caruby-tissue 1.5.6 → 2.1.1

data/examples/galena/spec/annotation_spec.rb

@@ -0,0 +1,46 @@
+require File.dirname(__FILE__) + '/spec_helper'
+
+module Galena::Annotation
+  TARGET = CaTissue::SpecimenCollectionGroup::Pathology::RadicalProstatectomyPathologyAnnotation
+  
+  describe 'migration' do
+    include_context 'a migration'
+
+    before(:all) do
+     @pth = migrate(:annotation, :target => TARGET).first
+    end
+
+    it 'should save the annotation' do
+      @pth.should_not be nil
+    end
+
+    it 'should set the comment' do
+      @pth.comment.should_not be nil
+    end
+
+    it 'should migrate the Gleason score' do
+      gls = @pth.gleason_score
+      gls.should_not be nil
+      gls.primary_pattern_score.should == '3'
+    end
+
+    it 'should migrate the grades' do
+      grd = @pth.histologic_grades.first
+      grd.should_not be nil
+      grd.grade.should == '2'
+    end
+  end
+  
+  describe 'migration to database' do
+    include_context 'a migration'
+
+    before(:all) do
+     @pth = migrate_to_database(:annotation, :target => TARGET).first
+    end
+
+    it 'should save the annotation' do
+      @pth.should_not be nil
+      @pth.identifier.should_not be nil
+    end
+  end
+end

data/examples/galena/spec/filter_spec.rb

@@ -0,0 +1,94 @@
+require File.dirname(__FILE__) + '/spec_helper'
+require 'fileutils'
+
+module Galena::Filter
+  RESULTS = File.dirname(__FILE__) + '/../results'
+  
+  # The rejects file.
+  REJECTS = RESULTS + '/filter/rejects.csv'
+  
+  # The migration options.
+  OPTS = {:target => CaTissue::TissueSpecimen, :bad => REJECTS}
+  
+  describe 'migration' do
+    include_context 'a migration'
+
+    before(:all) do
+      FileUtils.rm_rf RESULTS
+      @spcs = migrate(:filter, OPTS)
+    end
+    
+    after(:all) do
+      FileUtils.rm_rf RESULTS
+    end
+    
+    it 'should migrate the valid specimens' do
+      @spcs.size.should be 3
+    end
+    
+    it 'should reject the invalid specimens' do
+      File.readlines(REJECTS).to_a.size.should be 1
+    end
+      
+    it 'should infer the fixed specimen' do
+      @spcs.select { |spc| spc.specimen_type == 'Fixed Tissue' }.size.should be 1
+    end
+    
+    it 'should infer the frozen specimens' do
+      @spcs.select { |spc| spc.specimen_type == 'Frozen Tissue' }.size.should be 2
+    end
+    
+    context 'specimen' do
+      subject { @spcs.first }
+
+      it 'should set the quantity' do
+        subject.initial_quantity.should == 3.4
+      end
+
+      it 'should reference a SCG with a SPN' do
+        scg = subject.specimen_collection_group
+        scg.should_not be nil
+        scg.surgical_pathology_number.should == '4001'
+      end
+
+      it 'should register a participant with the name given by the parsed initials' do
+        reg = subject.specimen_collection_group.registration
+        reg.should_not be nil
+        pnt = reg.participant
+        pnt.should_not be nil
+        pnt.first_name.should == 'U'
+        pnt.last_name.should == 'Z'
+      end
+
+      it 'should set the received date' do
+        rep = subject.received_event_parameters
+        rep.should_not be nil
+        rep.timestamp.year.should == 2007
+        rep.timestamp.month.should == 1
+        rep.timestamp.day.should == 4
+      end
+    end
+  end
+  
+  describe 'migration to database' do
+    include_context 'a migration'
+
+    before(:all) do
+      FileUtils.rm_rf RESULTS
+      @spcs = migrate_to_database(:filter, OPTS)
+    end
+    
+    after(:all) do
+      FileUtils.rm_rf RESULTS
+    end
+    
+    it 'should save the valid specimens' do
+      @spcs.size.should be 3
+      @spcs.each { |spc| spc.identifier.should_not be nil }
+    end
+    
+    it 'should reject the invalid specimens' do
+      File.readlines(REJECTS).size.should be 1
+    end
+  end
+end

data/examples/galena/spec/frozen_spec.rb

@@ -0,0 +1,39 @@
+require File.dirname(__FILE__) + '/spec_helper'
+
+module Galena::Frozen
+  describe 'migration' do
+    include_context 'a migration'
+
+    before(:all) do
+      @spc = migrate(:frozen, :target => CaTissue::TissueSpecimen).first
+    end
+    
+    it 'should migrate the specimen' do
+      @spc.should_not be nil
+    end
+    
+    it 'should set the specimen type to frozen' do
+      @spc.specimen_type.should == 'Frozen Tissue'
+    end
+    
+    it 'should store the specimen' do
+      pos = @spc.position
+      pos.should_not be nil
+      pos.holder.should_not be nil
+      pos.occupant.should be @spc
+    end
+  end
+  
+  describe 'migration to database' do
+    include_context 'a migration'
+
+    before(:all) do
+      @spc = migrate_to_database(:frozen, :target => CaTissue::TissueSpecimen).first
+    end
+    
+    it 'should save the specimen' do
+      @spc.should_not be nil
+      @spc.identifier.should_not be nil
+    end
+  end
+end

data/examples/galena/spec/general_spec.rb

@@ -0,0 +1,62 @@
+require File.dirname(__FILE__) + '/spec_helper'
+
+module Galena::General
+  describe 'migration' do
+    include_context 'a migration'
+
+    before(:all) do
+      # The general migration does not have defaults.
+      @spc = migrate(:general, :defaults => nil, :target => CaTissue::TissueSpecimen).first
+    end
+    
+    it 'should migrate the specimen' do
+      @spc.should_not be nil
+    end
+    
+    it 'should set the specimen type to frozen' do
+      @spc.specimen_type.should == 'Frozen Tissue'
+    end
+    
+    it 'should set the quantity' do
+      @spc.initial_quantity.should == 3.4
+    end
+    
+    it 'should set the SPN' do
+      scg = @spc.specimen_collection_group
+      scg.should_not be nil
+      scg.surgical_pathology_number.should == '3001'
+    end
+    
+    it 'should set the PPI' do
+      reg = @spc.specimen_collection_group.registration
+      reg.should_not be nil
+      reg.protocol_participant_identifier.should == '301'
+    end
+    
+    it 'should set the participant name' do
+      pnt = @spc.specimen_collection_group.registration.participant
+      pnt.should_not be nil
+      pnt.first_name.should == 'Rufus'
+      pnt.last_name.should == 'Firefly'
+    end
+    
+    it 'should set the MRN' do
+      pmi = @spc.specimen_collection_group.registration.participant.participant_medical_identifiers.first
+      pmi.should_not be nil
+      pmi.medical_record_number.should == '30001'
+    end
+  end
+  
+  describe 'migration to database' do
+    include_context 'a migration'
+
+    before(:all) do
+      @spc = migrate_to_database(:general, :defaults => nil, :target => CaTissue::TissueSpecimen).first
+    end
+    
+    it 'should save the specimen' do
+      @spc.should_not be nil
+      @spc.identifier.should_not be nil
+    end
+  end
+end

data/examples/galena/spec/registration_spec.rb

@@ -0,0 +1,37 @@
+require File.dirname(__FILE__) + '/spec_helper'
+
+module Galena::Registration
+  describe 'migration' do
+    include_context 'a migration'
+
+    before(:all) do
+      @reg = migrate(:registration, :target => CaTissue::CollectionProtocolRegistration).first
+    end
+    
+    it 'should migrate the registration' do
+      @reg.should_not be nil
+    end
+    
+    it 'should set the PPI to the MRN' do
+      pnt = @reg.participant
+      pnt.should_not be nil
+      pmi = pnt.participant_medical_identifiers.first
+      pmi.should_not be nil
+      pmi.medical_record_number.should == '10001'
+      pmi.medical_record_number.should == @reg.protocol_participant_identifier
+    end
+  end
+  
+  describe 'migration to database' do
+    include_context 'a migration'
+
+    before(:all) do
+      @reg = migrate_to_database(:registration, :target => CaTissue::CollectionProtocolRegistration).first
+    end
+    
+    it 'should save the registration' do
+      @reg.should_not be nil
+      @reg.identifier.should_not be nil
+    end
+  end
+end

data/examples/galena/spec/seed.rb

@@ -0,0 +1,107 @@
+require 'jinx/helpers/inflector'
+require 'jinx/migration/migratable'
+require 'galena/seed'
+
+module CaTissue
+  # Augment the classes below with sufficient content to pass the create mandatory attribute validation.
+  # This simulates an existing administrative object for testing purposes.
+  #
+  # This file is not placed in the specs support directory, since it is dynamically loaded as a shim.
+  shims CollectionProtocol, CollectionProtocolEvent, Site, StorageContainer, User
+
+  class CollectionProtocol
+    # Augments +Jinx::Migratable.migrate+ for the Galena example by adding the following defaults:
+    # * the CP principal_investigator defaults to the {Galena::Seed#protocol} PI
+    # * if the sites is empty, then the {Galena::Seed#tissue_bank} is added
+    #   to the CP sites
+    #
+    # @param (see Jinx::Migratable#migrate)
+    def migrate(row, migrated)
+      super
+      self.title ||= Galena.administrative_objects.protocol.title
+      self.principal_investigator ||= Galena.administrative_objects.protocol.principal_investigator
+      sites << Galena.administrative_objects.tissue_bank if sites.empty?
+      coordinators << Galena.administrative_objects.tissue_bank.coordinator if coordinators.empty?
+    end
+  end
+  
+  class CollectionProtocolEvent
+    # Augments +Jinx::Migratable.migrate+ for the example by adding the following defaults:
+    # * create a {CaTissue::TissueSpecimenRequirement}
+    # * copy the event point from {Galena::Seed}
+    #
+    # @param (see Jinx::Migratable#migrate)
+    def migrate(row, migrated)
+      super
+      cpe = Galena.administrative_objects.protocol.events.first
+      self.event_point ||= cpe.event_point
+      rqmt = cpe.requirements.first
+      CaTissue::TissueSpecimenRequirement.new(:collection_event => self, :specimen_type => rqmt.specimen_type)
+    end
+  end
+
+  class Site
+    # Augments +Jinx::Migratable.migrate+ for the example by merging the content of the
+    # {Galena::Seed} site which matches on this Site's name, if any.
+    #
+    # @param (see Jinx::Migratable#migrate)
+    def migrate(row, migrated)
+      super
+      # Match the site by name. Account for uniquification by a partial match, e.g.
+      # 'Galena_Hospital_41893443' matches the site named 'Galena Hospital'.
+      tmpl = TEMPLATES.detect { |site| name[site.name.gsub('_', ' ')] }
+      # merge the default mandatory attribute values
+      if tmpl then merge(tmpl, mandatory_attributes) end
+    end
+    
+    private
+    
+    TEMPLATES ||= [Galena.administrative_objects.hospital, Galena.administrative_objects.tissue_bank]
+  end
+
+  class StorageContainer
+    # Augments +Jinx::Migratable.migrate+ for the example by setting the
+    # the container site and type to the {Galena::Seed}
+    # box site and type, resp.
+    #
+    # @param (see Jinx::Migratable#migrate)
+    def migrate(row, migrated)
+      super
+      self.site ||= Galena.administrative_objects.tissue_bank
+      self.storage_type ||= Galena.administrative_objects.box_type
+    end
+  end
+  
+  class SpecimenEventParameters
+    # Fills in the event parameters user details.
+    #
+    # @param (see Jinx::Migratable#migrate)
+    def migrate(row, migrated)
+      user.migrate(row, migrated) if user
+    end
+  end
+  
+  class User
+    # Augments +Jinx::Migratable.migrate+ for the example as follows:
+    # * infer the first and last name from the email address
+    # * copy the address and organizations from the tissue bank coordinator 
+    #
+    # @param (see Jinx::Migratable#migrate)
+    def migrate(row, migrated)
+      super
+      # Invent the mandatory name fields based on the login, if necessary.
+      if login_name then
+        last, first = login_name[/[^@]+/].split('.').reverse.map { |s| s.capitalize }
+        first ||= 'Oscar'
+        self.first_name ||= first
+        self.last_name ||= last
+      end
+      # the coordinator serves as the User content template
+      coord = Galena.administrative_objects.hospital.coordinator
+      # deep copy of the address
+      self.address ||= coord.address.copy
+      # shallow copy of the mandatory references
+      merge(coord, [:cancer_research_group, :department, :institution])
+    end
+  end
+end

data/examples/galena/spec/simple_spec.rb

@@ -0,0 +1,58 @@
+require File.dirname(__FILE__) + '/spec_helper'
+
+module Galena::Simple
+  describe 'migration' do
+    include_context 'a migration'
+
+    before(:all) do
+      @spc = migrate(:simple, :target => CaTissue::TissueSpecimen).first
+    end
+    
+    it 'should save the specimen' do
+      @spc.should_not be nil
+    end
+
+    it 'should set the quantity' do
+      @spc.initial_quantity.should == 3.0
+    end
+
+    it 'should reference a SCG which includes the specimen' do
+      scg = @spc.specimen_collection_group
+      scg.should_not be nil
+      scg.specimens.size.should be 1
+      scg.specimens.first.should be @spc
+    end
+
+    it 'should register a participant with last name the same as the MRN' do
+      reg = @spc.specimen_collection_group.registration
+      reg.should_not be nil
+      pnt = reg.participant
+      pnt.should_not be nil
+      pnt.participant_medical_identifiers.size.should be 1
+      pmi = pnt.participant_medical_identifiers.first
+      pmi.medical_record_number.should == '20001'
+      pnt.last_name.should == pmi.medical_record_number
+    end
+
+    it 'should set the received date' do
+      rep = @spc.received_event_parameters
+      rep.should_not be nil
+      rep.timestamp.year.should == 2007
+      rep.timestamp.month.should == 12
+      rep.timestamp.day.should == 4
+    end
+  end
+  
+  describe 'migration to database' do
+    include_context 'a migration'
+
+    before(:all) do
+      @spc = migrate_to_database(:simple, :target => CaTissue::TissueSpecimen).first
+    end
+    
+    it 'should save the specimen' do
+      @spc.should_not be nil
+      @spc.identifier.should_not be nil
+    end
+  end
+end