caruby-tissue 1.5.6 → 2.1.1

data/lib/catissue/domain.rb

@@ -1,26 +0,0 @@
-require 'caruby/domain'
-require 'catissue/resource'
-require 'catissue/annotation/annotatable_class'
-require 'catissue/wustl/logger'
-
-module CaTissue
-  
-  private
-  
-  # The required Java package name.
-  PKG = 'edu.wustl.catissuecore.domain'
-  
-  # The domain class definitions.
-  SRC_DIR = File.join(File.dirname(__FILE__), 'domain')
-
-  # Enable the resource metadata aspect.
-  md_proc = Proc.new { |klass| AnnotatableClass.extend_class(klass) }
-  CaRuby::Domain.extend_module(self, :mixin => Resource, :metadata => md_proc, :package => PKG)
-  
-  # Set up the caTissue client logger before loading the class definitions.
-  Wustl::Logger.configure
-  
-  # Load the class definitions.
-  load_dir(SRC_DIR)
-end
-

data/lib/catissue/extract/command.rb

@@ -1,31 +0,0 @@
-require 'catissue/cli/command'
-require 'catissue/extract/delta'
-require 'catissue/extract/extractor'
-
-module CaTissue
-  # ExtractCommand extracts target CaTissue domain class objects whose modification date is
-  # within a time interval to a CSV file based on a CSV mapping file.
-  class ExtractCommand < CaTissue::Command
-    # Creates a new ExtractCommand.
-    # The delta range is given by the required :since option and optional :before option.
-    # The default before value is the current DateTime. These are used to build a Delta
-    # which is passed to {CaRuby::Command#initialize} as the :ids option.
-    # The :log option specifies a log file.
-    # Other supported options are described in {Extractor#initialize}.
-    def initialize
-      # prep the options
-      since = opts.delete(:since)
-      raise ArgumentError.new("Missing required beginning of date selection range option") unless since
-      before = opts.delete(:before) || DateTime.now
-       # the data acquirer
-      opts[:ids] = Delta.new(@target, since, before)
-      # make the command
-      super(opts)
-    end
-
-    # Starts an Extractor with the command-line options.
-    def run
-      super { |opts| Extractor.new(opts) }
-    end
-  end
-end

data/lib/catissue/extract/delta.rb

@@ -1,58 +0,0 @@
-require 'date'
-require 'caruby/csv/csvio'
-require 'caruby/util/log'
-require 'caruby/util/collection'
-require 'caruby/util/pretty_print'
-require 'catissue/database'
-
-module CaTissue
-  # Delta determines caTissue objects which changed within a time interval.
-  class Delta
-    include Enumerable
-
-    # Creates a new Delta for objects of the given target type which changed
-    # at or after the since Date and earlier but not at the before Date.
-    # The default before Date is now.
-    def initialize(target, since, before=nil)
-      # convert the required target to a CaTissue class if necessary
-      @matcher = create_table_regex(target)
-      @since = since
-      @before = before || DateTime.now
-    end
-
-    # Calls the given block on each caTissue identifier satisfying the delta condition.
-    # This method submits the delta SQL and filters the result on the target class.
-    # This method always submits the query; the caller is responsible for preserving
-    # the result if necessary using {#to_a}.
-    def each(&block)
-      execute_query(&block)
-    end
-
-    private
-
-    SQL_FILE = File.join(File.dirname(__FILE__), '..', '..', '..', 'sql', 'delta.sql')
-
-    # Returns the result of running the delta SQL on the target CaTissue domain class.
-    def execute_query
-      sql = File.open(SQL_FILE) { |file| file.read }
-      logger.debug { "Executing identifier change set selection range #{@since} - #{@before}, SQL:\n#{sql}" }
-      CaTissue::Database.executor.execute do |dbh|
-        dbh.select_all(sql, @since, @before) do |row|
-          table, identifier = row
-          yield identifier.to_i if table =~ @matcher
-        end
-      end
-    end
-
-    # Returns the table match REs for the given target class.
-    def create_table_regex(target)
-      # The class => table RE hash. Make this hash rather than defining a constant in order to enable
-      # logging before touching a domain class.
-      @cls_tbl_hash ||= {
-        CaTissue::Specimen => /catissue_[[:alpha:]]+_specimen/i,
-        CaTissue::SpecimenCollectionGroup => /catissue_specimen_coll_group/i
-      }
-      @cls_tbl_hash.detect_value { |klass, table| table if target <= klass }
-    end
-  end
-end

data/lib/catissue/extract/extractor.rb

@@ -1,99 +0,0 @@
-require 'caruby/util/properties'
-require 'caruby/csv/csv_mapper'
-require 'caruby/csv/csvio'
-
-module CaTissue
-  # Extracts caTissue objects.
-  class Extractor
-    include Enumerable
-
-    # The default name of this migrator.
-    DEF_NAME = 'caTissue Extractor'
-
-    # The extract output file
-    attr_reader :output
-
-    # Creates a new Extractor with the given options.
-    #
-    # @option options [String] :file the extract configuration file name
-    # @option options [String] :name name of this Migrator (default is +caTissue Migrator+)
-    # @option options [String] :output optional output CSV file name
-    # @option options [String] :target required target domain class or class name
-    # @option options [String] :ids the database identifiers of the target objects to extract
-    # @option options [String] :log log file (default +log/extract.log+)
-    def initialize(options={})
-      conf_file = options.delete(:file)
-      if conf_file then
-        CaRuby::Properties.new(conf_file, :array => [:shims]).each { |key, value| options[key.to_sym] ||= value }
-      end
-      # tailor the options
-      name = options[:name] || DEF_NAME
-      super(name)
-      @ids = options[:ids]
-      raise ArgumentError.new("Missing required ids option") unless @ids
-      # convert the required target to a CaTissue class if necessary
-      @target = target_class_from_option(options[:target])
-      @target ||= CaTissue::Specimen
-      # the CSV output file
-      @output = options[:output]
-      raise ArgumentError.new("Missing required extract output file option") unless @output
-      # the field mapping configuration
-      fld_conf = options[:mapping]
-      mapper = CaRuby::CsvMapper.new(fld_conf, @target, @output, :mode => "w")
-      @csvio = mapper.csvio
-      @fld_path_hash = {}
-      mapper.paths.each do |path|
-        fld = mapper.header(path)
-        # the path node is either an attribute symbol or attribute metadata;
-        # if metadata, then use the reader method.
-        @fld_path_hash[fld] = path.map { |attr_or_md| CaRuby::Domain::Attribute === attr_or_md ? attr_or_md.reader : attr_or_md }
-      end
-      logger.debug { "Extract field => path map: #{@fld_path_hash.transform { |path| path.join('.') }.pp_s}" }
-    end
-
-    # Exports the selected target records from the database to the output file.
-    def run
-      begin
-        extract { |obj| write(obj) }
-      ensure
-        @csvio.close
-      end
-    end
-
-    # Executes this extractor CSV file and calls the block given to this method on each target domain object.
-    def extract
-      logger.debug { "Found #{@ids.size} extract targets." }
-      CaTissue::Database.instance.open do
-        @ids.each do |identifier|
-          obj = @target.new(:identifier => identifier)
-          logger.debug { "Finding extract target #{obj}..." }
-          if obj.find then
-            logger.debug { "Extractor fetched #{obj}." }
-            yield obj
-          else
-            logger.debug { "Extract target #{obj} not found." }
-          end
-        end
-      end
-    end
-
-    alias :each :extract
-
-    private
-
-    def write(obj)
-      # collect the field values in order by resolving the path on obj
-      rec = @csvio.headers.map do |fld|
-        obj.path_value(@fld_path_hash[fld])
-      end
-      @csvio << rec
-      logger.debug { "Extractor wrote #{obj} to CSV output file." }
-    end
-
-    def target_class_from_option(option)
-      return if option.nil?
-      return option if Class === option
-      CaTissue.const_get(option)
-    end
-  end
-end

data/lib/catissue/migration/uniquify.rb

@@ -1,2 +0,0 @@
-require 'caruby/migration/uniquify'
-require 'catissue/util/uniquify'

data/lib/catissue/util/collectible_event_parameters.rb

@@ -1,71 +0,0 @@
-module CaTissue
-  # A CollectibleEventParameters is a SpecimenEventParameters which pertains to Specimen
-  # or SpecimenCollectionGroup collection at the point of tissue acquisition from the participant
-  # or receival at the tissue bank.
-  module CollectibleEventParameters
-    # Returns the SpecimenEventParameters in others which matches this CollectibleEventParameters in the scope of an owner Specimen or SCG.
-    # This method relaxes {CaRuby::Resource#match_in_owner_scope} for a CollectibleEventParameters that matches any SpecimenEventParameters
-    # in others of the same class, since there can be at most one CollectibleEventParameters of a given class for a given SCG.
-    def match_in_owner_scope(others)
-      others.detect { |other| minimal_match?(other) }
-    end
-    
-    private
-    
-    # Injects validation to ensure that a CollectibleEventParameters instance cannot be owned by
-    # both a specimen and a SCG.
-    # 
-    # @param [Class] klass the including class
-    def self.included(klass)
-      klass.class_eval do
-        owner_attributes.each do |attr|
-          wtr = attribute_metadata(attr).writer
-          redefine_method(wtr) do |base|
-            lambda do |obj|
-              validate_no_owner_confict(attr, obj)
-              send(base, obj)
-            end
-          end
-        end
-      end
-    end
-    
-    # @param attribute the owner attribute to set
-    # @param obj the owner to set
-    # @raise [] if there is already a different owner attribute value
-    def validate_no_owner_confict(attribute, obj)
-      return if obj.nil?
-      self.class.owner_attributes.each do |attr|
-        next if attr == attribute
-        other = send(attr)
-        if other then
-          raise ValidationError.new("Cannot add #{qp} to #{attribute} #{obj.qp}, since it is already owned by #{attr} #{other}")
-        end
-      end
-    end
-    
-    # Overrides {CaRuby::Migratable#migratable__migrate_owner} to give owner preference to a migrated SCG
-    # over a migrated Specimen.
-    #
-    # @param (see CaRuby::Migratable#migratable__migrate_owner)
-    def migratable__migrate_owner(row, migrated, mth_hash=nil)
-      migratable__set_scg(row, migrated, mth_hash) or migratable__set_specimen(row, migrated, mth_hash)
-    end
-    
-    # @param (see #migratable__migrate_owner)
-    # @return [CaTissue::SpecimenCollectionGroup, nil] the migrated SCG, if any
-    def migratable__set_scg(row, migrated, mth_hash=nil)
-      attr_md = self.class.attribute_metadata(:specimen_collection_group)
-      scg = migratable__target_value(attr_md, row, migrated, mth_hash)
-      if scg then self.specimen_collection_group = scg end
-    end
-    
-    # @param (see #migratable__migrate_owner)
-    # @return [CaTissue::Specimen, nil] the migrated specimen, if any
-    def migratable__set_specimen(row, migrated, mth_hash=nil)
-      attr_md = self.class.attribute_metadata(:specimen)
-      spc = migratable__target_value(attr_md, row, migrated, mth_hash)
-      if spc then self.specimen = spc end
-    end
-  end
-end

data/lib/catissue/util/controlled_value.rb

@@ -1,29 +0,0 @@
-require 'caruby/util/controlled_value'
-
-module CaTissue
-  class ControlledValue < CaRuby::ControlledValue
-
-    PUBLIC_ID_ALIAS_MAP = {:tissue_site => 'Tissue_Site_PID', :clinical_diagnosis => 'Clinical_Diagnosis_PID'}
-
-    # Returns the standard public id string for the given public_id_or_alias.
-    def self.standard_public_id(public_id_or_alias)
-      PUBLIC_ID_ALIAS_MAP[public_id_or_alias.to_sym] or public_id_or_alias.to_s
-    end
-
-    attr_accessor :identifier, :public_id
-
-    attr_reader :identifier
-
-    def parent_identifier
-      parent.identifier if parent
-    end
-
-    def public_id=(public_id_or_alias)
-      @public_id = self.class.standard_public_id(public_id_or_alias)
-    end
-
-    def to_s
-      "#{value}"
-    end
-  end
-end

data/lib/catissue/util/uniquify.rb

@@ -1,86 +0,0 @@
-require 'caruby/domain/uniquify'
-
-module CaTissue
-  class CollectionProtocol
-    include CaRuby::Resource::Unique
-    
-    # Makes this CP's short and long title unique.
-    def uniquify
-      super
-      self.short_title = title
-    end
-  end
-
-  class CollectionProtocolEvent
-    include CaRuby::Resource::Unique
-  end
-
-  class Container
-    include CaRuby::Resource::Unique
-    
-    # Makes this Container and all of its subcontainers unique.
-    def uniquify
-      super
-      subcontainers.each { |ctr| ctr.uniquify }
-    end
-  end
-
-  class ParticipantMedicalIdentifier
-    include CaRuby::Resource::Unique
-  end
-
-  class CollectionProtocolRegistration
-    include CaRuby::Resource::Unique
-    
-    # Makes this CPR's PPI unique.
-    def uniquify
-      oldval = protocol_participant_identifier || return
-      newval = uniquify_value(oldval)
-      self.protocol_participant_identifier = newval
-      logger.debug { "Reset #{qp} PPI from #{oldval} to unique value #{newval}." }
-    end
-  end
-
-  class SpecimenCollectionGroup
-    include CaRuby::Resource::Unique
-    
-    # Makes this SCG's SPN unique.
-    def uniquify
-      super
-      oldval = surgical_pathology_number || return
-      newval = uniquify_value(oldval)
-      self.surgical_pathology_number = newval
-      logger.debug { "Reset #{qp} SPN from #{oldval} to unique value #{newval}." }
-    end
-  end
-
-  class Specimen
-    include CaRuby::Resource::Unique
-  end
-
-  class ExternalIdentifier
-    include CaRuby::Resource::Unique
-    
-    # Makes this ExternalIdentifier's value unique.
-    def uniquify
-      oldval = value || return
-      newval = uniquify_value(oldval)
-      self.value = newval
-      logger.debug { "Reset #{qp} value from #{oldval} to unique value #{newval}." }
-    end
-  end
-
-  class User
-    include CaRuby::Resource::Unique
-    
-    # Makes this User's login id and email address unique.
-    # The result is in the form _name___suffix_+@test.com+
-    # where:
-    # * _name_ is the name prefix portion of the original email address
-    # * _suffix_ is a unique number
-    def uniquify
-      email = email_address ||= self.login_name || return
-      self.login_name = self.email_address = uniquify_value(email[/[^@]+/]) + '@test.com'
-    end
-  end
-end

data/test/fixtures/catissue/domain/conf/catissue_override.yaml

@@ -1,9 +0,0 @@
-# Tests merging attribute properites.
-
-secondary_key_attributes:
-  CollectionProtocol:
-    - title
-
-required_attributes:
-  CollectionProtocol:
-    - sequenceNumber

data/test/fixtures/catissue/extract/conf/scg_extract.yaml

@@ -1,3 +0,0 @@
-fields: test/fixtures/catissue/extract/conf/scg_fields.yaml
-output: test/results/catissue/extract/scg.csv
-target: SpecimenCollectionGroup

data/test/fixtures/catissue/extract/conf/scg_fields.yaml

@@ -1,3 +0,0 @@
-MRN: registration.participant_identifier
-SPN: surgical_pathology_number
-Collection Date: collection_event_parameters.timestamp

data/test/fixtures/catissue/extract/conf/spc_extract.yaml

@@ -1,3 +0,0 @@
-fields: test/fixtures/catissue/extract/conf/spc_fields.yaml
-output: test/results/catissue/extract/spc.csv
-target: TissueSpecimen

data/test/fixtures/catissue/extract/conf/spc_fields.yaml

@@ -1,4 +0,0 @@
-MRN: specimen_collection_group.registration.participant_identifier
-SPN: specimen_collection_group.surgical_pathology_number
-Collection Date: specimen_collection_group.collection_event_parameters.timestamp
-Quantity: initial_quantity