caruby-tissue 1.5.4 → 1.5.5

data/test/lib/catissue/domain/participant_test.rb

@@ -1,6 +1,8 @@
 require File.join(File.dirname(__FILE__), '..', 'test_case')
 require 'caruby/util/uniquifier'
 
+require 'json'
+
 class ParticipantTest < Test::Unit::TestCase
   include CaTissue::TestCase
 
@@ -91,6 +93,15 @@ class ParticipantTest < Test::Unit::TestCase
       assert_raises(CaTissue::AnnotationError, "Chemotherapy is not deprecated.") { CaTissue::Participant::Clinical::Chemotherapy.new}
     end
   end
+  
+  def test_json
+    CaTissue::Race.new(:participant => @pnt, :race_name => 'White')
+    dup = JSON[@pnt.to_json]
+    race = dup.races.first
+    assert_not_nil(race, "Race not serialized")
+    assert_equal('White', race.race_name, "Race name not serialized correctly")
+    assert_same(dup, race.participant, "Race participant not serialized correctly")
+  end
 
    ## DATABASE TEST CASES
 

data/test/lib/catissue/domain/specimen_collection_group_test.rb

@@ -33,28 +33,46 @@ class SpecimenCollectionGroupTest < Test::Unit::TestCase
     assert_equal(collection_event, @scg.collection_event, 'Collection event not set to default')
   end
 
-  def test_prostate_annotation
-    scg = CaTissue::SpecimenCollectionGroup.new
+  def test_prostatectomy_annotation
     assert(CaTissue::SpecimenCollectionGroup.annotation_attribute?(:pathology))
-    pths = scg.pathology
+    pths = @scg.pathology
     assert(pths.empty?, "Pathology annotations not empty at start")
     pa = CaTissue::SpecimenCollectionGroup::Pathology::RadicalProstatectomyPathologyAnnotation.new
-    pa.merge_attributes(:specimen_procedure => 'Biopsy', :specimen_collection_group => scg)
+    pa.merge_attributes(:specimen_collection_group => @scg)
     assert_equal(1, pths.size, "SCG pathology proxy not created")
     pth = pths.first
     pas = pth.radical_prostatectomy_pathology_annotations
     epx = CaTissue::SpecimenCollectionGroup::Pathology::ExtraprostaticExtension.new
     epx.merge_attributes(:status => 'Present', :radical_prostatectomy_pathology_annotation => pa)
-    assert_not_nil(pas.first, "Prostatectomy annotation not added to #{scg} annotations")
-    assert_same(pa, pas.first, "Prostatectomy annotation incorrect")
-    assert_same(pth, pa.pathology, "Prostatectomy annotation proxy not set")
-    assert_same(pth, pa.proxy, "Prostatectomy annotation proxy alias not set")
-    assert_same(scg, pth.hook, "Annotation proxy hook not set")
-    assert_same(scg, pa.hook, "Prostatectomy annotation hook not set")
-    assert_not_nil(pa.extraprostatic_extension, "#{pa} extraprostatic extension not set")
+    assert_not_nil(pas.first, "#{@scg} prostatectomy annotation not added")
+    assert_same(pa, pas.first, "#{@scg} prostatectomy annotation incorrect")
+    assert_same(pth, pa.pathology, "#{@scg} prostatectomy annotation #{pa} proxy incorrect")
+    assert_same(pth, pa.proxy, "#{@scg} prostatectomy annotation proxy #{pa} alias incorrect")
+    assert_same(@scg, pth.hook, "#{@scg} prostatectomy annotation proxy hook incorrect")
+    assert_same(@scg, pa.hook, "#{@scg} prostatectomy annotation hook incorrect")
+    assert_not_nil(pa.extraprostatic_extension, "#{pa} extraprostatic extension incorrect")
     assert_same(epx, pa.extraprostatic_extension, "{pa} extraprostatic extension incorrect")
   end
   
+  def test_prostate_biopsy_annotation
+    pths = @scg.pathology
+    assert(pths.empty?, "Pathology annotations not empty at start")
+    pa = CaTissue::SpecimenCollectionGroup::Pathology::NeedleBiopsyProstatePathologyAnnotation.new
+    pa.merge_attributes(:specimen_procedure => 'Biopsy', :specimen_collection_group => @scg)
+    invn =  CaTissue::SpecimenCollectionGroup::Pathology::Invasion.new
+    invn.merge_attributes(:lymphatic_invasion => 'Present', :base_solid_tissue_pathology_annotation => pa)
+    assert_equal(1, pths.size, "SCG pathology proxy not created")
+    pth = pths.first
+    pas = pth.needle_biopsy_prostate_pathology_annotations
+    assert_not_nil(pas.first, "#{@scg} prostate biopsy annotation not added")
+    assert_same(pa, pas.first, "#{@scg} prostate biopsy annotation incorrect")
+    assert_same(pth, pa.pathology, "#{@scg} prostate biopsy annotation #{pa} proxy incorrect")
+    assert_same(pth, pa.proxy, "#{@scg} prostate biopsy annotation proxy #{pa} alias incorrect")
+    assert_same(@scg, pth.hook, "#{@scg} prostate biopsy annotation proxy #{pth} hook incorrect")
+    assert_same(@scg, pa.hook, "#{@scg} prostate biopsy annotation hook incorrect")
+    assert_same(invn, pa.invasion, "#{@scg} prostate biopsy annotation #{pa} invasion incorrect")
+  end
+  
   def test_collect
     scg = CaTissue::SpecimenCollectionGroup.new
     cdt = DateTime.now
@@ -245,7 +263,7 @@ class SpecimenCollectionGroupTest < Test::Unit::TestCase
     verify_save(scg)
   end
   
-  def test_save_prostate_annotation
+  def test_save_prostatectomy_annotation
     pa = CaTissue::SpecimenCollectionGroup::Pathology::RadicalProstatectomyPathologyAnnotation.new
     pa.specimen_collection_group = @scg
     htype = CaTissue::SpecimenCollectionGroup::Pathology::HistologicType.new
@@ -267,6 +285,38 @@ class SpecimenCollectionGroupTest < Test::Unit::TestCase
     assert_not_nil(margin.identifier, "#{@scg} annotation #{margin} not saved")
   end
   
+  # Verifies that SCG create also creates the registered participant clinical annotation. This test
+  # exercises the {CaTissue::Database#finder_parameter} work-around.
+  def test_save_participant_annotation
+    reg = @scg.registration
+    pcl = reg.protocol
+    # unset the registration protocol until the protocol is created
+    reg.protocol = nil
+    # create the protocol
+    pcl.create
+    # reset the registration protocol to the now-existing CP
+    reg.protocol = pcl
+    # the SCG -> CPR -> participant
+    pnt = reg.participant
+    # make a participant annotation
+    lab = CaTissue::Participant::Clinical::LabAnnotation.new
+    lab.merge_attributes(:lab_test_name => 'Test Lab', :participant => pnt)
+    # save the SCG
+    verify_save(@scg)
+    # the SCG -> CPR -> participant annotation should be saved as well
+    assert_not_nil(lab.identifier, "#{@scg} participant #{pnt} annotation #{lab} not saved")
+  end
+  
+  def test_save_prostate_biopsy_annotation
+    pa = CaTissue::SpecimenCollectionGroup::Pathology::NeedleBiopsyProstatePathologyAnnotation.new
+    pa.merge_attributes(:specimen_procedure => 'Biopsy', :specimen_collection_group => @scg)
+    invn =  CaTissue::SpecimenCollectionGroup::Pathology::Invasion.new
+    invn.merge_attributes(:lymphatic_invasion => 'Present', :base_solid_tissue_pathology_annotation => pa)
+    verify_save(pa)
+    assert_not_nil(pa.identifier, "#{@scg} annotation #{pa} not saved")
+    assert_not_nil(invn.identifier, "#{@scg} annotation #{invn} not saved")
+  end
+  
   # Tests saving a participant lab annotation indirectly by saving a SCG. 
   def test_save_lab_annotation_by_saving_scg
     pnt = @scg.collection_protocol_registration.participant

data/test/lib/catissue/domain/specimen_test.rb

@@ -164,7 +164,6 @@ class SpecimenTest < Test::Unit::TestCase
 
   # Verifies that caRuby Tissue is compatible with both the caTissue 1.1 and 1.2 Specimen annotation class names. 
   def test_rename
-    assert_same(CaTissue::Specimen::Pathology::ProstateSpecimenPathologyAnnotation, CaTissue::Specimen::Pathology::ProstatePathologyAnnotation, "caTissue 1.2 annotation class rename unsupported")
     assert_same(CaTissue::Specimen::Pathology::SpecimenAdditionalFinding, CaTissue::Specimen::Pathology::AdditionalFinding, "caTissue 1.2 annotation class rename unsupported")
     assert_same(CaTissue::Specimen::Pathology::SpecimenBaseSolidTissuePathologyAnnotation, CaTissue::Specimen::Pathology::SpecimenBaseSolidTissuePathologyAnnotation, "caTissue 1.2 annotation class rename unsupported")
     assert_same(CaTissue::Specimen::Pathology::SpecimenDetails, CaTissue::Specimen::Pathology::Details, "caTissue 1.2 annotation class rename unsupported")

data/test/lib/catissue/test_case.rb

@@ -192,8 +192,8 @@ module CaTissue
     # @param [Resource] actual the fetched value
     def verify_that_saved_matches_fetched(expected, actual)
       expected.class.saved_nondomain_attributes.each do |attr|
-        # TODO - available_quantity broken for spc type Not Specified
-        # compare attributes that are fetched and set on create
+        # available_quantity broken for spc type Not Specified; see quirk above.
+        # TODO - Compare attributes that are fetched and set on create.
         attr_md = expected.class.attribute_metadata(attr)
         if verify_saved_attribute?(attr_md) then
           eval = expected.database.lazy_loader.suspend { expected.send(attr) }

data/test/lib/examples/galena/tissue/migration/seedify.rb

@@ -8,7 +8,7 @@ module CaTissue
   shims CollectionProtocol, CollectionProtocolEvent, Site, StorageContainer, User
   
   class CollectionProtocol
-    # Augments +CaRuby::Migratable.migrate+ for the Galena example by adding the following defaults:
+    # Augments {CaRuby::Migratable#migrate} for the Galena example by adding the following defaults:
     # * the CP principal_investigator defaults to the {Galena::Seed::Defaults#protocol} PI
     # * if the sites is empty, then the {Galena::Seed::Defaults#tissue_bank} is added
     #   to the CP sites
@@ -35,7 +35,7 @@ module CaTissue
   end
   
   class CollectionProtocolEvent
-    # Augments +CaRuby::Migratable.migrate+ for the example by adding the following defaults:
+    # Augments {CaRuby::Migratable#migrate} for the example by adding the following defaults:
     # * create a {CaTissue::TissueSpecimenRequirement}
     # * copy the event point from the matching {Galena::Seed::Defaults} CPE, if any
     #
@@ -57,7 +57,7 @@ module CaTissue
   end
 
   class Site
-    # Augments +CaRuby::Migratable.migrate+ for the example by merging the content of the
+    # Augments {CaRuby::Migratable#migrate} for the example by merging the content of the
     # {Galena::Seed::Defaults} site which matches on this Site's name, if any.
     #
     # @param (see CaRuby::Migratable#migrate)
@@ -76,7 +76,7 @@ module CaTissue
   end
 
   class StorageContainer
-    # Augments +CaRuby::Migratable.migrate+ for the example by setting the
+    # Augments {CaRuby::Migratable#migrate} for the example by setting the
     # the container site and type to the {Galena::Seed::Defaults}
     # box site and type, resp.
     #
@@ -89,7 +89,7 @@ module CaTissue
   end
   
   class User
-    # Augments +CaRuby::Migratable.migrate+ for the example as follows:
+    # Augments {CaRuby::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 
     #

data/test/lib/examples/galena/tissue/migration/test_case.rb

@@ -44,13 +44,17 @@ module Galena
         opts[:target] ||= CaTissue::TissueSpecimen
         opts[:mapping] ||= File.join(CONFIGS, "#{fixture}_fields.yaml")
         unless opts.has_key?(:defaults) then
-          def_file = File.join(CONFIGS, "#{fixture}_defaults.yaml")
-          if File.exists?(def_file) then opts[:defaults] = def_file end
+          f = File.join(CONFIGS, "#{fixture}_defaults.yaml")
+          if File.exists?(f) then opts[:defaults] = f end
+        end
+        unless opts.has_key?(:filters) then
+          f = File.join(CONFIGS, "#{fixture}_values.yaml")
+          if File.exists?(f) then opts[:filters] = f end
         end
         unless opts.has_key?(:shims) then
-          shims = File.join(SHIMS, "#{fixture}_shims.rb")
-          if File.exists?(shims) then
-            opts[:shims] = [shims]
+          f = File.join(SHIMS, "#{fixture}_shims.rb")
+          if File.exists?(f) then
+            opts[:shims] = [f]
           end    
         end
         mgtr = super

metadata

@@ -1,13 +1,13 @@
 --- !ruby/object:Gem::Specification 
 name: caruby-tissue
 version: !ruby/object:Gem::Version 
-  hash: 11
+  hash: 9
   prerelease: false
   segments: 
   - 1
   - 5
-  - 4
-  version: 1.5.4
+  - 5
+  version: 1.5.5
 platform: ruby
 authors: 
 - OHSU
@@ -26,12 +26,12 @@ dependencies:
     requirements: 
     - - ">="
       - !ruby/object:Gem::Version 
-        hash: 5
+        hash: 9
         segments: 
         - 1
         - 5
-        - 3
-        version: 1.5.3
+        - 5
+        version: 1.5.5
   type: :runtime
   version_requirements: *id001
 description: "    The caruby-tissue gem applies the caRuby facade to the caTissue application.\n"
@@ -52,23 +52,14 @@ files:
 - bin/crtextract
 - bin/crtmigrate
 - bin/crtsmoke
-- conf/extract/simple_fields.yaml
-- conf/migration/filter_fields.yaml
-- conf/migration/filter_migration.yaml
-- conf/migration/frozen_fields.yaml
-- conf/migration/frozen_migration.yaml
-- conf/migration/general_fields.yaml
-- conf/migration/general_migration.yaml
-- conf/migration/simple_fields.yaml
-- conf/migration/simple_migration.yaml
-- conf/migration/small_fields.yaml
-- conf/migration/small_migration.yaml
 - conf/wustl/log4j.properties
 - examples/galena/bin/seed
 - examples/galena/conf/extract/simple_fields.yaml
 - examples/galena/conf/migration/annotation_defaults.yaml
 - examples/galena/conf/migration/annotation_fields.yaml
+- examples/galena/conf/migration/filter_defaults.yaml
 - examples/galena/conf/migration/filter_fields.yaml
+- examples/galena/conf/migration/filter_values.yaml
 - examples/galena/conf/migration/frozen_defaults.yaml
 - examples/galena/conf/migration/frozen_fields.yaml
 - examples/galena/conf/migration/general_fields.yaml

data/conf/extract/simple_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

data/conf/migration/filter_fields.yaml

@@ -1,7 +0,0 @@
-Protocol: CollectionProtocol.title
-MRN: ParticipantMedicalIdentifier.medical_record_number
-Initials: Participant.first_name, Participant.last_name
-Frozen?: TissueSpecimen.specimen_type
-SPN: SpecimenCollectionGroup.surgical_pathology_number
-Collection Date: ReceivedEventParameters.timestamp
-Quantity: TissueSpecimen.initial_quantity

data/conf/migration/filter_migration.yaml

@@ -1,9 +0,0 @@
-# This is the Galena filter example migration configuration file.
-
-# The field heading => CaTissue mapping file.
-mapping: examples/galena/conf/migration/filter_fields.yaml
-
-# The filter code.
-shims: examples/galena/lib/galena/migration/filter_shims.rb
-
-target: TissueSpecimen

data/conf/migration/frozen_fields.yaml

@@ -1,11 +0,0 @@
-# This is the Galena frozen example migration field mapping file.
-# This example extends the simple migration with storage fields
-# and the frozen defaults.
-
-MRN: ParticipantMedicalIdentifier.medical_record_number, Participant.last_name
-SPN: SpecimenCollectionGroup.surgical_pathology_number
-Collection Date: ReceivedEventParameters.timestamp
-Quantity: TissueSpecimen.initial_quantity
-Box: SpecimenPosition.container.name
-X: SpecimenPosition.position_dimension_one
-Y: SpecimenPosition.position_dimension_two

data/conf/migration/frozen_migration.yaml

@@ -1,9 +0,0 @@
-# This is the Galena frozen example migration configuration file.
-# The frozen example extends the simple example with storage fields
-# and shims.
-
-mapping: examples/galena/conf/migration/frozen_fields.yaml
-
-shims: examples/galena/lib/galena/migration/frozen_shims.rb
-
-target: TissueSpecimen

data/conf/migration/general_fields.yaml

@@ -1,44 +0,0 @@
-# This is the Galena general example migration field mapping file in the format:
-#   input field: caTissue property
-
-Protocol: CollectionProtocol.title
-
-Collection Site: Site.name
-
-SPN: SpecimenCollectionGroup.surgical_pathology_number
-
-PPI: CollectionProtocolRegistration.protocol_participant_identifier
-
-MRN: ParticipantMedicalIdentifier.medical_record_number
-
-First Name: Participant.first_name
-
-Last Name: Participant.last_name
-
-Collection Point: CollectionProtocolEvent.event_point
-
-Receiver: ReceivedEventParameters.user.login_name
-
-Received Timestamp: ReceivedEventParameters.timestamp
-
-Collector: CollectionEventParameters.user.login_name
-
-Collected Timestamp: CollectionEventParameters.timestamp
-
-Diagnosis: SpecimenCollectionGroup.clinical_diagnosis
-
-Anatomic Site: SpecimenCharacteristics.tissue_site
-
-Development: TissueSpecimen.pathological_status
-
-Label: TissueSpecimen.label
-
-Type: TissueSpecimen.specimen_type
-
-Quantity: TissueSpecimen.initial_quantity
-
-Box: SpecimenPosition.container.name
-
-X: SpecimenPosition.position_dimension_one
-
-Y: SpecimenPosition.position_dimension_two

data/conf/migration/general_migration.yaml

@@ -1,9 +0,0 @@
-#
-# This is the Galena general example migration configuration file.
-#
-
-# The field heading => CaTissue mapping file.
-mapping: examples/galena/conf/migration/general_fields.yaml
-
-# The migration target class for each record.
-target: TissueSpecimen

data/conf/migration/simple_fields.yaml

@@ -1,30 +0,0 @@
-# This is the Galena simple example migration field mapping file.
-# Each entry is in the format:
-#   heading: paths
-# The heading is the CSV file label in the leading heading record.
-# The paths is a comma-separated list of CaTissue domain object attribute paths specifying
-# how the CSV heading maps to a CaTissue attribute value. Each attribute path is in the format:
-#   class.attribute[.attribute]
-# where class is a CaTissue class and attribute is a Ruby accessor method defined in the CaTissue class.
-# The accessor method can be one of the following:
-# * a Java property name, e.g. lastName
-# * the pre-defined Rubyized underscore form of the Java property, e.g. last_name
-
-# The collection protocol title for the specimen
-Protocol: CollectionProtocol.title
-
-# The input MRN field is used for the PMI MRN, CPR PPI and Participant last name.
-# Since the migration source is for a single collection site, the MRN is unique within the protocol.
-# The simple input does not have a Participant name field. It is a useful practice to set the caTissue
-# name to some value, since caTissue uses the name for display and sorting. For want of a better
-# value, the name is set to the MRN.
-MRN: ParticipantMedicalIdentifier.medical_record_number, Participant.last_name
-
-# The input SPN field is the SCG SPN value.
-SPN: SpecimenCollectionGroup.surgical_pathology_number
-
-# The input Collection Date is the Specimen received timestamp.
-Collection Date: ReceivedEventParameters.timestamp
-
-# The input Quantity is the target Specimen initial quantity.
-Quantity: Specimen.initial_quantity

data/conf/migration/simple_migration.yaml

@@ -1,7 +0,0 @@
-# This is the Galena simple example migration configuration file.
-
-# The field heading => CaTissue mapping file.
-mapping: examples/galena/conf/migration/simple_fields.yaml
-
-# The migration target class for each record.
-target: TissueSpecimen

data/conf/migration/small_fields.yaml

@@ -1,24 +0,0 @@
-# This is the Galena example tiny migration field mapping file.
-# This example input has all of the fields necessary to create a specimen.
-# The example does not use a shim.
-
-# The collection protocol title for the specimen
-Protocol: CollectionProtocol.title
-
-# The input MRN field is used for the PMI MRN, CPR PPI and Participant last name
-MRN: ParticipantMedicalIdentifier.medical_record_number, Participant.last_name
-
-# The input SPN field is the SCG SPN value
-SPN: SpecimenCollectionGroup.surgical_pathology_number
-
-# The date the specimen was received
-Received Date: ReceivedEventParameters.timestamp
-
-# The specimen label
-Label: TissueSpecimen.label
-
-# The type of the specimen
-Type: TissueSpecimen.specimen_type
-
-# The specimen amount
-Quantity: TissueSpecimen.initial_quantity