -0
data/lib/catissue/domain/container.rb +234 -0
data/lib/catissue/domain/container_position.rb +21 -0
data/lib/catissue/domain/container_type.rb +131 -0
data/lib/catissue/domain/department.rb +13 -0
data/lib/catissue/domain/disposal_event_parameters.rb +13 -0
data/lib/catissue/domain/embedded_event_parameters.rb +10 -0
data/lib/catissue/domain/external_identifier.rb +22 -0
data/lib/catissue/domain/frozen_event_parameters.rb +10 -0
data/lib/catissue/domain/institution.rb +13 -0
data/lib/catissue/domain/new_specimen_array_order_item.rb +35 -0
data/lib/catissue/domain/order_details.rb +25 -0
data/lib/catissue/domain/participant.rb +138 -0
data/lib/catissue/domain/participant_medical_identifier.rb +38 -0
data/lib/catissue/domain/password.rb +11 -0
data/lib/catissue/domain/race.rb +11 -0
data/lib/catissue/domain/received_event_parameters.rb +25 -0
data/lib/catissue/domain/scg_event_parameters.rb +11 -0
data/lib/catissue/domain/site.rb +30 -0
data/lib/catissue/domain/specimen.rb +456 -0
data/lib/catissue/domain/specimen_array.rb +47 -0
data/lib/catissue/domain/specimen_array_content.rb +19 -0
data/lib/catissue/domain/specimen_array_type.rb +20 -0
data/lib/catissue/domain/specimen_characteristics.rb +20 -0
data/lib/catissue/domain/specimen_collection_group.rb +412 -0
data/lib/catissue/domain/specimen_event_parameters.rb +111 -0
data/lib/catissue/domain/specimen_position.rb +38 -0
data/lib/catissue/domain/specimen_protocol.rb +34 -0
data/lib/catissue/domain/specimen_requirement.rb +143 -0
data/lib/catissue/domain/storage_container.rb +204 -0
data/lib/catissue/domain/storage_type.rb +82 -0
data/lib/catissue/domain/transfer_event_parameters.rb +53 -0
data/lib/catissue/domain/user.rb +100 -0
data/lib/catissue/extract/command.rb +31 -0
data/lib/catissue/extract/delta.rb +62 -0
data/lib/catissue/extract/extractor.rb +99 -0
data/lib/catissue/migration/migrator.rb +101 -0
data/lib/catissue/migration/shims.rb +108 -0
data/lib/catissue/migration/uniquify.rb +111 -0
data/lib/catissue/resource.rb +84 -0
data/lib/catissue/util/controlled_value.rb +29 -0
data/lib/catissue/util/location.rb +116 -0
data/lib/catissue/util/log.rb +30 -0
data/lib/catissue/util/person.rb +31 -0
data/lib/catissue/util/position.rb +54 -0
data/lib/catissue/util/storable.rb +34 -0
data/lib/catissue/util/storage_type_holder.rb +30 -0
data/lib/catissue/version.rb +7 -0
metadata +212 -0

data/examples/galena/doc/top-level-namespace.html ADDED Viewed

@@ -0,0 +1,112 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+  "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
+  <head>
+    <meta name="Content-Type" content="text/html; charset=utf-8" />
+<title>Top Level Namespace</title>
+<link rel="stylesheet" href="css/style.css" type="text/css" media="screen" charset="utf-8" />
+<link rel="stylesheet" href="css/common.css" type="text/css" media="screen" charset="utf-8" />
+<script type="text/javascript" charset="utf-8">
+  relpath = '';
+  if (relpath != '') relpath += '/';
+</script>
+<script type="text/javascript" charset="utf-8" src="js/jquery.js"></script>
+<script type="text/javascript" charset="utf-8" src="js/app.js"></script>
+  </head>
+  <body>
+    <script type="text/javascript" charset="utf-8">
+      if (window.top.frames.main) document.body.className = 'frames';
+    </script>
+    <div id="header">
+      <div id="menu">
+    <a href="_index.html">Index</a> &raquo;
+    <span class="title">Top Level Namespace</span>
+  <div class="noframes"><span class="title">(</span><a href="." target="_top">no frames</a><span class="title">)</span></div>
+</div>
+      <div id="search">
+  <a id="class_list_link" href="#">Class List</a>
+  <a id="method_list_link" href="#">Method List</a>
+  <a id ="file_list_link" href="#">File List</a>
+</div>
+      <div class="clear"></div>
+    </div>
+    <iframe id="search_frame"></iframe>
+    <div id="content"><h1>Top Level Namespace
+</h1>
+<dl class="box">
+</dl>
+<div class="clear"></div>
+<h2>Defined Under Namespace</h2>
+<p class="children">
+      <strong class="modules">Modules:</strong> <span class='object_link'><a href="CaTissue.html" title="CaTissue (module)">CaTissue</a></span>, <span class='object_link'><a href="Galena.html" title="Galena (module)">Galena</a></span>
+</p>
+  <h2>Constant Summary</h2>
+    <dl class="constants">
+        <dt id="DEF_LOG_FILE-constant" class="">DEF_LOG_FILE =
+          <div class="docstring">
+  <div class="discussion">
+    <p>
+the default log file
+</p>
+  </div>
+</div>
+<div class="tags">
+</div>
+        </dt>
+        <dd><pre class="code"><span class='string val'>'log/migration.log'</span>
+</pre></dd>
+    </dl>
+</div>
+    <div id="footer">
+  Generated on Tue Nov 23 11:38:43 2010 by
+  <a href="http://yardoc.org" title="Yay! A Ruby Documentation Tool" target="_parent">yard</a>
+  0.6.1 (ruby-1.8.6).
+</div>
+  </body>
+</html>

data/examples/galena/lib/README.html ADDED Viewed

@@ -0,0 +1,33 @@
+<h1>Galena Cancer Center Tissue Bank Migrator example</h1>
+<p>
+This migration example demonstrates how to load the content of a hypothetical
+custom tissue bank into caTissue. The use case illustrates several common
+migration impediments:
+<ul>
+<li>Different terminology than caTissue
+<li>Different associations than caTissue
+<li>Incomplete input for caTissue
+<li>Denormalized input
+<li>Inconsistent input
+<li>Input data scrubbing
+<li>Aliquot inference
+<li>Pre-defined caTissue protocol
+</ul>
+These migration features are described in the migration process below.
+</p>
+<h2>Migration Process</h2>
+<h2>Input data</h2>
+<p>
+The hypothetical Galena Tissue Bank data resides in the <tt>data/galena.csv</tt>
+CSV file included in the example. The CSV file holds one row for each specimen.
+The fields are as follows:
+<dl>
+<dt>MRN</dt><dd>Patient Medical Record Number</dd>
+<dt>Initials</dt><dd>Patient name initials</dd>
+<dt>Frozen?</dt><dd>Flag indicating whether the specimen is frozen</dd>
+<dt>SPN</dt><dd>Surgical Pathology Number</dd>
+<dt>Collection Date</dt><dd>Specimen date of collection</dd>
+<dt>Quantity</dt><dd>Amount collected</dd>
+</dl>
+</p>

data/examples/galena/lib/galena.rb ADDED Viewed

@@ -0,0 +1,8 @@
+# The caRuby Tissue Galena example module.
+module Galena
+  # @param [String] the path (without wildcards) of the desired file relative to the gem root directory
+  # @return [String, nil] the file in this gem which matches the given path
+  def self.resource(path)
+    File.expand_path(File.join(File.dirname(__FILE__), '..', path))
+  end
+end

data/examples/galena/lib/galena/cli/seed.rb ADDED Viewed

@@ -0,0 +1,43 @@
+#!/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/examples/galena/lib/galena/migration/filter_shims.rb ADDED Viewed

@@ -0,0 +1,43 @@
+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/examples/galena/lib/galena/migration/frozen_shims.rb ADDED Viewed

@@ -0,0 +1,54 @@
+require 'galena/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::Migration::Defaults#box_type} in a
+    # freezer of type {Galena::Migration::Defaults#freezer_type}.
+    #
+    # @return [StorageContainer] the new box
+    def create_box
+      defs = Galena::Seed.defaults
+      self.storage_type = defs.box_type
+      self.site = defs.tissue_bank
+      # 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/examples/galena/lib/galena/seed/defaults.rb ADDED Viewed

@@ -0,0 +1,97 @@
+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.
+    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)
+        @freezer_type.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)
+        @protocol = CaTissue::CollectionProtocol.new(:short_title => 'Galena CP',
+          :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')
+        # a storage container
+        @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'
+      end
+    end
+  end
+end

data/lib/catissue.rb ADDED Viewed

@@ -0,0 +1,26 @@
+# This file is the entry point included by applications which reference a CaTissue object or service.
+# the caRuby core gem
+require 'rubygems'
+begin
+  gem 'caruby-core'
+rescue LoadError
+  # if the gem is not available, then try a local development source
+  $:.unshift File.join(File.dirname(__FILE__), '..', '..', 'caruby', 'lib')
+end
+require 'caruby/util/log'
+require 'catissue/util/log'
+require 'catissue/resource'
+require 'catissue/database'
+# CaTissue wraps the caTissue Java API.
+# See the caRuby[http://http://caruby.rubyforge.org/] home page for more information.
+module CaTissue
+  # @param [<String>] nodes the path components relative to the caRuby Tissue source directory
+  # @return [String] the file path to the specified path components
+  def self.path(*nodes)
+    root = File.join(File.dirname(__FILE__), '..')
+    File.expand_path(File.join(*nodes), root)
+  end
+end

data/lib/catissue/cli/command.rb ADDED Viewed

@@ -0,0 +1,51 @@
+# the standard log file
+DEF_LOG_FILE = 'log/catissue.log' unless defined?(DEF_LOG_FILE)
+begin
+  require 'catissue'
+rescue Exception => e
+  logger.error("caTissue client load was unsuccessful - #{e}:\n#{e.backtrace.qp}")
+  puts "caTissue client load was unsuccessful - #{e}."
+  puts "See the log at #{CaRuby::Log.instance.file} for more information."
+  exit 1
+end
+require 'caruby/cli/command'
+require 'catissue/version'
+module CaTissue
+  module CLI
+    # Augments {CaRuby::CLI::Command} with caTissue-specific command line option handlers.
+    class Command < CaRuby::CLI::Command
+      # @see {CaRuby::CLI::Command#initialize}
+      def initialize(specs=[], &executor)
+        specs << VERSION_OPT
+        super { |opts| handle_catissue_options(opts, &executor) }
+      end
+      private
+      # If the version option is set, then prints the version and exits.
+      # Otherwise, extracts the connection command line options, adds them
+      # to {CaTissue.access_properties}, and yields to the executor block.
+      #
+      # @param [{Symbol => Object}] opts the command line argument and option symbol => value hash
+      def handle_catissue_options(opts)
+        if opts[:version] then
+          puts "#{CaTissue::VERSION} for caTissue v#{CaTissue::CATISSUE_VERSIONS}"
+        else
+          CaRuby::ACCESS_OPTS.each do |opt, *spec|
+            value = opts.delete(opt)
+            CaTissue.access_properties[opt] = value if value
+          end
+          yield(opts)
+        end
+      end
+      private
+      VERSION_OPT = [:version, "--version", "Prints the version of caRuby Tissue and the supported caTissue releases and exits"]
+    end
+  end
+end